Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/k/khmer/khmer_2.1.2+dfsg-8_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/khmer-2.1.2+dfsg-8jynv89d6/khmer_2.1.2+dfsg-8_amd64.buildinfo Get source package info: khmer=2.1.2+dfsg-8 Source URL: http://snapshot.notset.fr/mr/package/khmer/2.1.2+dfsg-8/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=asciidoctor=2.0.12-1 autoconf=2.69-14 automake=1:1.16.3-2 autopoint=0.21-3 autotools-dev=20180224.1+nmu1 base-files=11 base-passwd=3.5.48 bash=5.1-2 binutils=2.35.1-6 binutils-common=2.35.1-6 binutils-x86-64-linux-gnu=2.35.1-6 bsdextrautils=2.36.1-4 bsdutils=1:2.36.1-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20200601 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.1-3 cython3=0.29.21-3+b1 dash=0.5.11+git20200708+dd9ef66-5 debconf=1.5.74 debhelper=13.3.1 debianutils=4.11.2 dh-autoreconf=19 dh-exec=0.23.2 dh-python=4.20201102 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-5 docutils-common=0.16+dfsg-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13+20201015-2 file=1:5.39-3 findutils=4.7.0+git20201010-2 fonts-glyphicons-halflings=1.009~3.4.1+dfsg-1 fonts-liberation=1:1.07.4-11 g++=4:10.2.0-1 g++-10=10.2.1-3 gcc=4:10.2.0-1 gcc-10=10.2.1-3 gcc-10-base=10.2.1-3 gettext=0.21-3 gettext-base=0.21-3 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-9 libarchive-zip-perl=1.68-1 libasan6=10.2.1-3 libatomic1=10.2.1-3 libattr1=1:2.4.48-6 libaudit-common=1:3.0-1 libaudit1=1:3.0-1 libbinutils=2.35.1-6 libblkid1=2.36.1-4 libbz2-1.0=1.0.8-4 libbz2-dev=1.0.8-4 libc-bin=2.31-7 libc-dev-bin=2.31-7 libc6=2.31-7 libc6-dev=2.31-7 libcap-ng0=0.7.9-2.2+b1 libcc1-0=10.2.1-3 libcom-err2=1.45.6-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-6 libctf0=2.35.1-6 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.256 libdebhelper-perl=13.3.1 libdpkg-perl=1.20.5 libelf1=0.182-2 libexpat1=2.2.10-1 libexpat1-dev=2.2.10-1 libffi7=3.3-5 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.1-3 libgcc-s1=10.2.1-3 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libgmp10=2:6.2.1+dfsg-1 libgomp1=10.2.1-3 libgpg-error0=1.38-2 libgssapi-krb5-2=1.18.3-4 libicu67=67.1-5 libisl23=0.23-1 libitm1=10.2.1-3 libjs-bootstrap=3.4.1+dfsg-1 libjs-jquery=3.5.1+dfsg+~3.5.5-4 libjs-sphinxdoc=3.4.1-1 libjs-underscore=1.9.1~dfsg-1 libk5crypto3=1.18.3-4 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-4 libkrb5support0=1.18.3-4 liblsan0=10.2.1-3 liblz4-1=1.9.3-1 liblzma5=5.2.5-1.0 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.36.1-4 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncursesw6=6.2+20201114-2 libnettle8=3.6-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-2 libpam-modules-bin=1.4.0-2 libpam-runtime=1.4.0-2 libpam0g=1.4.0-2 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.0-6 libpipeline1=1.5.3-1 libpython3-all-dev=3.9.1-1 libpython3-dev=3.9.1-1 libpython3-stdlib=3.9.1-1 libpython3.9=3.9.1-1 libpython3.9-dev=3.9.1-1 libpython3.9-minimal=3.9.1-1 libpython3.9-stdlib=3.9.1-1 libquadmath0=10.2.1-3 libreadline8=8.1-1 libruby2.7=2.7.2-3 libseccomp2=2.5.1-1 libselinux1=3.1-2+b2 libsigsegv2=2.12-3 libsmartcols1=2.36.1-4 libsqlite3-0=3.34.0-1 libssl1.1=1.1.1i-1 libstdc++-10-dev=10.2.1-3 libstdc++6=10.2.1-3 libsub-override-perl=0.09-2 libsystemd0=247.2-4 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.1-1 libtirpc-dev=1.3.1-1 libtirpc3=1.3.1-1 libtool=2.4.6-14 libtsan0=10.2.1-3 libubsan1=10.2.1-3 libuchardet0=0.0.7-1 libudev1=247.2-4 libunistring2=0.9.10-4 libuuid1=2.36.1-4 libxml2=2.9.10+dfsg-6.3+b1 libyaml-0-2=0.2.2-1 libzstd1=1.4.8+dfsg-1 linux-libc-dev=5.10.4-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 mailcap=3.68 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 media-types=1.1.0 mime-support=3.66 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 openssl=1.1.1i-1 patch=2.7.6-6 perl=5.32.0-6 perl-base=5.32.0-6 perl-modules-5.32=5.32.0-6 po-debconf=1.0.21+nmu1 python-babel-localedata=2.8.0+dfsg.1-5 python3=3.9.1-1 python3-alabaster=0.7.8-1.1 python3-all=3.9.1-1 python3-all-dev=3.9.1-1 python3-attr=20.3.0-1 python3-babel=2.8.0+dfsg.1-5 python3-bz2file=0.98-3 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-dev=3.9.1-1 python3-distutils=3.9.1-2 python3-docutils=0.16+dfsg-3 python3-guzzle-sphinx-theme=0.7.11-5 python3-idna=2.10-1 python3-imagesize=1.2.0-2 python3-importlib-metadata=1.6.0-2 python3-iniconfig=1.1.1-1 python3-jinja2=2.11.2-1 python3-lib2to3=3.9.1-2 python3-markupsafe=1.1.1-1+b3 python3-minimal=3.9.1-1 python3-more-itertools=4.2.0-3 python3-packaging=20.8-1 python3-pkg-resources=51.1.0-1 python3-pluggy=0.13.0-5 python3-py=1.10.0-1 python3-pygments=2.7.1+dfsg-1 python3-pyparsing=2.4.7-1 python3-pytest=6.0.2-2 python3-pytest-runner=2.11.1-1.2 python3-requests=2.25.1+dfsg-2 python3-roman=2.0.0-5 python3-screed=1.0.4-1 python3-setuptools=51.1.0-1 python3-six=1.15.0-2 python3-snowballstemmer=2.0.0-2 python3-sphinx=3.4.1-1 python3-sphinxcontrib.autoprogram=0.1.5-2 python3-toml=0.10.1-1 python3-tz=2020.5-1 python3-urllib3=1.26.2-1 python3-zipp=1.0.0-3 python3.9=3.9.1-1 python3.9-dev=3.9.1-1 python3.9-minimal=3.9.1-1 rake=13.0.1-4 rdfind=1.4.1-1+b3 readline-common=8.1-1 ruby=1:2.7+2 ruby-asciidoctor=2.0.12-1 ruby-minitest=5.13.0-1 ruby-net-telnet=0.1.1-2 ruby-power-assert=1.1.7-1 ruby-rubygems=3.2.0~rc.2-5 ruby-test-unit=3.3.5-1 ruby-xmlrpc=0.3.0-2 ruby2.7=2.7.2-3 rubygems-integration=1.17.3 sed=4.7-1 sensible-utils=0.0.12+nmu1 sgml-base=1.30 sphinx-common=3.4.1-1 sysvinit-utils=2.96-5 tar=1.32+dfsg-1 tzdata=2020f-1 util-linux=2.36.1-4 xml-core=0.18+nmu1 xz-utils=5.2.5-1.0 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210104T143637Z/ 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-8 && mkdir -p /build/khmer-NP0VRJ && dpkg-source --no-check -x /*.dsc /build/khmer-NP0VRJ/khmer-2.1.2+dfsg && chown -R builduser:builduser /build/khmer-NP0VRJ" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/khmer-NP0VRJ/khmer-2.1.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609766292" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/khmer-NP0VRJ /tmp/khmer-2.1.2+dfsg-8jynv89d6 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20210104T143637Z 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.a44NM_AIOt 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.a44NM_AIOt Reading package lists... Building dependency tree... util-linux is already the newest version (2.36.1-4). 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/20210104T143637Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210104T143637Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (866 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 ... 4647 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-7) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210104T143637Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.a44NM_AIOt Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210104T143637Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 19s (1208 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.a44NM_AIOt I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d khmer=2.1.2+dfsg-8 && mkdir -p /build/khmer-NP0VRJ && dpkg-source --no-check -x /*.dsc /build/khmer-NP0VRJ/khmer-2.1.2+dfsg && chown -R builduser:builduser /build/khmer-NP0VRJ"' exec /tmp/mmdebstrap.a44NM_AIOt 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/20210814T212851Z bookworm/main khmer 2.1.2+dfsg-8 (dsc) [2679 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main khmer 2.1.2+dfsg-8 (tar) [18.1 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main khmer 2.1.2+dfsg-8 (diff) [14.1 kB] Fetched 18.1 MB in 14s (1276 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'khmer_2.1.2+dfsg-8.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting khmer in /build/khmer-NP0VRJ/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-8.