Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/u/unifrac/unifrac_0.10.0-3+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/unifrac-0.10.0-3+b1fe4y37ow/unifrac_0.10.0-3+b1_amd64.buildinfo Get source package info: unifrac=0.10.0-3 Source URL: http://snapshot.notset.fr/mr/package/unifrac/0.10.0-3/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-5 binutils=2.37-10 binutils-common=2.37-10 binutils-x86-64-linux-gnu=2.37-10 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 ca-certificates=20211016 chrpath=0.16-2+b1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-12 cython3=0.29.24-1+b1 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-exec=0.23.4 dh-python=5.20211114 dh-strip-nondeterminism=1.12.1-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 fonts-dejavu-core=2.37-2 fonts-lyx=2.3.6-1 g++=4:11.2.0-2 g++-11=11.2.0-12 gcc=4:11.2.0-2 gcc-11=11.2.0-12 gcc-11-base=11.2.0-12 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hdf5-helpers=1.10.7+repack-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaec-dev=1.0.6-1 libaec0=1.0.6-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-12 libatomic1=11.2.0-12 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37-10 libblas3=3.10.0-1 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-12 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-10 libctf0=2.37-10 libcurl4=7.79.1-2 libcurl4-openssl-dev=7.79.1-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.1-3 libexpat1-dev=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.1-1 libfreetype6=2.11.0+dfsg-1 libfribidi0=1.0.8-2 libgcc-11-dev=11.2.0-12 libgcc-s1=11.2.0-12 libgcrypt20=1.9.4-4 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran5=11.2.0-12 libglib2.0-0=2.70.1-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-12 libgpg-error0=1.42-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 libharfbuzz0b=2.7.4-1 libhdf5-103-1=1.10.7+repack-4 libhdf5-cpp-103-1=1.10.7+repack-4 libhdf5-dev=1.10.7+repack-4 libhdf5-fortran-102=1.10.7+repack-4 libhdf5-hl-100=1.10.7+repack-4 libhdf5-hl-cpp-100=1.10.7+repack-4 libhdf5-hl-fortran-100=1.10.7+repack-4 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libimagequant0=2.12.2-1.1 libisl23=0.24-2 libitm1=11.2.0-12 libjbig0=2.1-3.1+b2 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.13.0+dfsg-1 libjs-sphinxdoc=4.3.1-1 libjs-underscore=1.9.1~dfsg-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblapack3=3.10.0-1 liblbfgsb0=3.0+dfsg.3-9 liblcms2-2=2.12~rc1-2 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-12 liblz4-1=1.9.3-2 liblzf1=3.6-3 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libopenjp2-7=2.4.0-3 libp11-kit0=0.24.0-5 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpng16-16=1.6.37-3 libprocps8=2:3.3.17-5 libpsl5=0.21.0-1.2 libpython3-all-dev=3.9.8-1 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.10=3.10.0-5 libpython3.10-dev=3.10.0-5 libpython3.10-minimal=3.10.0-5 libpython3.10-stdlib=3.10.0-5 libpython3.9=3.9.9-1 libpython3.9-dev=3.9.9-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libqhull-r8.0=2020.2-4 libquadmath0=11.2.0-12 libraqm0=0.7.0-4 libreadline8=8.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl-dev=1.1.1l-1 libssl1.1=1.1.1l-1 libssw0=1.1-13 libstdc++-11-dev=11.2.0-12 libstdc++6=11.2.0-12 libsub-override-perl=0.09-2 libsystemd0=249.7-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtiff5=4.3.0-2 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-12 libubsan1=11.2.0-12 libuchardet0=0.0.7-1 libudev1=249.7-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libwebp6=0.6.1-2.1 libwebpdemux2=0.6.1-2.1 libwebpmux3=0.6.1-2.1 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxml2=2.9.12+dfsg-5+b1 libxslt1.1=1.1.34-4 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.70+nmu1 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.3-1 ncurses-bin=6.3-1 openssl=1.1.1l-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 procps=2:3.3.17-5 python-matplotlib-data=3.5.0-2 python3=3.9.8-1 python3-all=3.9.8-1 python3-all-dev=3.9.8-1 python3-appdirs=1.4.4-1 python3-attr=20.3.0-1 python3-backcall=0.2.0-2 python3-biom-format=2.1.10-3 python3-brotli=1.0.9-2+b3 python3-cachecontrol=0.12.10-1 python3-certifi=2020.6.20-1 python3-chardet=4.0.0-1 python3-click=8.0.2-1 python3-colorama=0.4.4-1 python3-cycler=0.11.0-1 python3-dateutil=2.8.1-6 python3-decorator=4.4.2-2 python3-dev=3.9.8-1 python3-distutils=3.9.9-2 python3-fonttools=4.27.1-1+b1 python3-fs=2.4.12-1 python3-h5py=3.5.0-2 python3-h5py-serial=3.5.0-2+b1 python3-hdmedians=0.14.2-1+b1 python3-idna=2.10-1 python3-ipython=7.27.0-1 python3-jedi=0.18.0-1 python3-joblib=0.17.0-4 python3-kiwisolver=1.3.2-1+b1 python3-lib2to3=3.9.9-2 python3-lockfile=1:0.12.2-2.2 python3-lxml=4.6.4-1 python3-lz4=3.1.3+dfsg-1+b1 python3-matplotlib=3.5.0-2 python3-matplotlib-inline=0.1.3-1 python3-minimal=3.9.8-1 python3-mpmath=1.2.1-2 python3-msgpack=1.0.2-2+b1 python3-natsort=7.1.0-1 python3-numpy=1:1.21.4-2 python3-packaging=21.3-1 python3-pandas=1.3.4+dfsg-7 python3-pandas-lib=1.3.4+dfsg-7 python3-parso=0.8.1-1 python3-pexpect=4.8.0-2 python3-pickleshare=0.7.5-5 python3-pil=8.4.0-1 python3-pkg-resources=59.4.0-1 python3-prompt-toolkit=3.0.22-1 python3-ptyprocess=0.7.0-3 python3-pygments=2.7.1+dfsg-2.1 python3-pyparsing=2.4.7-1 python3-requests=2.25.1+dfsg-2 python3-scipy=1.7.1-2+b1 python3-setuptools=59.4.0-1 python3-six=1.16.0-2 python3-skbio=0.5.6-6 python3-sklearn=1.0.1-1 python3-sklearn-lib=1.0.1-1 python3-sympy=1.7.1-3 python3-threadpoolctl=2.1.0-1 python3-traitlets=5.1.1-1 python3-tz=2021.3-1 python3-ufolib2=0.11.1+dfsg1-1 python3-urllib3=1.26.5-1~exp1 python3-wcwidth=0.1.9+dfsg1-2 python3.10=3.10.0-5 python3.10-dev=3.10.0-5 