Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/k/khmer/khmer_2.1.2+dfsg-10_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/khmer-2.1.2+dfsg-102hci5iiu/khmer_2.1.2+dfsg-10_all.buildinfo Get source package info: khmer=2.1.2+dfsg-10 Source URL: http://snapshot.notset.fr/mr/package/khmer/2.1.2+dfsg-10/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.16-2 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 cython3=0.29.24-1+b1 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-exec=0.23.4 dh-python=5.20211114 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 docutils-common=0.17.1+dfsg-2 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 fonts-glyphicons-halflings=1.009~3.4.1+dfsg-2 fonts-liberation=1:1.07.4-11 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblkid1=2.37.2-4 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-5 libbz2-dev=1.0.8-5 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdpkg-perl=1.20.9 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.1-3 libexpat1-dev=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.24-2 libitm1=11.2.0-12 libjs-bootstrap=3.4.1+dfsg-2 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc=4.3.1-1 libjs-underscore=1.9.1~dfsg-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpython3-all-dev=3.9.8-1 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.10=3.10.0-5 libpython3.10-dev=3.10.0-5 libpython3.10-minimal=3.10.0-5 libpython3.10-stdlib=3.10.0-5 libpython3.9=3.9.9-1 libpython3.9-dev=3.9.9-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libquadmath0=11.2.0-12 libreadline8=8.1-2 libruby2.7=2.7.4-1+b1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5+b1 libyaml-0-2=0.2.2-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.70+nmu1 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.3-1 ncurses-bin=6.3-1 openssl=1.1.1l-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 python-babel-localedata=2.8.0+dfsg.1-7 python3=3.9.8-1 python3-alabaster=0.7.12-1 python3-all=3.9.8-1 python3-all-dev=3.9.8-1 python3-attr=20.3.0-1 python3-babel=2.8.0+dfsg.1-7 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-dev=3.9.8-1 python3-distutils=3.9.9-2 python3-docutils=0.17.1+dfsg-2 python3-guzzle-sphinx-theme=0.7.11-5 python3-idna=2.10-1 python3-imagesize=1.3.0-1 python3-importlib-metadata=4.6.4-1 python3-iniconfig=1.1.1-1 python3-jinja2=3.0.1-2 python3-lib2to3=3.9.9-2 python3-markupsafe=2.0.1-2+b1 python3-minimal=3.9.8-1 python3-more-itertools=8.10.0-2 python3-packaging=21.3-1 python3-pkg-resources=59.4.0-1 python3-pluggy=0.13.0-7.1 python3-py=1.10.0-1 python3-pygments=2.7.1+dfsg-2.1 python3-pyparsing=2.4.7-1 python3-pytest=6.2.5-1 python3-pytest-runner=2.11.1-1.2 python3-requests=2.25.1+dfsg-2 python3-roman=3.3-1 python3-screed=1.0.5-3 python3-setuptools=59.4.0-1 python3-six=1.16.0-2 python3-snowballstemmer=2.2.0-1 python3-sphinx=4.3.1-1 python3-sphinxcontrib.autoprogram=0.1.7-1 python3-toml=0.10.2-1 python3-tz=2021.3-1 python3-urllib3=1.26.5-1~exp1 python3-zipp=1.0.0-3 python3.10=3.10.0-5 python3.10-dev=3.10.0-5 python3.10-minimal=3.10.0-5 python3.9=3.9.9-1 python3.9-dev=3.9.9-1 python3.9-minimal=3.9.9-1 rake=13.0.3-1 rdfind=1.5.0-1.1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 ruby=1:2.7.6 ruby-asciidoctor=2.0.16-2 ruby-minitest=5.13.0-1 ruby-net-telnet=0.1.1-2 ruby-power-assert=1.1.7-2 ruby-rubygems=3.2.27-3 ruby-test-unit=3.3.9-1 ruby-xmlrpc=0.3.2-1 ruby2.7=2.7.4-1+b1 rubygems-integration=1.18 sed=4.8-1 sensible-utils=0.0.17 sgml-base=1.30 sphinx-common=4.3.1-1 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-4 xml-core=0.18+nmu1 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211209T025217Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211209T025217Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211205T145050Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d khmer=2.1.2+dfsg-10 && mkdir -p /build/khmer-ratrfy && dpkg-source --no-check -x /*.dsc /build/khmer-ratrfy/khmer-2.1.2+dfsg && chown -R builduser:builduser /build/khmer-ratrfy" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/khmer-ratrfy/khmer-2.1.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638565179" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/khmer-ratrfy /tmp/khmer-2.1.2+dfsg-102hci5iiu bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211205T145050Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.kkAtyyv5k5 as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.kkAtyyv5k5 Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211205T145050Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211205T145050Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (936 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4673 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211209T025217Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211209T025217Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211205T145050Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.kkAtyyv5k5 Get:1 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm InRelease [129 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211205T145050Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.1 MB in 19s (1198 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.kkAtyyv5k5 I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d khmer=2.1.2+dfsg-10 && mkdir -p /build/khmer-ratrfy && dpkg-source --no-check -x /*.dsc /build/khmer-ratrfy/khmer-2.1.2+dfsg && chown -R builduser:builduser /build/khmer-ratrfy"' exec /tmp/mmdebstrap.kkAtyyv5k5 Reading package lists... NOTICE: 'khmer' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/khmer.git Please use: git clone https://salsa.debian.org/med-team/khmer.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 18.1 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main khmer 2.1.2+dfsg-10 (dsc) [2687 B] Get:2 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main khmer 2.1.2+dfsg-10 (tar) [18.1 MB] Get:3 http://snapshot.notset.fr/archive/debian/20211209T025217Z bookworm/main khmer 2.1.2+dfsg-10 (diff) [14.9 kB] Fetched 18.1 MB in 14s (1275 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'khmer_2.1.2+dfsg-10.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting khmer in /build/khmer-ratrfy/khmer-2.1.2+dfsg dpkg-source: info: unpacking khmer_2.1.2+dfsg.orig.tar.gz dpkg-source: info: unpacking khmer_2.1.2+dfsg-10.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying update-manifest dpkg-source: info: applying setup-py-py3 dpkg-source: info: applying local-libs dpkg-source: info: applying older-setuptools dpkg-source: info: applying disable_google_analytics dpkg-source: info: applying get_version dpkg-source: info: applying install-prefix dpkg-source: info: applying cpython-bug-empty-exceptions dpkg-source: info: applying amend-skip dpkg-source: info: applying setup.py-py3 dpkg-source: info: applying python3 dpkg-source: info: applying fix_liboxli_test dpkg-source: info: applying gcc11.patch dpkg-source: info: applying bz2.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/khmer-ratrfy/khmer-2.1.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638565179" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.kkAtyyv5k5 dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 2.1.2+dfsg-10 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' dh_auto_clean || /bin/true install -d /build/khmer-ratrfy/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --clean -i python{version} -p "3.10 3.9" I: pybuild base:237: python3.10 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running clean removing '/build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:237: python3.9 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running clean removing '/build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; cd src/oxli && /usr/bin/make clean make[2]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/khmer-common.substvars debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars debian/files rm -fr -- debian/khmer-common/ debian/tmp/ debian/khmer/ debian/liboxli1/ debian/liboxli-dev/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-indep dh binary-indep --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -i -O--buildsystem=pybuild dh_autoreconf -i -O--buildsystem=pybuild dh_auto_configure -i -O--buildsystem=pybuild install -d /build/khmer-ratrfy/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --configure -i python{version} -p "3.10 3.9" I: pybuild base:237: python3.10 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running config I: pybuild base:237: python3.9 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' dh_auto_build pybuild --build -i python{version} -p "3.10 3.9" I: pybuild base:237: /usr/bin/python3.10 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running build running build_py creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/khmer_args.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/khmer_logger.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/thread_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/trimming.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer copying khmer/kfile.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/graph_features.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_banding.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_cython_assembly.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_hll.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_lump.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/build_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli copying oxli/partition.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli running egg_info creating khmer.egg-info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt writing manifest file 'khmer.egg-info/SOURCES.txt' reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.cpp' under directory 'khmer/_oxli' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli UPDATING /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py set /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py to '2.1.2' running build_ext cythoning khmer/_oxli/assembly.pyx to khmer/_oxli/assembly.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-ratrfy/khmer-2.1.2+dfsg/khmer/_oxli/assembly.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/graphs.pyx to khmer/_oxli/graphs.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-ratrfy/khmer-2.1.2+dfsg/khmer/_oxli/graphs.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/hashing.pyx to khmer/_oxli/hashing.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-ratrfy/khmer-2.1.2+dfsg/khmer/_oxli/hashing.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning khmer/_oxli/parsing.pyx to khmer/_oxli/parsing.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-ratrfy/khmer-2.1.2+dfsg/khmer/_oxli/parsing.