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 I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/khmer-NP0VRJ/khmer-2.1.2+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1609766292" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.a44NM_AIOt dpkg-buildpackage: info: source package khmer dpkg-buildpackage: info: source version 2.1.2+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' dh_auto_clean || /bin/true install -d /build/khmer-NP0VRJ/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --clean --test-pytest -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc make[2]: Leaving directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg/src/oxli' rm -rf __pycache__ .eggs make[1]: Leaving directory '/build/khmer-NP0VRJ/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-arch dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild install -d /build/khmer-NP0VRJ/khmer-2.1.2\+dfsg/debian/.debhelper/generated/_source/home pybuild --configure --test-pytest -i python{version} -p 3.9 I: pybuild base:232: python3.9 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' dh_auto_build pybuild --build --test-pytest -i python{version} -p 3.9 I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/_version.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/kfile.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/khmer_args.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/khmer_logger.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/thread_utils.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/trimming.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer copying khmer/utils.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/graph_features.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_banding.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_countgraph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_counting_single.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_counttable.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cpython_hierarchy.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cython_assembly.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_cython_parsing.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_filter_abund.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_functions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_hashset.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_hll.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_labelhash.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_lump.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_nibblestorage.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_nodegraph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_normalize_by_median.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_oxli_functions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_aligner.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_handling.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_sandbox_scripts.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_script_arguments.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_script_output.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_scripts.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_sequence_validation.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_streaming_io.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_subset_graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_tabletype.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_threaded_sequence_processor.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_version.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/test_read_parsers.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests copying tests/khmer_tst_utils.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/build_graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/functions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli copying oxli/partition.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_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 writing manifest file 'khmer.egg-info/SOURCES.txt' copying tests/.gitignore -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests creating /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/README.rst -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/all-A.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ct -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k12.ht -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.stoptags -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/badversion-k32.tagset -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/banding-reads.fq -> /build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/bogus.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/empty-file.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/fakelump.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k12.ht -> /build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.stoptags -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/goodversion-k32.tagset -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/multi-output.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/normC20k20.ct -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-mixed.fq -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired-slash1.fq -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fa.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/paired.malformat.fq -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-default.json -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/readaligner-k12.json -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/simple-genome.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/single-read.fq -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-empty.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph2.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-graph5.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-labels.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-large.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-multi.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap1.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-overlap2.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-reads.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-short.fa -> /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/test-transcript.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/truncated.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying tests/test-data/unclean-reads.fastq -> /build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data copying khmer/_oxli/assembly.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/assembly.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hllcounter.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/oxli_types.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/traversal.