python3.10-minimal=3.10.0-5 python3.9=3.9.9-1 python3.9-dev=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tar=1.34+dfsg-1 tzdata=2021e-1 unicode-data=14.0.0-1.1 util-linux=2.37.2-4 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210916T024755Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210916T024755Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211203T090951Z/ 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 unifrac=0.10.0-3 && mkdir -p /build/unifrac-GAoX32 && dpkg-source --no-check -x /*.dsc /build/unifrac-GAoX32/unifrac-0.10.0 && cd /build/unifrac-GAoX32/unifrac-0.10.0 && { printf '%s' 'unifrac (0.10.0-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Add Python 3.10 as supported version -- amd64 Build Daemon (x86-grnet-01) Fri, 03 Dec 2021 17:32:37 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/unifrac-GAoX32" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/unifrac-GAoX32/unifrac-0.10.0 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638552757" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/unifrac-GAoX32 /tmp/unifrac-0.10.0-3+b1fe4y37ow bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211203T090951Z 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.wwRr9BcSxP 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.wwRr9BcSxP Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211203T090951Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211203T090951Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1011 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4673 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210916T024755Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210916T024755Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211203T090951Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.wwRr9BcSxP Get:1 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211203T090951Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main Sources [11.6 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages [12.4 MB] Fetched 35.5 MB in 29s (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.wwRr9BcSxP I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d unifrac=0.10.0-3 && mkdir -p /build/unifrac-GAoX32 && dpkg-source --no-check -x /*.dsc /build/unifrac-GAoX32/unifrac-0.10.0 && cd /build/unifrac-GAoX32/unifrac-0.10.0 && { printf '%s' 'unifrac (0.10.0-3+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Add Python 3.10 as supported version -- amd64 Build Daemon (x86-grnet-01) Fri, 03 Dec 2021 17:32:37 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/unifrac-GAoX32"' exec /tmp/mmdebstrap.wwRr9BcSxP Reading package lists... NOTICE: 'unifrac' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/unifrac.git Please use: git clone https://salsa.debian.org/med-team/unifrac.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 106 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main unifrac 0.10.0-3 (dsc) [2380 B] Get:2 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main unifrac 0.10.0-3 (tar) [95.5 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210916T024755Z bookworm/main unifrac 0.10.0-3 (diff) [7664 B] Fetched 106 kB in 0s (746 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'unifrac_0.10.0-3.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting unifrac in /build/unifrac-GAoX32/unifrac-0.10.0 dpkg-source: info: unpacking unifrac_0.10.0.orig.tar.gz dpkg-source: info: unpacking unifrac_0.10.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use-cython-post-clean.patch dpkg-source: info: applying Fix-Makefile.patch dpkg-source: info: applying remove-check-for-pkg-version.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/unifrac-GAoX32/unifrac-0.10.0 && env DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1638552757" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.wwRr9BcSxP dpkg-buildpackage: info: source package unifrac dpkg-buildpackage: info: source version 0.10.0-3+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 Build Daemon (x86-grnet-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0' dh_auto_clean I: pybuild base:237: python3.10 setup.py clean running clean removing '/build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:237: python3.9 setup.py clean running clean removing '/build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/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 find . -name "*.o" -delete rm -rf .pybuild/ build/ sucpp/ssu unifrac/_api.cpp sucpp/test_su sucpp/test_api sucpp/libssu.so.0 sucpp/faithpd sucpp/libssu.so rm -rf unifrac.egg-info make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:237: python3.10 setup.py config /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/unifrac-GAoX32/unifrac-0.10.0/unifrac/_api.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling unifrac/_api.pyx because it changed. [1/1] Cythonizing unifrac/_api.pyx running config I: pybuild base:237: python3.9 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py build running build running build_py creating /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac copying unifrac/_meta.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac copying unifrac/_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac copying unifrac/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac creating /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests copying unifrac/tests/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests copying unifrac/tests/test_api.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests copying unifrac/tests/test_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests creating /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.tre -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e1.