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: khmer/_oxli/parsing.pxd:159:25: Declarations should not be declared inline. warning: khmer/_oxli/parsing.pxd:161:34: Declarations should not be declared inline. cythoning khmer/_oxli/utils.pyx to khmer/_oxli/utils.cpp /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/khmer-ratrfy/khmer-2.1.2+dfsg/khmer/_oxli/utils.pxd tree = Parsing.p_module(s, pxd, full_module_name) building 'khmer._khmer' extension creating build creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/src creating build/temp.linux-x86_64-3.10/src/khmer creating build/temp.linux-x86_64-3.10/src/oxli creating build/temp.linux-x86_64-3.10/third-party creating build/temp.linux-x86_64-3.10/third-party/smhasher x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension creating build/temp.linux-x86_64-3.10/khmer creating build/temp.linux-x86_64-3.10/khmer/_oxli x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-3.10/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:544: note: this is the location of the previous definition 544 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:551: note: this is the location of the previous definition 551 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:548: note: this is the location of the previous definition 548 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-3.10/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:544: note: this is the location of the previous definition 544 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:551: note: this is the location of the previous definition 551 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:548: note: this is the location of the previous definition 548 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-3.10/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-3.10/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5749:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5749 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-3.10/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/khmer/_oxli/utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.10 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.10 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.10 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.10 copying and adjusting scripts/count-median.py -> build/scripts-3.10 copying and adjusting scripts/do-partition.py -> build/scripts-3.10 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.10 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.10 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.10 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.10 copying and adjusting scripts/filter-abund.py -> build/scripts-3.10 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.10 copying and adjusting scripts/find-knots.py -> build/scripts-3.10 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.10 copying and adjusting scripts/load-graph.py -> build/scripts-3.10 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.10 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.10 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.10 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.10 copying and adjusting scripts/partition-graph.py -> build/scripts-3.10 copying and adjusting scripts/readstats.py -> build/scripts-3.10 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.10 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.10 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.10 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.10 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.10 changing mode of build/scripts-3.10/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.10/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.10/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.10/count-median.py from 644 to 755 changing mode of build/scripts-3.10/do-partition.py from 644 to 755 changing mode of build/scripts-3.10/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.10/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.10/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.10/filter-abund-single.py from 644 to 755 changing mode of build/scripts-3.10/filter-abund.py from 644 to 755 changing mode of build/scripts-3.10/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.10/find-knots.py from 644 to 755 changing mode of build/scripts-3.10/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.10/load-graph.py from 644 to 755 changing mode of build/scripts-3.10/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.10/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.10/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.10/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.10/partition-graph.py from 644 to 755 changing mode of build/scripts-3.10/readstats.py from 644 to 755 changing mode of build/scripts-3.10/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.10/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.10/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.10/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.10/extract-paired-reads.py from 644 to 755 I: pybuild base:237: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running build running build_py creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/khmer_args.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/khmer_logger.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/thread_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/trimming.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/kfile.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/graph_features.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_banding.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cython_assembly.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_hll.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_lump.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/build_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/partition.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/biglump-random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/casava_18-pe.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/combine_parts_1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-none-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/filter-test-B.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/old-style-format-w-comments.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badleft -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.badright -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken2.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken3.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-broken4.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-broken.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired_one.base.dif.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-X2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.even.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fa.part -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-a.odd.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-20-b.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/random-31-c.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-small.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/real-partition-tiny.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-3.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-impaired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read-paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-abund-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-error-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-n-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-fastq-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-output-partitions.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-contigs.fp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-sweep-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/valid-read-testing.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli UPDATING /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/src creating build/temp.linux-x86_64-3.9/src/khmer creating build/temp.linux-x86_64-3.9/src/oxli creating build/temp.linux-x86_64-3.9/third-party creating build/temp.linux-x86_64-3.9/third-party/smhasher x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension creating build/temp.linux-x86_64-3.9/khmer creating build/temp.linux-x86_64-3.9/khmer/_oxli x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:544: note: this is the location of the previous definition 544 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:551: note: this is the location of the previous definition 551 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:548: note: this is the location of the previous definition 548 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:544: note: this is the location of the previous definition 544 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:551: note: this is the location of the previous definition 551 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:548: note: this is the location of the previous definition 548 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5749:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5749 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -fopenmp running build_scripts creating build/scripts-3.9 copying and adjusting scripts/abundance-dist-single.py -> build/scripts-3.9 copying and adjusting scripts/abundance-dist.py -> build/scripts-3.9 copying and adjusting scripts/annotate-partitions.py -> build/scripts-3.9 copying and adjusting scripts/count-median.py -> build/scripts-3.9 copying and adjusting scripts/do-partition.py -> build/scripts-3.9 copying and adjusting scripts/extract-long-sequences.py -> build/scripts-3.9 copying and adjusting scripts/extract-partitions.py -> build/scripts-3.9 copying and adjusting scripts/fastq-to-fasta.py -> build/scripts-3.9 copying and adjusting scripts/filter-abund-single.py -> build/scripts-3.9 copying and adjusting scripts/filter-abund.py -> build/scripts-3.9 copying and adjusting scripts/filter-stoptags.py -> build/scripts-3.9 copying and adjusting scripts/find-knots.py -> build/scripts-3.9 copying and adjusting scripts/interleave-reads.py -> build/scripts-3.9 copying and adjusting scripts/load-graph.py -> build/scripts-3.9 copying and adjusting scripts/load-into-counting.py -> build/scripts-3.9 copying and adjusting scripts/make-initial-stoptags.py -> build/scripts-3.9 copying and adjusting scripts/merge-partitions.py -> build/scripts-3.9 copying and adjusting scripts/normalize-by-median.py -> build/scripts-3.9 copying and adjusting scripts/partition-graph.py -> build/scripts-3.9 copying and adjusting scripts/readstats.py -> build/scripts-3.9 copying and adjusting scripts/sample-reads-randomly.py -> build/scripts-3.9 copying and adjusting scripts/split-paired-reads.py -> build/scripts-3.9 copying and adjusting scripts/trim-low-abund.py -> build/scripts-3.9 copying and adjusting scripts/unique-kmers.py -> build/scripts-3.9 copying and adjusting scripts/extract-paired-reads.py -> build/scripts-3.9 changing mode of build/scripts-3.9/abundance-dist-single.py from 644 to 755 changing mode of build/scripts-3.9/abundance-dist.py from 644 to 755 changing mode of build/scripts-3.9/annotate-partitions.py from 644 to 755 changing mode of build/scripts-3.9/count-median.py from 644 to 755 changing mode of build/scripts-3.9/do-partition.py from 644 to 755 changing mode of build/scripts-3.9/extract-long-sequences.py from 644 to 755 changing mode of build/scripts-3.9/extract-partitions.py from 644 to 755 changing mode of build/scripts-3.9/fastq-to-fasta.py from 644 to 755 changing mode of build/scripts-3.9/filter-abund-single.py from 644 to 755 changing mode of build/scripts-3.9/filter-abund.py from 644 to 755 changing mode of build/scripts-3.9/filter-stoptags.py from 644 to 755 changing mode of build/scripts-3.9/find-knots.py from 644 to 755 changing mode of build/scripts-3.9/interleave-reads.py from 644 to 755 changing mode of build/scripts-3.9/load-graph.py from 644 to 755 changing mode of build/scripts-3.9/load-into-counting.py from 644 to 755 changing mode of build/scripts-3.9/make-initial-stoptags.py from 644 to 755 changing mode of build/scripts-3.9/merge-partitions.py from 644 to 755 changing mode of build/scripts-3.9/normalize-by-median.py from 644 to 755 changing mode of build/scripts-3.9/partition-graph.py from 644 to 755 changing mode of build/scripts-3.9/readstats.py from 644 to 755 changing mode of build/scripts-3.9/sample-reads-randomly.py from 644 to 755 changing mode of build/scripts-3.9/split-paired-reads.py from 644 to 755 changing mode of build/scripts-3.9/trim-low-abund.py from 644 to 755 changing mode of build/scripts-3.9/unique-kmers.py from 644 to 755 changing mode of build/scripts-3.9/extract-paired-reads.py from 644 to 755 ln -sf "`pwd`"/.pybuild/pythonX.Y_*/build/khmer/*.so khmer && \ ./setup.py develop --user && ./setup.py build_sphinx /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running develop /usr/lib/python3/dist-packages/setuptools/command/easy_install.py:158: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools. warnings.warn( /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp creating build/lib.linux-x86_64-3.9 creating build/lib.linux-x86_64-3.9/khmer x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.assembly' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/assembly.