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli UPDATING /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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_64-3.9 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:74:2: 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:412:2: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:1737:2: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:203:31: 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:203:31: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_9Alphabets_get(PyObject*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_4name___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_8sequence___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11description___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_7quality___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11cleaned_seq___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5733:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5733 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function ‘int __pyx_f_5khmer_5_oxli_7parsing__check_is_pair(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*, __pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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 running develop 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 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:74:2: 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:412:2: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:1737:2: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:203:31: 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:203:31: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/assembly.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/assembly.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/assembly.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/assembly.cpp:538: note: this is the location of the previous definition 538 | #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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:651: include/khmer/_cpy_utils.hh:17: warning: "PyInt_Check" redefined 17 | #define PyInt_Check(arg) PyLong_Check(arg) | khmer/_oxli/graphs.cpp:534: note: this is the location of the previous definition 534 | #define PyInt_Check(op) PyLong_Check(op) | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:18: warning: "PyInt_AsLong" redefined 18 | #define PyInt_AsLong(arg) PyLong_AsLong(arg) | khmer/_oxli/graphs.cpp:541: note: this is the location of the previous definition 541 | #define PyInt_AsLong PyLong_AsLong | In file included from include/khmer/_cpy_khmer.hh:49, from khmer/_oxli/graphs.cpp:651: include/khmer/_cpy_utils.hh:19: warning: "PyInt_FromLong" redefined 19 | #define PyInt_FromLong(arg) PyLong_FromLong(arg) | khmer/_oxli/graphs.cpp:538: note: this is the location of the previous definition 538 | #define PyInt_FromLong PyLong_FromLong | x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_9Alphabets_get(PyObject*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:2339:47: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 2339 | __pyx_t_4 = (__pyx_v_alphabet != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_alphabet) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_4name___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:3969:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 3969 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_name) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_8sequence___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4057:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4057 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_sequence) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11description___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4144:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4144 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_description) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_7quality___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4228:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4228 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_quality) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘PyObject* __pyx_pf_5khmer_5_oxli_7parsing_8Sequence_11cleaned_seq___get__(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:4312:16: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 4312 | __pyx_t_2 = (__Pyx_PyUnicode_IS_TRUE(__pyx_v_cleaned_seq) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp: In function ‘bool __pyx_f_5khmer_5_oxli_7parsing_sanitize_sequence(std::string&, std::string&, bool)’: khmer/_oxli/parsing.cpp:5733:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 5733 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { | ~~~~~~~~~~^~~~~~~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from khmer/_oxli/parsing.cpp:4: khmer/_oxli/parsing.cpp: In function ‘int __pyx_f_5khmer_5_oxli_7parsing__check_is_pair(__pyx_obj_5khmer_5_oxli_7parsing_Sequence*, __pyx_obj_5khmer_5_oxli_7parsing_Sequence*)’: /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11131:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11131 | __pyx_t_1 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:261:7: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 261 | PyUnicode_WSTR_LENGTH(op) : \ | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:262:52: warning: ‘Py_UNICODE* PyUnicode_AsUnicode(PyObject*)’ is deprecated [-Wdeprecated-declarations] 262 | ((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\ | ^ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( | ^~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:451:75: warning: ‘Py_ssize_t _PyUnicode_get_wstr_length(PyObject*)’ is deprecated [-Wdeprecated-declarations] 451 | #define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op) | ^ /usr/include/python3.9/cpython/unicodeobject.h:264:8: note: in expansion of macro ‘PyUnicode_WSTR_LENGTH’ 264 | PyUnicode_WSTR_LENGTH(op))) | ^~~~~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:453:108: note: in expansion of macro ‘PyUnicode_GET_SIZE’ 453 | #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) | ^~~~~~~~~~~~~~~~~~ khmer/_oxli/parsing.cpp:11304:49: note: in expansion of macro ‘__Pyx_PyUnicode_IS_TRUE’ 11304 | __pyx_t_4 = (__pyx_v_subpart1 != Py_None)&&(__Pyx_PyUnicode_IS_TRUE(__pyx_v_subpart1) != 0); | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing abundance-dist.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing annotate-partitions.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing count-median.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing do-partition.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-long-sequences.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-partitions.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing fastq-to-fasta.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund-single.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-abund.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing filter-stoptags.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing find-knots.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing interleave-reads.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-graph.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing load-into-counting.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing make-initial-stoptags.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing merge-partitions.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing normalize-by-median.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing partition-graph.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing readstats.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing sample-reads-randomly.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing split-paired-reads.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing trim-low-abund.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing unique-kmers.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installing extract-paired-reads.py script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Installed /build/khmer-NP0VRJ/khmer-2.1.2+dfsg Processing dependencies for khmer==2.1.2 Searching for screed==1.0.4 Best match: screed 1.0.4 Adding screed 1.0.4 to easy-install.pth file Installing screed script to /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/fakehome/.local/bin Using /usr/lib/python3/dist-packages Searching for bz2file==0.98 Best match: bz2file 0.98 Adding bz2file 0.98 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for Cython==0.29.21 Best match: Cython 0.29.21 Adding Cython 0.29.21 to easy-install.pth file Using /usr/lib/python3/dist-packages Finished processing dependencies for khmer==2.1.2 running build_sphinx Running Sphinx v3.4.1 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... 