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e2.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t1.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t2.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data copying unifrac/tests/data/test.faith.exp -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data running build_ext Compiling SSU make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' rm -f *.o ssu make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' building 'unifrac._api' extension creating build creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/sucpp creating build/temp.linux-x86_64-3.10/unifrac x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/unifrac-GAoX32/unifrac-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.10 -c sucpp/api.cpp -o build/temp.linux-x86_64-3.10/sucpp/api.o -std=c++11 -I/usr/include/hdf5/serial sucpp/api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: sucpp/api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ sucpp/api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: sucpp/api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ sucpp/api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/unifrac-GAoX32/unifrac-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.10 -c unifrac/_api.cpp -o build/temp.linux-x86_64-3.10/unifrac/_api.o -std=c++11 -I/usr/include/hdf5/serial In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from unifrac/_api.cpp:675: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ unifrac/_api.cpp: In function ‘PyObject* __pyx_pf_7unifrac_4_api_ssu(PyObject*, PyObject*, PyObject*, PyObject*, bool, double, bool, unsigned int)’: unifrac/_api.cpp:3236:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3236 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_16; __pyx_t_9+=1) { | ~~~~~~~~~~^~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/unifrac-GAoX32/unifrac-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/sucpp/api.o build/temp.linux-x86_64-3.10/unifrac/_api.o -Lsucpp/ -lssu -o /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/_api.cpython-310-x86_64-linux-gnu.so -std=c++11 I: pybuild base:237: /usr/bin/python3 setup.py build running build running build_py creating /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac copying unifrac/_meta.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac copying unifrac/_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac copying unifrac/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac creating /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests copying unifrac/tests/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests copying unifrac/tests/test_api.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests copying unifrac/tests/test_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests creating /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/crawford.tre -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e1.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/e2.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t1.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/t2.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data copying unifrac/tests/data/test.faith.exp -> /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data running build_ext Compiling SSU make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' rm -f *.o ssu make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' building 'unifrac._api' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/sucpp creating build/temp.linux-x86_64-3.9/unifrac x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/unifrac-GAoX32/unifrac-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.9 -c sucpp/api.cpp -o build/temp.linux-x86_64-3.9/sucpp/api.o -std=c++11 -I/usr/include/hdf5/serial sucpp/api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: sucpp/api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ sucpp/api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int sucpp/api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: sucpp/api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ sucpp/api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ sucpp/api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ sucpp/api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: sucpp/api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ sucpp/api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sucpp/api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/unifrac-GAoX32/unifrac-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Iunifrac -I/usr/lib/python3/dist-packages/numpy/core/include -Isucpp/ -I/usr/include/python3.9 -c unifrac/_api.cpp -o build/temp.linux-x86_64-3.9/unifrac/_api.o -std=c++11 -I/usr/include/hdf5/serial In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from unifrac/_api.cpp:675: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ unifrac/_api.cpp: In function ‘PyObject* __pyx_pf_7unifrac_4_api_ssu(PyObject*, PyObject*, PyObject*, PyObject*, bool, double, bool, unsigned int)’: unifrac/_api.cpp:3236:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3236 | for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_16; __pyx_t_9+=1) { | ~~~~~~~~~~^~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/unifrac-GAoX32/unifrac-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/sucpp/api.o build/temp.linux-x86_64-3.9/unifrac/_api.o -Lsucpp/ -lssu -o /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/_api.cpython-39-x86_64-linux-gnu.so -std=c++11 create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py install --root /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext Compiling SSU make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' rm -f *.o ssu make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' running install_lib creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10 creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/_meta.