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:544: note: this is the location of the previous definition 544 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:551: note: this is the location of the previous definition 551 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:661: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:548: note: this is the location of the previous definition 548 | #define PyInt_FromLong PyLong_FromLong | creating build/lib.linux-x86_64-3.9/khmer/_oxli x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/assembly.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.graphs' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/graphs.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o -O3 -std=c++11 -pedantic -fopenmp In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:544: note: this is the location of the previous definition 544 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:551: note: this is the location of the previous definition 551 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:661: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:548: note: this is the location of the previous definition 548 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/graphs.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.hashing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/hashing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/hashing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.parsing' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/parsing.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o -O3 -std=c++11 -pedantic -fopenmp khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5749:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5749 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/parsing.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -fopenmp building 'khmer._oxli.utils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c khmer/_oxli/utils.cpp -o build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/khmer/_oxli/utils.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o build/lib.linux-x86_64-3.9/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -fopenmp copying build/lib.linux-x86_64-3.9/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> khmer copying build/lib.linux-x86_64-3.9/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli copying build/lib.linux-x86_64-3.9/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> khmer/_oxli Creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/lib/python3.9/site-packages/khmer.egg-link (link to .) Adding khmer 2.1.2 to easy-install.pth file Installing abundance-dist-single.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing count-median.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing readstats.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing trim-low-abund.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing unique-kmers.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-paired-reads.py script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Installed /build/khmer-ratrfy/khmer-2.1.2+dfsg Processing dependencies for khmer==2.1.2 Searching for screed==1.0.5 Best match: screed 1.0.5 Adding screed 1.0.5 to easy-install.pth file Installing screed script to /build/khmer-ratrfy/khmer-2.1.2+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Searching for Cython==0.29.24 Best match: Cython 0.29.24 Adding Cython 0.29.24 to easy-install.pth file Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==2.1.2 /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running build_sphinx Running Sphinx v4.3.1 making output directory... done building [mo]: targets for 0 po files that are out of date building [html]: targets for 41 source files that are out of date updating environment: [new config] 41 added, 0 changed, 0 removed reading sources... [ 2%] LICENSE reading sources... [ 4%] citations reading sources... [ 7%] contributors reading sources... [ 9%] dev/CODE_OF_CONDUCT reading sources... [ 12%] dev/a-quick-guide-to-testing reading sources... [ 14%] dev/binary-file-formats reading sources... [ 17%] dev/codebase-guide reading sources... [ 19%] dev/development reading sources... [ 21%] dev/for-khmer-developers reading sources... [ 24%] dev/getting-started reading sources... [ 26%] dev/guidelines-continued-dev reading sources... [ 29%] dev/hackathon reading sources... [ 31%] dev/index reading sources... [ 34%] dev/python-api reading sources... 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[ 90%] user/index reading sources... [ 92%] user/install reading sources... [ 95%] user/known-issues reading sources... [ 97%] user/partitioning-big-data reading sources... [100%] user/scripts looking for now-outdated files... none found pickling environment... done checking consistency... /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/dev/python-api.rst: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 2%] LICENSE writing output... [ 4%] citations writing output... [ 7%] contributors writing output... [ 9%] dev/CODE_OF_CONDUCT writing output... [ 12%] dev/a-quick-guide-to-testing writing output... [ 14%] dev/binary-file-formats writing output... [ 17%] dev/codebase-guide writing output... [ 19%] dev/development writing output... [ 21%] dev/for-khmer-developers writing output... [ 24%] dev/getting-started writing output... 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[100%] user/scripts /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -N /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --n_tables /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -x /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --max-tablesize /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: -x /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: -N /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: -x /build/khmer-ratrfy/khmer-2.1.2+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: -N generating indices... genindex done writing additional pages... search done copying images... [ 50%] user/partitioning-workflow.png copying images... [100%] user/artifact-removal.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 10 warnings. The HTML pages are in build/sphinx/html. asciidoctor --backend manpage -a reproducible debian/khmer.1.adoc cd src/oxli && /usr/bin/make clean all make[2]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashtable.o hashtable.cc hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: hashtable.cc:512:1: required from here hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: hashtable.cc:529:1: required from here hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hashgraph.o hashgraph.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o hllcounter.o hllcounter.cc hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: hllcounter.cc:524:1: required from here hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_hash.o kmer_hash.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o labelhash.o labelhash.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o traversal.o traversal.cc In file included from traversal.cc:39: traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: traversal.cc:202:5: required from here ../../include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from traversal.cc:39: traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: traversal.cc:203:5: required from here ../../include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_aligner.o read_aligner.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o read_parsers.o read_parsers.cc In file included from ../../third-party/seqan/core/include/seqan/basic.h:62, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/seq_io.h:64, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:116, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ ../../third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:166, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ ../../third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from ../../third-party/seqan/core/include/seqan/align.h:174, from ../../third-party/seqan/core/include/seqan/store.h:38, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ ../../third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107, from ../../third-party/seqan/core/include/seqan/store.h:41, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/bam_io.h:107, from ../../third-party/seqan/core/include/seqan/store.h:41, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from ../../third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from ../../third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from ../../third-party/seqan/core/include/seqan/basic.h:52, from ../../third-party/seqan/core/include/seqan/seq_io.h:44, from read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ../../third-party/seqan/core/include/seqan/store.h:61, from ../../third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from ../../third-party/seqan/core/include/seqan/seq_io.h:83, from read_parsers.cc:39: ../../third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: ../../third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ ../../third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o subset.o subset.cc subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o kmer_filters.o kmer_filters.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o assembler.o assembler.cc In file included from assembler.cc:38: ../../include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: ../../include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ ../../include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from assembler.cc:38: ../../include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: ../../include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ ../../include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from assembler.cc:38: ../../include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ ../../include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o alphabets.o alphabets.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -c -o murmur3.o ../../third-party/smhasher/MurmurHash3.