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[100%] user/scripts looking for now-outdated files... none found pickling environment... done checking consistency... /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/dev/hackathon.rst: WARNING: document isn't included in any toctree /build/khmer-NP0VRJ/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... [ 26%] dev/guidelines-continued-dev writing output... [ 29%] dev/hackathon writing output... [ 31%] dev/index writing output... [ 34%] dev/python-api writing output... 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[100%] user/scripts /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -N /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --n_tables /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py -x /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/choosing-table-sizes.rst:59: WARNING: unknown option: load-into-counting.py --max-tablesize /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: -x /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/scripts.rst:79: WARNING: unknown option: -N /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/doc/user/scripts.rst:87: WARNING: unknown option: -x /build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/src/oxli' rm -f *.o *.a *.so* oxli.pc g++ -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:203:31: 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:203:31: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:74:2: 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:412:2: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:1737:2: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/src/oxli' make[1]: Leaving directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild rm -f -- debian/khmer.substvars debian/liboxli1.substvars debian/liboxli-dev.substvars rm -fr -- debian/.debhelper/generated/khmer/ debian/khmer/ debian/tmp/ debian/.debhelper/generated/liboxli1/ debian/liboxli1/ debian/.debhelper/generated/liboxli-dev/ debian/liboxli-dev/ dh_auto_install -a -O--buildsystem=pybuild install -d /build/khmer-NP0VRJ/khmer-2.1.2\+dfsg/debian/tmp pybuild --install --test-pytest -i python{version} -p 3.9 --dest-dir /build/khmer-NP0VRJ/khmer-2.1.2\+dfsg/debian/tmp I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer '--install-scripts=/usr/lib/khmer/bin' running install 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 writing manifest file 'khmer.egg-info/SOURCES.txt' copying khmer/_oxli/assembly.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/graphs.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/hashing.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/parsing.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli copying khmer/_oxli/utils.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli UPDATING /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py set /build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 [-Wdeprecated-declarations] 92 | std::auto_ptr instance; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 105 | std::auto_ptr > _gzStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 108 | std::auto_ptr > _bz2Stream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 110 | std::auto_ptr > > _mmapString; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 111 | std::auto_ptr _plainStream; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 116 | std::auto_ptr, SinglePass<> > > _gzReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 119 | std::auto_ptr, SinglePass<> > > _bz2Reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 121 | std::auto_ptr >, SinglePass > > _mmapReaderSinglePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 122 | std::auto_ptr >, DoublePass > > _mmapReaderDoublePass; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 123 | std::auto_ptr > > _istreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 124 | std::auto_ptr > > _ifstreamReader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:74:2: 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:412:2: 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 [-Wdeprecated-declarations] 180 | std::auto_ptr _writer; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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 [-Wdeprecated-declarations] 182 | std::auto_ptr _reader; | ^~~~~~~~ In file included from /usr/include/c++/10/bits/locale_conv.h:41, from /usr/include/c++/10/locale:43, from /usr/include/c++/10/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++/10/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:1737:2: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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:203:31: 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:203:31: 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 -fdebug-prefix-map=/build/khmer-NP0VRJ/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9 creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/kfile.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_args.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/khmer_logger.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/thread_utils.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/trimming.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/utils.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/graph_features.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_banding.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_countgraph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counting_single.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_counttable.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cpython_hierarchy.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_assembly.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_cython_parsing.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_filter_abund.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_functions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hashset.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_hll.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_labelhash.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_lump.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nibblestorage.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_nodegraph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_normalize_by_median.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_oxli_functions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_aligner.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_handling.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sandbox_scripts.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_arguments.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_script_output.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_scripts.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_sequence_validation.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_streaming_io.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_subset_graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_tabletype.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_threaded_sequence_processor.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_version.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test_read_parsers.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/khmer_tst_utils.