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/test_api.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/test_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/crawford.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/crawford.tre -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/e1.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/e2.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/t1.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/t2.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/tests/data/test.faith.exp -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.10_unifrac/build/unifrac/_api.cpython-310-x86_64-linux-gnu.so -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/_meta.py to _meta.cpython-310.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/_methods.py to _methods.cpython-310.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/__init__.py to __init__.cpython-310.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/test_api.py to test_api.cpython-310.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac/tests/test_methods.py to test_methods.cpython-310.pyc running install_egg_info running egg_info creating unifrac.egg-info writing unifrac.egg-info/PKG-INFO writing dependency_links to unifrac.egg-info/dependency_links.txt writing requirements to unifrac.egg-info/requires.txt writing top-level names to unifrac.egg-info/top_level.txt writing manifest file 'unifrac.egg-info/SOURCES.txt' reading manifest file 'unifrac.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'unifrac.egg-info/SOURCES.txt' Copying unifrac.egg-info to /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.10/dist-packages/unifrac-0.10.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext Compiling SSU make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' rm -f *.o ssu make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c tree.cpp -o tree.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c biom.cpp -o biom.o biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: warning: implicitly-declared ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ is deprecated [-Wdeprecated-copy] 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5File.h:101:9: note: because ‘H5::H5File’ has user-provided ‘H5::H5File::H5File(const H5::H5File&)’ 101 | H5File(const H5File& original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’: /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared ‘H5::Group& H5::Group::operator=(const H5::Group&)’ is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5Group.h:57:9: note: because ‘H5::Group’ has user-provided ‘H5::Group::Group(const H5::Group&)’ 57 | Group(const Group& original); | ^~~~~ biom.cpp: In constructor ‘su::biom::biom(std::string)’: biom.cpp:21:51: note: synthesized method ‘H5::H5File& H5::H5File::operator=(const H5::H5File&)’ first required here 21 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp:24:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 24 | obs_indices = file.openDataSet(OBS_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:25:49: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 25 | obs_data = file.openDataSet(OBS_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:26:61: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 26 | sample_indices = file.openDataSet(SAMPLE_INDICES.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp:27:55: warning: implicitly-declared ‘H5::DataSet& H5::DataSet::operator=(const H5::DataSet&)’ is deprecated [-Wdeprecated-copy] 27 | sample_data = file.openDataSet(SAMPLE_DATA.c_str()); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:45, from biom.hpp:1, from biom.cpp:4: /usr/include/hdf5/serial/H5DataSet.h:100:9: note: because ‘H5::DataSet’ has user-provided ‘H5::DataSet::DataSet(const H5::DataSet&)’ 100 | DataSet(const DataSet& original); | ^~~~~~~ biom.cpp: In member function ‘void su::biom::load_ids(const char*, std::vector >&)’: biom.cpp:115:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 115 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 116 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘void su::biom::load_indptr(const char*, std::vector&)’: biom.cpp:141:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 141 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 142 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_obs_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:184:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 184 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 185 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:190:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 191 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function ‘unsigned int su::biom::get_sample_data_direct(std::string, uint32_t*&, double*&)’: biom.cpp:238:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 238 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 239 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:244:47: warning: format ‘%zd’ expects argument of type ‘signed size_t’, but argument 3 has type ‘long long unsigned int’ [-Wformat=] 244 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 245 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac.cpp -o unifrac.o In file included from