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -c -o storage.o storage.cc g++ -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC -Wall -Wstrict-null-sentinel -std=c++11 -I ../../include/ -I ../../third-party/seqan/core/include/ -I ../../third-party/smhasher/ -Wdate-time -D_FORTIFY_SOURCE=2 -DSEQAN_HAS_ZLIB=1 -DSEQAN_HAS_BZIP2=1 -O3 -fPIC -Wall -fopenmp -DVERSION= -DNO_UNIQUE_RC=0 -Wl,-z,relro -Wl,-z,now -lz -lbz2 -Wl,-soname=liboxli.so.1 -shared -o liboxli.so.1 hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ln -sf liboxli.so.1 liboxli.so ar rcs liboxli.a hashtable.o hashgraph.o hllcounter.o kmer_hash.o labelhash.o traversal.o read_aligner.o read_parsers.o subset.o kmer_filters.o assembler.o alphabets.o murmur3.o storage.o ranlib liboxli.a sed -e 's,@prefix@,/usr/local,' -e 's,@VERSION@,,' oxli.pc.in >oxli.pc make[2]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg/src/oxli' make[1]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -i -O--buildsystem=pybuild dh_prep -i -O--buildsystem=pybuild rm -f -- debian/khmer-common.substvars rm -fr -- debian/.debhelper/generated/khmer-common/ debian/khmer-common/ debian/tmp/ dh_auto_install -i -O--buildsystem=pybuild install -d /build/khmer-ratrfy/khmer-2.1.2\+dfsg/debian/tmp pybuild --install -i python{version} -p "3.10 3.9" --dest-dir /build/khmer-ratrfy/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:237: /usr/bin/python3.10 setup.py install --root /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer '--install-scripts=/usr/lib/khmer/bin' /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli UPDATING /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py set /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.10/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.10/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.10/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.10/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.10 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10 creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_args.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/khmer_logger.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/thread_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/trimming.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/kfile.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/graph_features.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_banding.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_assembly.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_hll.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_lump.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/.gitignore -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test-data creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpython-310-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpython-310-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpython-310-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpython-310-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpython-310-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/khmer/_khmer.cpython-310-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli/build_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli/functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.10_khmer/build/oxli/partition.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/__init__.py to __init__.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_args.py to khmer_args.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/thread_utils.py to thread_utils.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/trimming.py to trimming.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/utils.py to utils.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/kfile.py to kfile.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-310.pyc /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.10/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_version.py to test_version.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer/_version.py to _version.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli/__init__.py to __init__.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli/build_graph.py to build_graph.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli/functions.py to functions.cpython-310.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/oxli/partition.py to partition.cpython-310.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.10/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/abundance-dist-single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/abundance-dist.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/annotate-partitions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/count-median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/do-partition.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-long-sequences.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-partitions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/fastq-to-fasta.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund-single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/filter-stoptags.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/find-knots.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/interleave-reads.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/load-graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/load-into-counting.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/make-initial-stoptags.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/merge-partitions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/normalize-by-median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/partition-graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/readstats.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/sample-reads-randomly.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/split-paired-reads.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/trim-low-abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/unique-kmers.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.10/extract-paired-reads.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer '--install-scripts=/usr/lib/khmer/bin' /usr/lib/python3/dist-packages/setuptools/dist.py:717: UserWarning: Usage of dash-separated 'include-dirs' will not be supported in future versions. Please use the underscore name 'include_dirs' instead warnings.warn( running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing khmer.egg-info/PKG-INFO writing dependency_links to khmer.egg-info/dependency_links.txt writing requirements to khmer.egg-info/requires.txt writing top-level names to khmer.egg-info/top_level.txt reading manifest file 'khmer.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'ChangeLog' warning: no files found matching 'ez_setup.py' warning: no files found matching 'IDEAS' warning: no files found matching 'README.md' warning: no files found matching 'TODO' warning: no files found matching '.ycm_extra_conf.py' warning: no files found matching '*.hh' under directory 'lib' warning: no files found matching '*.cc' under directory 'lib' warning: no files found matching '[Mm]akefile*' under directory 'lib' warning: no files found matching 'get_version.py' under directory 'lib' warning: no files found matching '*.hh' under directory 'khmer' warning: no files found matching '*.1' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'sample*' under directory 'third-party' warning: no files found matching 'words*' under directory 'third-party' warning: no files found matching '*.sh' under directory 'third-party' warning: no files found matching '*.c' under directory 'third-party' warning: no files found matching 'manual*' under directory 'third-party' warning: no files found matching '[Mm]akefile*' under directory 'third-party' warning: no files found matching '*.pl' under directory 'third-party' warning: no files found matching '*.dsp' under directory 'third-party' warning: no files found matching 'CHANGES' under directory 'third-party' warning: no files found matching '*.txt' under directory 'third-party' warning: no files found matching 'FAQ' under directory 'third-party' warning: no files found matching 'INDEX' under directory 'third-party' warning: no files found matching 'configure' under directory 'third-party' warning: no files found matching '*.xsl' under directory 'third-party' warning: no files found matching 'bzip.css' under directory 'third-party/bzip2' warning: no files found matching 'entities.xml' under directory 'third-party/bzip2' warning: no files found matching 'libbz2.def' under directory 'third-party/bzip2' warning: no files found matching 'LICENSE' under directory 'third-party/bzip2' warning: no files found matching 'third-party/zlib/zconf.h.in' warning: no files found matching 'third-party/zlib/zlib.pc.in' warning: no previously-included files found matching 'third-party/zlib/Makefile' warning: no previously-included files found matching 'third-party/zlib/zconf.h' warning: no files found matching 'README.txt' under directory 'scripts' warning: no previously-included files matching '*.orig' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'khmer.egg-info/SOURCES.txt' UPDATING /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py to '2.1.2' running build_ext skipping 'khmer/_oxli/assembly.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/graphs.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/hashing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/parsing.cpp' Cython extension (up-to-date) skipping 'khmer/_oxli/utils.cpp' Cython extension (up-to-date) building 'khmer._khmer' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_countgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_counttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_graphlabels.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashset.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hashtable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_hllcounter.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_khmer.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodegraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_nodetable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readaligner.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_readparsers.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcountgraph.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_smallcounttable.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_subsetpartition.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/khmer/_cpy_utils.cc -o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/alphabets.cc -o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/assembler.cc -o build/temp.linux-x86_64-3.9/src/oxli/assembler.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::LinearAssembler::LinearAssembler(const oxli::Hashgraph*)’: include/oxli/assembler.hh:80:23: warning: ‘oxli::LinearAssembler::graph’ will be initialized after [-Wreorder] 80 | const Hashgraph * graph; | ^~~~~ include/oxli/assembler.hh:79:16: warning: ‘oxli::WordLength oxli::LinearAssembler::_ksize’ [-Wreorder] 79 | WordLength _ksize; | ^~~~~~ src/oxli/assembler.cc:52:1: warning: when initialized here [-Wreorder] 52 | LinearAssembler::LinearAssembler(const Hashgraph * ht) : | ^~~~~~~~~~~~~~~ src/oxli/assembler.cc: In destructor ‘oxli::SimpleLabeledAssembler::~SimpleLabeledAssembler()’: src/oxli/assembler.cc:189:5: warning: deleting object of polymorphic class type ‘oxli::LinearAssembler’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 189 | delete this->linear_asm; | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh: In constructor ‘oxli::JunctionCountAssembler::JunctionCountAssembler(oxli::Hashgraph*)’: include/oxli/assembler.hh:158:16: warning: ‘oxli::JunctionCountAssembler::_ksize’ will be initialized after [-Wreorder] 158 | WordLength _ksize; | ^~~~~~ include/oxli/assembler.hh:153:15: warning: ‘oxli::Traverser oxli::JunctionCountAssembler::traverser’ [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/assembler.cc:38: include/oxli/assembler.hh:153:15: warning: ‘oxli::JunctionCountAssembler::traverser’ will be initialized after [-Wreorder] 153 | Traverser traverser; | ^~~~~~~~~ include/oxli/assembler.hh:151:21: warning: ‘oxli::LinearAssembler oxli::JunctionCountAssembler::linear_asm’ [-Wreorder] 151 | LinearAssembler linear_asm; | ^~~~~~~~~~ src/oxli/assembler.cc:346:1: warning: when initialized here [-Wreorder] 346 | JunctionCountAssembler::JunctionCountAssembler(Hashgraph * ht) : | ^~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashgraph.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hashtable.cc -o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile(oxli::read_parsers::ReadParserPtr&, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:512:1: required from here src/oxli/hashtable.cc:103:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 103 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ src/oxli/hashtable.cc: In instantiation of ‘void oxli::Hashtable::consume_seqfile_banding(oxli::read_parsers::ReadParserPtr&, unsigned int, unsigned int, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hashtable.cc:529:1: required from here src/oxli/hashtable.cc:133:18: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 133 | } catch (NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/hllcounter.cc -o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/hllcounter.cc: In instantiation of ‘void oxli::HLLCounter::consume_seqfile(oxli::read_parsers::ReadParserPtr&, bool, unsigned int&, long long unsigned int&) [with SeqIO = oxli::read_parsers::FastxReader; oxli::read_parsers::ReadParserPtr = std::unique_ptr >]’: src/oxli/hllcounter.cc:524:1: required from here src/oxli/hllcounter.cc:428:40: warning: catching polymorphic type ‘struct oxli::read_parsers::NoMoreReadsAvailable’ by value [-Wcatch-value=] 428 | } catch (read_parsers::NoMoreReadsAvailable) { | ^~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_filters.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/kmer_hash.cc -o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/labelhash.cc -o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_aligner.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/read_parsers.cc -o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o -O3 -std=c++11 -pedantic -fopenmp In file included from third-party/seqan/core/include/seqan/basic.h:62, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/basic/test_system.h:92:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:105:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:110:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:111:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:116:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:119:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:121:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:122:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:123:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/seq_io.h:64, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/seq_io/sequence_stream_impl.h:124:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:116, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/dp_cell_affine.h: In member function ‘seqan::DPCell_ >& seqan::DPCell_ >::operator=(const seqan::DPCell_ >&)’: third-party/seqan/core/include/seqan/align/dp_cell_affine.h:84:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 84 | if (this != &other) | ^~ third-party/seqan/core/include/seqan/align/dp_cell_affine.h:86:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 86 | _horizontalScore = other._horizontalScore; | ^~~~~~~~~~~~~~~~ In file included from third-party/seqan/core/include/seqan/align.h:166, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h: In function ‘int seqan::_globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersBitVector&)’: third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:70:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 70 | if (length(seqH) < length(seqV)) | ^~ third-party/seqan/core/include/seqan/align/global_alignment_myers_impl.h:74:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 74 | const unsigned int BLOCK_SIZE = BitsPerValue::VALUE; | ^~~~~ In file included from third-party/seqan/core/include/seqan/align.h:174, from third-party/seqan/core/include/seqan/store.h:38, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In function ‘seqan::Pair > seqan::_alignBandedSmithWatermanTrace(seqan::LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, TId, TId, TScore&, TDiagonal, TDiagonal)’: third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:409:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 409 | if ((actualCol == 0) || (actualRow == 0)) | ^~ third-party/seqan/core/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:412:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 412 | if (actualCol < len1) _alignTracePrint(finder.trace, seqH, seqV, id1, actualCol, id2, actualRow, len1 - actualCol, Horizontal); | ^~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h: At global scope: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:180:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/bam_io.h:107, from third-party/seqan/core/include/seqan/store.h:41, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/bam_io/bam_stream.h:182:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/11/bits/locale_conv.h:41, from /usr/include/c++/11/locale:43, from /usr/include/c++/11/iomanip:43, from third-party/seqan/core/include/seqan/basic/debug_test_system.h:46, from third-party/seqan/core/include/seqan/basic/basic_debug.h:52, from third-party/seqan/core/include/seqan/basic.h:52, from third-party/seqan/core/include/seqan/seq_io.h:44, from src/oxli/read_parsers.cc:39: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from third-party/seqan/core/include/seqan/store.h:61, from third-party/seqan/core/include/seqan/seq_io/fai_index.h:40, from third-party/seqan/core/include/seqan/seq_io.h:83, from src/oxli/read_parsers.cc:39: third-party/seqan/core/include/seqan/store/store_all.h: In function ‘void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&)’: third-party/seqan/core/include/seqan/store/store_all.h:1733:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1733 | if (alignQualityStoreLengthPre == 0u) | ^~ third-party/seqan/core/include/seqan/store/store_all.h:1737:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1737 | sortAlignedReads(store.alignedReadStore, SortBeginPos()); | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/storage.cc -o build/temp.linux-x86_64-3.9/src/oxli/storage.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/subset.cc -o build/temp.linux-x86_64-3.9/src/oxli/subset.o -O3 -std=c++11 -pedantic -fopenmp src/oxli/subset.cc: In member function ‘size_t oxli::SubsetPartition::output_partitioned_file(const string&, const string&, bool, oxli::CallbackFn, void*)’: src/oxli/subset.cc:136:24: warning: unused variable ‘ksize’ [-Wunused-variable] 136 | const unsigned int ksize = _ht->ksize(); | ^~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c src/oxli/traversal.cc -o build/temp.linux-x86_64-3.9/src/oxli/traversal.o -O3 -std=c++11 -pedantic -fopenmp In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = false; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:202:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from src/oxli/traversal.cc:39: src/oxli/traversal.cc: In instantiation of ‘oxli::NodeGatherer::NodeGatherer(const oxli::Hashgraph*, oxli::KmerFilterList) [with bool direction = true; oxli::KmerFilterList = std::__cxx11::list >]’: src/oxli/traversal.cc:203:5: required from here include/oxli/traversal.hh:79:23: warning: ‘oxli::NodeGatherer::graph’ will be initialized after [-Wreorder] 79 | const Hashgraph * graph; | ^~~~~ include/oxli/traversal.hh:76:20: warning: ‘oxli::KmerFilterList oxli::NodeGatherer::filters’ [-Wreorder] 76 | KmerFilterList filters; | ^~~~~~~ src/oxli/traversal.cc:53:1: warning: when initialized here [-Wreorder] 53 | NodeGatherer::NodeGatherer(const Hashgraph * ht, | ^~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DVERSION=2.1.2 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -UNO_UNIQUE_RC -Iinclude -I. -Iinclude -Ithird-party/seqan/core/include -Ithird-party/smhasher -I/usr/include/python3.9 -c third-party/smhasher/MurmurHash3.cc -o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -O3 -std=c++11 -pedantic -fopenmp x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/khmer-ratrfy/khmer-2.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/src/khmer/_cpy_countgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_counttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_graphlabels.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashset.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hashtable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_hllcounter.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodegraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_nodetable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readaligner.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcountgraph.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_smallcounttable.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_subsetpartition.o build/temp.linux-x86_64-3.9/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.9/src/oxli/alphabets.o build/temp.linux-x86_64-3.9/src/oxli/assembler.o build/temp.linux-x86_64-3.9/src/oxli/hashgraph.o build/temp.linux-x86_64-3.9/src/oxli/hashtable.o build/temp.linux-x86_64-3.9/src/oxli/hllcounter.o build/temp.linux-x86_64-3.9/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.9/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.9/src/oxli/labelhash.o build/temp.linux-x86_64-3.9/src/oxli/read_aligner.o build/temp.linux-x86_64-3.9/src/oxli/read_parsers.o build/temp.linux-x86_64-3.9/src/oxli/storage.o build/temp.linux-x86_64-3.9/src/oxli/subset.o build/temp.linux-x86_64-3.9/src/oxli/traversal.o build/temp.linux-x86_64-3.9/third-party/smhasher/MurmurHash3.o -lz -lbz2 -o /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -fopenmp running build_scripts running install_lib creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9 creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_args.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_logger.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/thread_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/trimming.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/kfile.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/graph_features.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_banding.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_assembly.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hll.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_lump.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/.gitignore -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer creating /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__init__.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/build_graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/functions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-ratrfy/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/partition.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_args.py to khmer_args.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/khmer_logger.py to khmer_logger.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/thread_utils.py to thread_utils.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/trimming.py to trimming.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/utils.py to utils.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/kfile.py to kfile.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/graph_features.py to graph_features.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_banding.py to test_banding.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_countgraph.py to test_countgraph.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counting_single.py to test_counting_single.