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/.gitignore -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/100-reads.fq.truncated.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/README.rst -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/all-A.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ct -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k12.ht -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.stoptags -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/badversion-k32.tagset -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/banding-reads.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/biglump-random-20-a.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/bogus.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/casava_18-pe.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/combine_parts_1.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-all-paired-all-keep.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-none-paired.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/dn-test-some-paired-all-keep.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/empty-file.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/fakelump.fa.stoptags.txt -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-A.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/filter-test-B.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k12.ht.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.stoptags -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/goodversion-k32.tagset -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/multi-output.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/normC20k20.ct -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/old-style-format-w-comments.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badleft -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.badright -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken.fq.paired_bad -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken2.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken3.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-broken4.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-2.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-broken.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed-witherror.fa.pe -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.pe -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fa.se -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.pe -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-mixed.fq.se -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired-slash1.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fa.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.1 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired.malformat.fq.2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/paired_one.base.dif.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-X2.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.even.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fa.part -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.fq.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-a.odd.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-20-b.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/random-31-c.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-default.json -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/readaligner-k12.json -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-small.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/real-partition-tiny.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome-reads.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/simple-genome.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/single-read.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fa.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-2.paired2.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-3.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-impaired.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read-paired.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-abund-read.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-empty.fa.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-error-reads.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-n-reads.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-fastq-reads.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-filter-abund-Ns.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph2.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-graph5.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-labels.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-large.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-multi.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-output-partitions.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap1.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-overlap2.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.bz2 -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-reads.fq.gz -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-short.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-contigs.fp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-sweep-reads.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/test-transcript.fa -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/truncated.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/unclean-reads.fastq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/tests/test-data/valid-read-testing.fq -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/tests/test-data creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hllcounter.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/oxli_types.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/traversal.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pxd -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.pyx -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/assembly.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/graphs.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/hashing.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/parsing.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_oxli/utils.cpp -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer/_oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_version.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/khmer/_khmer.cpython-39-x86_64-linux-gnu.so -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/khmer creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/__init__.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/build_graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/functions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli copying /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/.pybuild/cpython3_3.9_khmer/build/oxli/partition.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/python3.9/dist-packages/oxli byte-compiling /build/khmer-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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-NP0VRJ/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 creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer creating /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist-single.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/abundance-dist.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/annotate-partitions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/count-median.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/do-partition.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-long-sequences.