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_counttable.py to test_counttable.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cpython_hierarchy.py to test_cpython_hierarchy.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_assembly.py to test_cython_assembly.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_cython_parsing.py to test_cython_parsing.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_filter_abund.py to test_filter_abund.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_functions.py to test_functions.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_graph.py to test_graph.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hashset.py to test_hashset.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_hll.py to test_hll.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_labelhash.py to test_labelhash.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_lump.py to test_lump.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nibblestorage.py to test_nibblestorage.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_nodegraph.py to test_nodegraph.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_normalize_by_median.py to test_normalize_by_median.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_oxli_functions.py to test_oxli_functions.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_aligner.py to test_read_aligner.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_handling.py to test_read_handling.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sandbox_scripts.py to test_sandbox_scripts.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_arguments.py to test_script_arguments.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_script_output.py to test_script_output.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_scripts.py to test_scripts.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_sequence_validation.py to test_sequence_validation.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_streaming_io.py to test_streaming_io.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py to test_subset_graph.cpython-39.pyc /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:61: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:82: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="? /usr/lib/python3.9/dist-packages/khmer/tests/test_subset_graph.py:509: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_tabletype.py to test_tabletype.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_threaded_sequence_processor.py to test_threaded_sequence_processor.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_version.py to test_version.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test_read_parsers.py to test_read_parsers.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/khmer_tst_utils.py to khmer_tst_utils.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_version.py to _version.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/__init__.py to __init__.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/build_graph.py to build_graph.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/functions.py to functions.cpython-39.pyc byte-compiling /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli/partition.py to partition.cpython-39.pyc running install_egg_info Copying khmer.egg-info to /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer-2.1.2.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.9/abundance-dist-single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/annotate-partitions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/count-median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/do-partition.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-long-sequences.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-partitions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/fastq-to-fasta.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund-single.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-stoptags.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/find-knots.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/interleave-reads.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-into-counting.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/make-initial-stoptags.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/merge-partitions.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/normalize-by-median.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/partition-graph.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/readstats.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/sample-reads-randomly.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/split-paired-reads.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/trim-low-abund.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/unique-kmers.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-paired-reads.py -> /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 rm -f debian/khmer-common.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' cd src/oxli && /usr/bin/make PREFIX=../debian/tmp install make[2]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg/src/oxli' rm -rf ../debian/tmp/include/oxli ../debian/tmp/include/khmer mkdir -p ../debian/tmp/lib ../debian/tmp/lib/pkgconfig ../debian/tmp/include/oxli cp -r ../../include/oxli/hashtable.hh ../../include/oxli/hashgraph.hh ../../include/oxli/hllcounter.hh ../../include/oxli/oxli_exception.hh ../../include/oxli/oxli.hh ../../include/oxli/kmer_hash.hh ../../include/oxli/labelhash.hh ../../include/oxli/traversal.hh ../../include/oxli/read_aligner.hh ../../include/oxli/read_parsers.hh ../../include/oxli/subset.hh ../../include/oxli/kmer_filters.hh ../../include/oxli/assembler.hh ../../include/oxli/alphabets.hh ../../include/oxli/storage.hh \ ../../third-party/smhasher/MurmurHash3.h \ ../debian/tmp/include/oxli/ cp oxli.pc ../debian/tmp/lib/pkgconfig/ cp liboxli.so.1 liboxli.a ../debian/tmp/lib/ ln -sf ../debian/tmp/lib/liboxli.so.1 ../debian/tmp/lib/liboxli.so make[2]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg/src/oxli' dh_install install -d debian/khmer-common/usr/share/file/khmer cp --reflink=auto -a ./include/oxli/magic debian/khmer-common/usr/share/file/khmer/ install -d debian/.debhelper/generated/khmer-common install -d debian/.debhelper/generated/khmer install -d debian/.debhelper/generated/liboxli1 install -d debian/.debhelper/generated/liboxli-dev find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' dh_installdocs -i -O--buildsystem=pybuild install -d debian/khmer-common/usr/share/doc/khmer-common cd './build/sphinx/html/..' && find 'html' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/khmer-ratrfy/khmer-2.1.2+dfsg/debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./CITATION debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./README.rst debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./debian/README.test debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./debian/tests/run-unit-test debian/khmer-common/usr/share/doc/khmer-common cp --reflink=auto -a ./src/oxli/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common chmod -R u\+rw,go=rX debian/khmer-common/usr/share/doc install -p -m0644 debian/copyright debian/khmer-common/usr/share/doc/khmer-common/copyright install -d debian/khmer-common/usr/share/doc-base/ install -p -m0644 debian/doc-base debian/khmer-common/usr/share/doc-base/khmer-common.khmer rm -f debian/khmer-common.debhelper.log debian/rules override_dh_sphinxdoc make[1]: Entering directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' dh_sphinxdoc ln -sf ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -sf ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js ln -sf ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js ln -sf ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js ln -sf ../../../../javascript/sphinxdoc/1.0/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0), libjs-sphinxdoc (>= 2.0)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0), libjs-sphinxdoc (>= 1.8), libjs-sphinxdoc (>= 2.0)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Depends debian/khmer-common.substvars; echo "sphinxdoc:Depends=libjs-sphinxdoc (>= 1.0), libjs-sphinxdoc (>= 1.8), libjs-sphinxdoc (>= 2.0), libjs-sphinxdoc (>= 2.4.3-5~)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars (grep -a -s -v sphinxdoc:Built-Using debian/khmer-common.substvars; echo "sphinxdoc:Built-Using=sphinx (= 4.3.1-1)") > debian/khmer-common.substvars.new mv debian/khmer-common.substvars.new debian/khmer-common.substvars rdfind -makesymlinks true -followsymlinks true\ /usr/lib/python3/dist-packages/guzzle_sphinx_theme \ debian/khmer-common debian/khmer-common/usr debian/khmer-common/usr/share debian/khmer-common/usr/share/file debian/khmer-common/usr/share/file/khmer debian/khmer-common/usr/share/file/khmer/magic debian/khmer-common/usr/share/doc debian/khmer-common/usr/share/doc/khmer-common debian/khmer-common/usr/share/doc/khmer-common/html debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo debian/khmer-common/usr/share/doc/khmer-common/html/LICENSE.html debian/khmer-common/usr/share/doc/khmer-common/html/_images debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png debian/khmer-common/usr/share/doc/khmer-common/html/_sources debian/khmer-common/usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/contributors.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/CODE_OF_CONDUCT.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/a-quick-guide-to-testing.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/binary-file-formats.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/codebase-guide.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/development.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/for-khmer-developers.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/getting-started.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/guidelines-continued-dev.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/hackathon.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/python-api.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/release.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/scripts-and-sandbox.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/introduction.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.1.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.1.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.2.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.3.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.4.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.0.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.1.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/roadmap.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/api-examples.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/biblio.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/blog-posts.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/choosing-table-sizes.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/examples.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/galaxy.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/getting-help.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/guide.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/index.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/install.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/known-issues.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/partitioning-big-data.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/scripts.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_static debian/khmer-common/usr/share/doc/khmer-common/html/_static/basic.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/documentation_options.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot 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debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/guzzle.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png debian/khmer-common/usr/share/doc/khmer-common/html/_static/pygments.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html debian/khmer-common/usr/share/doc/khmer-common/html/dev debian/khmer-common/usr/share/doc/khmer-common/html/dev/CODE_OF_CONDUCT.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/a-quick-guide-to-testing.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/binary-file-formats.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/codebase-guide.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/development.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/for-khmer-developers.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/getting-started.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/guidelines-continued-dev.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/hackathon.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/index.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/python-api.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/release.html debian/khmer-common/usr/share/doc/khmer-common/html/dev/scripts-and-sandbox.html debian/khmer-common/usr/share/doc/khmer-common/html/genindex.html debian/khmer-common/usr/share/doc/khmer-common/html/index.html debian/khmer-common/usr/share/doc/khmer-common/html/introduction.html debian/khmer-common/usr/share/doc/khmer-common/html/objects.inv debian/khmer-common/usr/share/doc/khmer-common/html/release-notes debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/index.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.1.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.1.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.2.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.3.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.4.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.0.html debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.1.html debian/khmer-common/usr/share/doc/khmer-common/html/roadmap.html debian/khmer-common/usr/share/doc/khmer-common/html/search.html debian/khmer-common/usr/share/doc/khmer-common/html/searchindex.js debian/khmer-common/usr/share/doc/khmer-common/html/user debian/khmer-common/usr/share/doc/khmer-common/html/user/api-examples.html debian/khmer-common/usr/share/doc/khmer-common/html/user/biblio.html debian/khmer-common/usr/share/doc/khmer-common/html/user/blog-posts.html debian/khmer-common/usr/share/doc/khmer-common/html/user/choosing-table-sizes.html debian/khmer-common/usr/share/doc/khmer-common/html/user/examples.html debian/khmer-common/usr/share/doc/khmer-common/html/user/galaxy.html debian/khmer-common/usr/share/doc/khmer-common/html/user/getting-help.html debian/khmer-common/usr/share/doc/khmer-common/html/user/guide.html debian/khmer-common/usr/share/doc/khmer-common/html/user/index.html debian/khmer-common/usr/share/doc/khmer-common/html/user/install.html debian/khmer-common/usr/share/doc/khmer-common/html/user/known-issues.html debian/khmer-common/usr/share/doc/khmer-common/html/user/partitioning-big-data.html debian/khmer-common/usr/share/doc/khmer-common/html/user/scripts.html debian/khmer-common/usr/share/doc/khmer-common/README.rst debian/khmer-common/usr/share/doc/khmer-common/README.test debian/khmer-common/usr/share/doc/khmer-common/run-unit-test debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc debian/khmer-common/usr/share/doc/khmer-common/copyright debian/khmer-common/usr/share/doc-base debian/khmer-common/usr/share/doc-base/khmer-common.khmer Now scanning "/usr/lib/python3/dist-packages/guzzle_sphinx_theme", found 117 files. Now scanning "debian/khmer-common"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 195 files. Now scanning "debian/khmer-common/usr"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 195 files. Now scanning "debian/khmer-common/usr/share"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 195 files. Now scanning "debian/khmer-common/usr/share/file", found 1 files. Now scanning "debian/khmer-common/usr/share/file/khmer", found 1 files. Now scanning "debian/khmer-common/usr/share/file/khmer/magic", found 1 files. Now scanning "debian/khmer-common/usr/share/doc"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 193 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 193 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 187 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/.buildinfo", found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/LICENSE.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images", found 2 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources", found 41 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/LICENSE.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/contributors.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/CODE_OF_CONDUCT.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/a-quick-guide-to-testing.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/binary-file-formats.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/codebase-guide.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/development.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/for-khmer-developers.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/getting-started.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/guidelines-continued-dev.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/hackathon.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/python-api.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/release.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/dev/scripts-and-sandbox.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/introduction.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes", found 9 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.0.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.2.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.3.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-1.4.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.0.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/release-notes/release-2.1.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/roadmap.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/api-examples.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/biblio.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/blog-posts.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/choosing-table-sizes.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/examples.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/galaxy.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/getting-help.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/guide.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/index.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/install.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/known-issues.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/partitioning-big-data.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_sources/user/scripts.rst.txt", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 99 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/basic.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css", found 3 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//doctools.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/documentation_options.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts", found 84 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans", found 41 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts", found 40 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro", found 35 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Black.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Bold.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-ExtraLight.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Light.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Regular.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/EOT/SourceSerifPro-Semibold.eot", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Black.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Bold.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-ExtraLight.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Light.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Regular.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/OTF/SourceSerifPro-Semibold.otf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/README.md", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/ReadMe.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/SourceSerifProReadMe.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Black.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Bold.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-ExtraLight.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Light.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Regular.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/TTF/SourceSerifPro-Semibold.ttf", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF", found 12 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Black.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Bold.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-ExtraLight.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Light.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Regular.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/OTF/SourceSerifPro-Semibold.otf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF", found 6 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Black.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-ExtraLight.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/bower.json", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/source-serif-pro.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/guzzle.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//jquery.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js", found 2 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/labibi.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//language_data.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/pygments.css", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//searchtools.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js"readfileinfo.cc:Something went wrong when reading file info from "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js" :No such file or directory failed to read file info on file "debian/khmer-common/usr/share/doc/khmer-common/html/_static//underscore.js , found 0 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/contributors.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/CODE_OF_CONDUCT.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/a-quick-guide-to-testing.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/binary-file-formats.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/codebase-guide.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/development.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/for-khmer-developers.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/getting-started.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/guidelines-continued-dev.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/hackathon.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/python-api.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/release.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/dev/scripts-and-sandbox.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/genindex.