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-partitions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/fastq-to-fasta.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund-single.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-abund.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/filter-stoptags.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/find-knots.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/interleave-reads.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/load-into-counting.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/make-initial-stoptags.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/merge-partitions.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/normalize-by-median.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/partition-graph.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/readstats.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/sample-reads-randomly.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/split-paired-reads.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/trim-low-abund.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/unique-kmers.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin copying build/scripts-3.9/extract-paired-reads.py -> /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist-single.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/abundance-dist.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/annotate-partitions.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/count-median.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/do-partition.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-long-sequences.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-partitions.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/fastq-to-fasta.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund-single.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-abund.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/filter-stoptags.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/find-knots.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/interleave-reads.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-graph.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/load-into-counting.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/make-initial-stoptags.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/merge-partitions.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/normalize-by-median.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/partition-graph.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/readstats.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/sample-reads-randomly.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/split-paired-reads.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/trim-low-abund.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/unique-kmers.py to 755 changing mode of /build/khmer-NP0VRJ/khmer-2.1.2+dfsg/debian/khmer/usr/lib/khmer/bin/extract-paired-reads.py to 755 rm -f debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' cd src/oxli && /usr/bin/make PREFIX=../debian/tmp install make[2]: Entering directory '/build/khmer-NP0VRJ/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-NP0VRJ/khmer-2.1.2+dfsg/src/oxli' dh_install install -d debian/.debhelper/generated/khmer-common install -d debian/khmer//usr/share/metainfo/ cp --reflink=auto -a ./debian/khmer.metainfo.xml debian/khmer//usr/share/metainfo// install -d debian/khmer/usr/bin/ cp --reflink=auto -a ./debian/bin/khmer debian/khmer/usr/bin// install -d debian/.debhelper/generated/khmer install -d debian/liboxli1/usr/lib/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.so.1 debian/liboxli1/usr/lib/x86_64-linux-gnu/ install -d debian/.debhelper/generated/liboxli1 install -d debian/liboxli-dev/usr/include/oxli cp --reflink=auto -a ./include/oxli/alphabets.hh ./include/oxli/assembler.hh ./include/oxli/hashgraph.hh ./include/oxli/hashtable.hh ./include/oxli/hllcounter.hh ./include/oxli/kmer_filters.hh ./include/oxli/kmer_hash.hh ./include/oxli/labelhash.hh ./include/oxli/oxli.hh ./include/oxli/oxli_exception.hh ./include/oxli/read_aligner.hh ./include/oxli/read_parsers.hh ./include/oxli/storage.hh ./include/oxli/subset.hh ./include/oxli/traversal.hh debian/liboxli-dev/usr/include/oxli/ install -d debian/liboxli-dev/usr/include/oxli/smhasher cp --reflink=auto -a ./third-party/smhasher/MurmurHash3.h debian/liboxli-dev/usr/include/oxli/smhasher/ install -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu cp --reflink=auto -a ./src/oxli/liboxli.a ./src/oxli/liboxli.so debian/liboxli-dev/usr/lib/x86_64-linux-gnu/ install -d debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a ./src/oxli/oxli.pc debian/liboxli-dev/usr/lib/x86_64-linux-gnu/pkgconfig/ install -d debian/.debhelper/generated/liboxli-dev find debian/khmer -name .gitignore -delete make[1]: Leaving directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' dh_installdocs -a -O--buildsystem=pybuild install -d debian/khmer/usr/share/doc/khmer install -p -m0644 debian/copyright debian/khmer/usr/share/doc/khmer/copyright install -d debian/liboxli1/usr/share/doc/liboxli1 install -p -m0644 debian/copyright debian/liboxli1/usr/share/doc/liboxli1/copyright install -d debian/liboxli-dev/usr/share/doc/liboxli-dev install -p -m0644 debian/copyright debian/liboxli-dev/usr/share/doc/liboxli-dev/copyright rm -f debian/khmer.debhelper.log debian/liboxli-dev.debhelper.log debian/liboxli1.debhelper.log debian/rules override_dh_sphinxdoc make[1]: Entering directory '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' find: ‘debian/khmer-common’: No such file or directory dh_sphinxdoc dh_sphinxdoc: warning: Sphinx documentation not found rdfind -makesymlinks true -followsymlinks true\ /usr/lib/python3/dist-packages/guzzle_sphinx_theme \ Now scanning "/usr/lib/python3/dist-packages/guzzle_sphinx_theme", found 116 files. Now have 116 files in total. Removed 14 files due to nonunique device and inode. Total size is 5330190 bytes or 5 MiB Removed 100 files due to unique sizes from list.2 files left. Now eliminating candidates based on first bytes:removed 2 files from list.0 files left. Now eliminating candidates based on last bytes:removed 0 files from list.0 files left. Now eliminating candidates based on sha1 checksum:removed 0 files from list.0 files left. It seems like you have 0 files that are not unique Totally, 0 B can be reduced. Now making results file results.txt Now making symbolic links. creating Making 0 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-NP0VRJ/khmer-2.1.2+dfsg' dh_installchangelogs -a -O--buildsystem=pybuild install -p -m0644 debian/changelog debian/khmer/usr/share/doc/khmer/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/khmer/usr/share/doc/khmer/changelog install -p -m0644 debian/changelog debian/liboxli1/usr/share/doc/liboxli1/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli1/usr/share/doc/liboxli1/changelog install -p -m0644 debian/changelog debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/liboxli-dev/usr/share/doc/liboxli-dev/changelog dh_installman -a -O--buildsystem=pybuild install -d debian/khmer/usr/share/man/man1/ install -p -m0644 ./debian/khmer.1 debian/khmer/usr/share/man/man1/khmer.1 man-recode --to-code UTF-8 --suffix .dh-new debian/khmer/usr/share/man/man1/khmer.1 mv debian/khmer/usr/share/man/man1/khmer.1.dh-new debian/khmer/usr/share/man/man1/khmer.1 chmod 0644 -- debian/khmer/usr/share/man/man1/khmer.1 dh_python3 -a -O--buildsystem=pybuild D: dh_python3 dh_python3:161: version: 4.20201102 D: dh_python3 dh_python3:162: argv: ['/usr/bin/dh_python3', '-a', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:163: options: {'guess_deps': True, 'skip_private': False, 'verbose': False, 'arch': True, '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 (default=3.9) D: dh_python3 debhelper:99: skipping package liboxli1 (missing ${python3:Depends} in Depends) D: dh_python3 debhelper:99: skipping package liboxli-dev (missing ${python3:Depends} in Depends) D: dh_python3 debhelper:152: source=khmer, binary packages=['khmer'] D: dh_python3 dh_python3:183: processing package khmer... D: dh_python3 fs:49: moving files from debian/khmer/usr/lib/python3.9/dist-packages to debian/khmer/usr/lib/python3/dist-packages/ D: dh_python3 tools:102: fix_shebang (debian/khmer/usr/bin/khmer): doesn't look like a shebang: #!