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/introduction.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/objects.inv", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes", found 9 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.0.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.2.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.3.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-1.4.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.0.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/release-notes/release-2.1.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/roadmap.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/search.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/searchindex.js", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user", found 13 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/api-examples.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/biblio.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/blog-posts.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/choosing-table-sizes.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/examples.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/galaxy.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/getting-help.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/guide.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/index.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/install.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/known-issues.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/partitioning-big-data.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/html/user/scripts.html", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/README.rst", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/README.test", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/run-unit-test", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/test-compile.cc", found 1 files. Now scanning "debian/khmer-common/usr/share/doc/khmer-common/copyright", found 1 files. Now scanning "debian/khmer-common/usr/share/doc-base", found 1 files. Now scanning "debian/khmer-common/usr/share/doc-base/khmer-common.khmer", found 1 files. Now have 1929 files in total. Removed 1631 files due to nonunique device and inode. Total size is 11822152 bytes or 11 MiB Removed 113 files due to unique sizes from list. 185 files left. Now eliminating candidates based on first bytes: removed 3 files from list. 182 files left. Now eliminating candidates based on last bytes: removed 0 files from list. 182 files left. Now eliminating candidates based on sha1 checksum: removed 0 files from list. 182 files left. It seems like you have 182 files that are not unique Totally, 5 MiB can be reduced. Now making results file results.txt Now making symbolic links. creating Making 91 links. if [ -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ]; then \ rm debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt && \ cd debian/khmer-common/usr/share/doc/khmer-common/html/_sources/ && \ ln -s ../../CITATION citations.rst.txt; fi make[1]: Leaving directory '/build/khmer-ratrfy/khmer-2.1.2+dfsg' dh_installchangelogs -i -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/khmer-common/usr/share/doc/khmer-common/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer-common/usr/share/doc/khmer-common/changelog dh_installman -i -O--buildsystem=pybuild dh_python3 -i -O--buildsystem=pybuild D: dh_python3 dh_python3:161: version: 5.20211114 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-i', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': False, 'arch': False, 'package': None, 'no_package': None, 'compile_all': False, 'vrange': None, 'regexpr': None, 'accept_upstream_versions': False, 'depends': None, 'depends_section': None, 'recommends': None, 'recommends_section': None, 'suggests': None, 'suggests_section': None, 'requires': None, 'shebang': None, 'ignore_shebangs': False, 'clean_dbg_pkg': True, 'no_ext_rename': False, 'no_shebang_rewrite': False, 'O': '--buildsystem=pybuild'} D: dh_python3 dh_python3:164: args: [] D: dh_python3 dh_python3:165: supported Python versions: 3.9,3.10 (default=3.9) D: dh_python3 debhelper:150: skipping package khmer-common (missing ${python3:Depends} in Depends) D: dh_python3 debhelper:157: source=khmer, binary packages=[] E: dh_python3 dh_python3:176: no package to act on (python3-foo or one with ${python3:Depends} in Depends) dh_installsystemduser -i -O--buildsystem=pybuild dh_perl -i -O--buildsystem=pybuild dh_link -i -O--buildsystem=pybuild rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/js/bootstrap.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/js/bootstrap.min.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Bold.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Semibold.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff ln -s ../../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Light.ttf.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/source-serif-pro/WOFF/TTF/SourceSerifPro-Regular.ttf.woff ln -s 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debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Bold-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Semibold-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Regular-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-LightItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-SemiboldItalic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Light-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBoldItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-ExtraBold-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-BoldItalic-webfont.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf ln -s ../../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/fonts/OpenSans-Italic-webfont.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css ln -s ../../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/open-sans/stylesheet.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/open-sans/stylesheet.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSans-Italic.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Italic.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSerif-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSerif-Regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/LiberationSans-Regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/LiberationSans-Regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.svg ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.svg debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.svg rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.ttf debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.ttf rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.woff debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.eot debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.eot rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2 ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/fonts/glyphicons-halflings-regular.woff2 debian/khmer-common/usr/share/doc/khmer-common/html/_static/fonts/glyphicons-halflings-regular.woff2 rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/bootstrap.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap.min.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/bootstrap-theme.min.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/bootstrap-theme.min.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css ln -s ../../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/css/font-face.css debian/khmer-common/usr/share/doc/khmer-common/html/_static/css/font-face.css rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js ln -s ../../../../../lib/python3/dist-packages/guzzle_sphinx_theme/guzzle_sphinx_theme/static/jquery.min.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.min.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js ln -s ../../../../javascript/sphinxdoc/1.0/underscore.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/underscore.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js ln -s ../../../../javascript/sphinxdoc/1.0/searchtools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/searchtools.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js ln -s ../../../../javascript/sphinxdoc/1.0/language_data.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/language_data.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js ln -s ../../../../javascript/sphinxdoc/1.0/jquery.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/jquery.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js ln -s ../../../../javascript/sphinxdoc/1.0/doctools.js debian/khmer-common/usr/share/doc/khmer-common/html/_static/doctools.js rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt ln -s ../../CITATION debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt dh_strip_nondeterminism -i -O--buildsystem=pybuild Using 1638565179 as canonical time Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_images/artifact-removal.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_images/partitioning-workflow.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/file.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/minus.png using File::StripNondeterminism::handlers::png Normalizing debian/khmer-common/usr/share/doc/khmer-common/html/_static/plus.png using File::StripNondeterminism::handlers::png dh_compress -i -O--buildsystem=pybuild cd debian/khmer-common chmod a-x usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian gzip -9nf usr/share/doc/khmer-common/CITATION usr/share/doc/khmer-common/changelog usr/share/doc/khmer-common/changelog.Debian cd '/build/khmer-ratrfy/khmer-2.1.2+dfsg' rm -f debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt.gz ln -s ../../CITATION.gz debian/khmer-common/usr/share/doc/khmer-common/html/_sources/citations.rst.txt.gz dh_fixperms -i -O--buildsystem=pybuild find debian/khmer-common ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/khmer-common/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer-common/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer-common/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer-common -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -i -O--buildsystem=pybuild dh_installdeb -i -O--buildsystem=pybuild install -d debian/khmer-common/DEBIAN cp -f debian/khmer-common.postinst debian/khmer-common/DEBIAN/postinst [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postinst" chmod 0755 -- debian/khmer-common/DEBIAN/postinst cp -f debian/khmer-common.postrm debian/khmer-common/DEBIAN/postrm [META] Replace #TOKEN#s in "debian/khmer-common/DEBIAN/postrm" chmod 0755 -- debian/khmer-common/DEBIAN/postrm dh_gencontrol -i -O--buildsystem=pybuild echo misc:Depends= >> debian/khmer-common.substvars echo misc:Pre-Depends= >> debian/khmer-common.substvars dpkg-gencontrol -pkhmer-common -ldebian/changelog -Tdebian/khmer-common.substvars -Pdebian/khmer-common chmod 0644 -- debian/khmer-common/DEBIAN/control dh_md5sums -i -O--buildsystem=pybuild cd debian/khmer-common >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/khmer-common/DEBIAN/md5sums dh_builddeb -i -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/khmer-common .. dpkg-deb: building package 'khmer-common' in '../khmer-common_2.1.2+dfsg-10_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../khmer_2.1.2+dfsg-10_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/khmer-ratrfy /tmp/khmer-2.1.2+dfsg-102hci5iiu I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.kkAtyyv5k5... I: success in 1175.9383 seconds md5: khmer-common_2.1.2+dfsg-10_all.deb: OK sha1: khmer-common_2.1.2+dfsg-10_all.deb: OK sha256: khmer-common_2.1.2+dfsg-10_all.deb: OK Checksums: OK