/bin/sh D: dh_python3 fs:260: package khmer details = {'requires.txt': {'debian/khmer/usr/lib/python3/dist-packages/khmer-2.1.2.egg-info/requires.txt'}, 'egg-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {'/usr/lib/khmer': {'shebangs': {/usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3, /usr/bin/python3}, 'compile': True}}, 'compile': True, 'ext_vers': {Version('3.9')}, 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package khmer D: dh_python3 pydist:142: trying to find dependency for Cython>=0.25.2 (python=None) D: dh_python3 pydist:142: trying to find dependency for bz2file (python=None) D: dh_python3 pydist:142: trying to find dependency for screed>=1.0 (python=None) D: dh_python3 depends:275: D={'python3 (<< 3.10)', 'python3-screed (>= 1.0)', 'python3:any', 'python3 (>= 3.9~)', 'cython3 (>= 0.26.1)', 'python3-bz2file'}; R=[]; S=[]; E=[], B=[]; RT=[('/usr/lib/khmer', '')] dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild install -d debian/khmer/usr/share/lintian/overrides install -p -m0644 debian/khmer.lintian-overrides debian/khmer/usr/share/lintian/overrides/khmer install -d debian/liboxli1/usr/share/lintian/overrides install -p -m0644 debian/liboxli1.lintian-overrides debian/liboxli1/usr/share/lintian/overrides/liboxli1 dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild rm -f debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.so ln -s liboxli.so.1 debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.so dh_strip_nondeterminism -a -O--buildsystem=pybuild Using 1609766292 as canonical time Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/100-reads.fq.truncated.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/empty-file.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/goodversion-k12.ht.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/random-20-a.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/test-abund-read-2.fa.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/khmer/usr/lib/python3/dist-packages/khmer/tests/test-data/test-reads.fq.gz using File::StripNondeterminism::handlers::gzip dh_compress -a -O--buildsystem=pybuild cd debian/khmer cd debian/liboxli1 cd debian/liboxli-dev chmod a-x usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 chmod a-x usr/share/doc/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian gzip -9nf usr/share/doc/khmer/changelog usr/share/doc/khmer/changelog.Debian usr/share/man/man1/khmer.1 chmod a-x usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian gzip -9nf usr/share/doc/liboxli-dev/changelog usr/share/doc/liboxli-dev/changelog.Debian gzip -9nf usr/share/doc/liboxli1/changelog usr/share/doc/liboxli1/changelog.Debian cd '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' cd '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' cd '/build/khmer-NP0VRJ/khmer-2.1.2+dfsg' dh_fixperms -a -O--buildsystem=pybuild find debian/khmer ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/liboxli1/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli1/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/liboxli-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/doc -type f -a -true -a ! -regex 'debian/khmer/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/khmer/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/liboxli1/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/khmer/usr/share/man debian/khmer/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/liboxli1 -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 find debian/liboxli-dev -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 find debian/khmer -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 find debian/liboxli1/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/liboxli-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/khmer/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/khmer/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -a -O--buildsystem=pybuild dh_dwz -a -a -O--buildsystem=pybuild install -d debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug -- debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so objcopy --compress-debug-sections debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu/khmer.debug dwz -- debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 dh_strip -a -a -O--buildsystem=pybuild strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/liboxli-dev/usr/lib/x86_64-linux-gnu/liboxli.a install -d debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/19/0799e64eed3cd2fe32ffb4a4877e5ebf5d803b.debug install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2f objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2f/973729f953a6efd57ff0cd797ca323e899e1db.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2f/973729f953a6efd57ff0cd797ca323e899e1db.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/2f/973729f953a6efd57ff0cd797ca323e899e1db.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/89 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/89/dab7d31339264b5de431846671453138d5f009.debug chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/19/0799e64eed3cd2fe32ffb4a4877e5ebf5d803b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 objcopy --add-gnu-debuglink debian/.debhelper/liboxli1/dbgsym-root/usr/lib/debug/.build-id/19/0799e64eed3cd2fe32ffb4a4877e5ebf5d803b.debug debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -d debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc ln -s liboxli1 debian/.debhelper/liboxli1/dbgsym-root/usr/share/doc/liboxli1-dbgsym chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/89/dab7d31339264b5de431846671453138d5f009.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/89/dab7d31339264b5de431846671453138d5f009.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b7 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b7/53c1691cd420c1a9c41f8d191fda8bc5653110.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b7/53c1691cd420c1a9c41f8d191fda8bc5653110.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/b7/53c1691cd420c1a9c41f8d191fda8bc5653110.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7a objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7a/074c7d9e5ef3983caa02eaef8bd65483ac74f2.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7a/074c7d9e5ef3983caa02eaef8bd65483ac74f2.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/7a/074c7d9e5ef3983caa02eaef8bd65483ac74f2.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a5 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a5/d26f00f82505f374f07ea7f088fa2128535a81.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a5/d26f00f82505f374f07ea7f088fa2128535a81.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a5/d26f00f82505f374f07ea7f088fa2128535a81.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a2 objcopy --only-keep-debug --compress-debug-sections debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a2/641d256467511273b2c74a6eefe51a3ac8ce36.debug chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a2/641d256467511273b2c74a6eefe51a3ac8ce36.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.build-id/a2/641d256467511273b2c74a6eefe51a3ac8ce36.debug debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so install -d debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/khmer/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/khmer/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/khmer/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/khmer/usr/lib/debug install -d debian/.debhelper/khmer/dbgsym-root/usr/share/doc ln -s khmer debian/.debhelper/khmer/dbgsym-root/usr/share/doc/khmer-dbgsym dh_makeshlibs -a -a -O--buildsystem=pybuild rm -f debian/khmer/DEBIAN/shlibs rm -f debian/liboxli1/DEBIAN/shlibs install -d debian/liboxli1/DEBIAN echo "liboxli 1 liboxli1 (>= 2.1.2+dfsg)" >> debian/liboxli1/DEBIAN/shlibs chmod 0644 -- debian/liboxli1/DEBIAN/shlibs mv debian/.debhelper/generated/liboxli1/triggers.new debian/.debhelper/generated/liboxli1/triggers rm -f debian/liboxli-dev/DEBIAN/shlibs dh_shlibdeps -a -a -O--buildsystem=pybuild dpkg-shlibdeps -Tdebian/liboxli1.substvars debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 install -d debian/khmer/DEBIAN dpkg-shlibdeps -Tdebian/khmer.substvars debian/khmer/usr/lib/python3/dist-packages/khmer/_khmer.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/assembly.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/graphs.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/hashing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/parsing.cpython-39-x86_64-linux-gnu.so debian/khmer/usr/lib/python3/dist-packages/khmer/_oxli/utils.cpython-39-x86_64-linux-gnu.so dpkg-shlibdeps: warning: symbol BZ2_bzRead used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzdirect used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateEnd used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzReadClose used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol crc32 used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzwrite used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol BZ2_bzReadOpen used by debian/liboxli1/usr/lib/x86_64-linux-gnu/liboxli.so.1 found in none of the libraries dpkg-shlibdeps: warning: 13 other similar warnings have been skipped (use -v to see them all) dh_installdeb -a -O--buildsystem=pybuild printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/postinst cat debian/khmer.postinst.debhelper >> debian/khmer/DEBIAN/postinst chmod 0755 -- debian/khmer/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/khmer/DEBIAN/prerm cat debian/khmer.prerm.debhelper >> debian/khmer/DEBIAN/prerm chmod 0755 -- debian/khmer/DEBIAN/prerm install -p -m0644 debian/.debhelper/generated/liboxli1/triggers debian/liboxli1/DEBIAN/triggers install -d debian/liboxli-dev/DEBIAN dh_gencontrol -a -O--buildsystem=pybuild echo misc:Depends= >> debian/liboxli-dev.substvars echo misc:Pre-Depends= >> debian/liboxli-dev.substvars dpkg-gencontrol -pliboxli-dev -ldebian/changelog -Tdebian/liboxli-dev.substvars -Pdebian/liboxli-dev echo misc:Depends= >> debian/khmer.substvars echo misc:Pre-Depends= >> debian/khmer.substvars install -d debian/.debhelper/khmer/dbgsym-root/DEBIAN dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -Pdebian/.debhelper/khmer/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=khmer-dbgsym "-DDepends=khmer (= \${binary:Version})" "-DDescription=debug symbols for khmer" "-DBuild-Ids=2f973729f953a6efd57ff0cd797ca323e899e1db 7a074c7d9e5ef3983caa02eaef8bd65483ac74f2 89dab7d31339264b5de431846671453138d5f009 a2641d256467511273b2c74a6eefe51a3ac8ce36 a5d26f00f82505f374f07ea7f088fa2128535a81 b753c1691cd420c1a9c41f8d191fda8bc5653110" -DSection=debug -UMulti-Arch -UReplaces -UBreaks echo misc:Depends= >> debian/liboxli1.substvars echo misc:Pre-Depends= >> debian/liboxli1.substvars install -d debian/.debhelper/liboxli1/dbgsym-root/DEBIAN dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/.debhelper/liboxli1/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=liboxli1-dbgsym "-DDepends=liboxli1 (= \${binary:Version})" "-DDescription=debug symbols for liboxli1" -DBuild-Ids=190799e64eed3cd2fe32ffb4a4877e5ebf5d803b -DSection=debug -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/control dpkg-gencontrol -pliboxli1 -ldebian/changelog -Tdebian/liboxli1.substvars -Pdebian/liboxli1 dpkg-gencontrol: warning: package khmer: substitution variable ${python3:Versions} unused, but is defined chmod 0644 -- debian/liboxli-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/control dpkg-gencontrol -pkhmer -ldebian/changelog -Tdebian/khmer.substvars -Pdebian/khmer chmod 0644 -- debian/liboxli1/DEBIAN/control dpkg-gencontrol: warning: package khmer: substitution variable ${python3:Versions} unused, but is defined chmod 0644 -- debian/khmer/DEBIAN/control dh_md5sums -a -O--buildsystem=pybuild cd debian/liboxli1 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/khmer >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/liboxli-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli1/DEBIAN/md5sums cd debian/.debhelper/liboxli1/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/liboxli-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/liboxli1/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/khmer/DEBIAN/md5sums cd debian/.debhelper/khmer/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/khmer/dbgsym-root/DEBIAN/md5sums dh_builddeb -a -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/khmer .. dpkg-deb --root-owner-group --build debian/.debhelper/khmer/dbgsym-root .. dpkg-deb --root-owner-group --build debian/.debhelper/liboxli1/dbgsym-root .. dpkg-deb --root-owner-group --build debian/liboxli1 .. dpkg-deb --root-owner-group --build debian/liboxli-dev .. dpkg-deb: building package 'khmer' in '../khmer_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'khmer-dbgsym' in '../khmer-dbgsym_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli1' in '../liboxli1_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli1-dbgsym' in '../liboxli1-dbgsym_2.1.2+dfsg-8_amd64.deb'. dpkg-deb: building package 'liboxli-dev' in '../liboxli-dev_2.1.2+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../khmer_2.1.2+dfsg-8_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/khmer-NP0VRJ /tmp/khmer-2.1.2+dfsg-8jynv89d6 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.a44NM_AIOt... I: success in 887.2819 seconds md5: Value of 'md5' differs for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb md5: Size differs for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb md5: Value of 'md5' differs for khmer_2.1.2+dfsg-8_amd64.deb md5: Size differs for khmer_2.1.2+dfsg-8_amd64.deb md5: liboxli-dev_2.1.2+dfsg-8_amd64.deb: OK md5: liboxli1-dbgsym_2.1.2+dfsg-8_amd64.deb: OK md5: liboxli1_2.1.2+dfsg-8_amd64.deb: OK sha1: Value of 'sha1' differs for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb sha1: Size differs for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb sha1: Value of 'sha1' differs for khmer_2.1.2+dfsg-8_amd64.deb sha1: Size differs for khmer_2.1.2+dfsg-8_amd64.deb sha1: liboxli-dev_2.1.2+dfsg-8_amd64.deb: OK sha1: liboxli1-dbgsym_2.1.2+dfsg-8_amd64.deb: OK sha1: liboxli1_2.1.2+dfsg-8_amd64.deb: OK sha256: Value of 'sha256' differs for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb sha256: Size differs for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb sha256: Value of 'sha256' differs for khmer_2.1.2+dfsg-8_amd64.deb sha256: Size differs for khmer_2.1.2+dfsg-8_amd64.deb sha256: liboxli-dev_2.1.2+dfsg-8_amd64.deb: OK sha256: liboxli1-dbgsym_2.1.2+dfsg-8_amd64.deb: OK sha256: liboxli1_2.1.2+dfsg-8_amd64.deb: OK Checksums: FAIL Cannot generate diffoscope for khmer-dbgsym_2.1.2+dfsg-8_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/5d1fe9de7a59291d8edfb746905853bcab1e1ba25286e50f691e5353417a2a71/download Cannot generate diffoscope for khmer_2.1.2+dfsg-8_amd64.deb: RetryError[]