unifrac.cpp:4: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition In file included from unifrac.cpp:4: affinity.hpp: In function ‘int bind_to_core(int)’: affinity.hpp:118:62: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘pthread_t’ {aka ‘long unsigned int’} [-Wformat=] 118 | fprintf(stderr, "Unable to bind this thread to core %d. Are sufficient processors available?", thread); | ~^ ~~~~~~ | | | | int pthread_t {aka long unsigned int} | %ld affinity.hpp:99:12: warning: variable ‘ret’ set but not used [-Wunused-but-set-variable] 99 | int j, ret; | ^~~ unifrac.cpp: In function ‘int sync_printf(const char*, ...)’: unifrac.cpp:42:1: warning: no return statement in function returning non-void [-Wreturn-type] 42 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c unifrac_task.cpp -o unifrac_task.o unifrac_task.cpp: In function ‘void su::_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double, const su::task_parameters*)’: unifrac_task.cpp:6:81: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 6 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ unifrac_task.cpp: In function ‘void su::_vaw_unnormalized_weighted_unifrac_task(std::vector&, std::vector&, double*, double*, double*, double, const su::task_parameters*)’: unifrac_task.cpp:56:85: warning: unused parameter ‘dm_stripes_total’ [-Wunused-parameter] 56 | std::vector &__restrict__ dm_stripes_total, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c api.cpp -o api.o api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_su.cpp -o test_su tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_su.cpp: In function ‘void test_bptree_postorder()’: test_su.cpp:387:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 387 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:389:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 389 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_preorder()’: test_su.cpp:405:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 405 | uint32_t obs[tree.nparens / 2]; | ^~~ test_su.cpp:407:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 407 | for(int i = 0; i < (tree.nparens / 2); i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_parent()’: test_su.cpp:425:14: warning: ISO C++ forbids variable length array ‘obs’ [-Wvla] 425 | uint32_t obs[tree.nparens - 2]; | ^~~ test_su.cpp:427:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 427 | for(int i = 0; i < (tree.nparens) - 2; i++) | ~~^~~~~~~~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_leftchild()’: test_su.cpp:519:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 519 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightchild()’: test_su.cpp:534:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 534 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_bptree_rightsibling()’: test_su.cpp:549:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 549 | for(int i = 0; i < tree.nparens; i++) { | ~~^~~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unifrac_set_proportions()’: test_su.cpp:614:12: warning: unused variable ‘sample_counts’ [-Wunused-variable] 614 | double sample_counts[] = {7, 3, 4, 6, 3, 4}; | ^~~~~~~~~~~~~ test_su.cpp: In function ‘void test_unweighted_unifrac()’: test_su.cpp:981:14: warning: unused variable ‘obs’ [-Wunused-variable] 981 | double **obs; | ^~~ test_su.cpp: In function ‘void test_unweighted_unifrac_fast()’: test_su.cpp:1021:14: warning: unused variable ‘obs’ [-Wunused-variable] 1021 | double **obs; | ^~~ test_su.cpp: In function ‘void test_normalized_weighted_unifrac()’: test_su.cpp:1061:14: warning: unused variable ‘obs’ [-Wunused-variable] 1061 | double **obs; | ^~~ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -Wno-unused-parameter test_api.cpp -o test_api tree.o biom.o unifrac.o unifrac_task.o api.o -pthread test_api.cpp: In function ‘void test_merge_partial_mat()’: test_api.cpp:207:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 207 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:210:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 210 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ test_api.cpp:224:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 224 | for(int i = 0; i < obs->cf_size; i++) { | ~~^~~~~~~~~~~~~~ test_api.cpp:227:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 227 | for(int i = 0; i < obs->n_samples; i++) | ~~^~~~~~~~~~~~~~~~ make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC -c cmd.cpp -o cmd.o h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC su.cpp -o ssu tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:115:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 115 | for(unsigned int p = 0; p < npartials; p++) { | ~~^~~~~~~~~~~ su.cpp: In function ‘int main(int, char**)’: su.cpp:304:24: warning: unused variable ‘report_bare’ [-Wunused-variable] 304 | const std::string &report_bare = input.getCmdOption("--report-bare"); | ^~~~~~~~~~~ su.cpp: In function ‘int mode_partial_report(std::string, int, bool)’: su.cpp:132:1: warning: control reaches end of non-void function [-Wreturn-type] 132 | } | ^ h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC faithpd.cpp -o faithpd tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lhdf5_cpp -pthread make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' h5c++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -Wextra -std=c++11 -pedantic -I. -O4 -fPIC api.cpp -c -o api.o -fPIC api.cpp: In function ‘compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:238:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 238 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:248:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 248 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘compute_status faith_pd_one_off(const char*, const char*, r_vec**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:273:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 273 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function ‘compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)’: api.cpp:32:81: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses] 32 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:290:5: note: in expansion of macro ‘PARSE_SYNC_TREE_TABLE’ 290 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:300:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 300 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int api.cpp: In function ‘IOStatus read_partial(const char*, partial_mat_t**)’: api.cpp:476:57: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~^~~ api.cpp:476:103: warning: comparison of constant ‘0’ with boolean expression is always false [-Wbool-compare] 476 | if(n_samples <= 0 || n_stripes <= 0 || stripe_start < 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 492 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp:503:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 503 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:501:9: warning: unused variable ‘current_to_load’ [-Wunused-variable] 501 | int current_to_load; | ^~~~~~~~~~~~~~~ api.cpp: In function ‘MergeStatus merge_partial(partial_mat_t**, int, unsigned int, mat_t**)’: api.cpp:538:39: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 538 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:557:54: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 557 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:568:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 568 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:583:75: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 583 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n"); | ~^ | | | int h5c++ -shared -o libssu.so.0 tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp -shlib -Wl,-soname,libssu.so.0 -Wl,-z,relro -Wl,-z,now ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -o libssu.a tree.o biom.o unifrac.o cmd.o unifrac_task.o api.o -lc -lhdf5_cpp make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0/sucpp' running install_lib creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9 creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/_meta.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/__init__.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/test_api.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/test_methods.py -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests creating /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/crawford.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/crawford.tre -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/e1.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/e2.biom -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/t1.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/t2.newick -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/tests/data/test.faith.exp -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/data copying /build/unifrac-GAoX32/unifrac-0.10.0/.pybuild/cpython3_3.9_unifrac/build/unifrac/_api.cpython-39-x86_64-linux-gnu.so -> /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/_meta.py to _meta.cpython-39.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/_methods.py to _methods.cpython-39.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/__init__.py to __init__.cpython-39.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/test_api.py to test_api.cpython-39.pyc byte-compiling /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac/tests/test_methods.py to test_methods.cpython-39.pyc running install_egg_info running egg_info writing unifrac.egg-info/PKG-INFO writing dependency_links to unifrac.egg-info/dependency_links.txt writing requirements to unifrac.egg-info/requires.txt writing top-level names to unifrac.egg-info/top_level.txt reading manifest file 'unifrac.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '*.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '.*.swp' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'unifrac.egg-info/SOURCES.txt' Copying unifrac.egg-info to /build/unifrac-GAoX32/unifrac-0.10.0/debian/python3-unifrac/usr/lib/python3.9/dist-packages/unifrac-0.10.0.egg-info Skipping SOURCES.txt running install_scripts dh_install -a -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/unifrac-GAoX32/unifrac-0.10.0' chrpath -d debian/libssu-tools/usr/bin/ssu chrpath -d debian/libssu-tools/usr/bin/faithpd chrpath -d debian/libssu0/usr/lib/x86_64-linux-gnu/libssu.so.0 make[1]: Leaving directory '/build/unifrac-GAoX32/unifrac-0.10.0' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_installman -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package libssu-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-unifrac: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'python3-unifrac-dbgsym' in '../python3-unifrac-dbgsym_0.10.0-3+b1_amd64.deb'. dpkg-deb: building package 'libssu0' in '../libssu0_0.10.0-3+b1_amd64.deb'. dpkg-deb: building package 'python3-unifrac' in '../python3-unifrac_0.10.0-3+b1_amd64.deb'. dpkg-deb: building package 'libssu-dev' in '../libssu-dev_0.10.0-3+b1_amd64.deb'. dpkg-deb: building package 'libssu0-dbgsym' in '../libssu0-dbgsym_0.10.0-3+b1_amd64.deb'. dpkg-deb: building package 'libssu-tools' in '../libssu-tools_0.10.0-3+b1_amd64.deb'. dpkg-deb: building package 'libssu-tools-dbgsym' in '../libssu-tools-dbgsym_0.10.0-3+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../unifrac_0.10.0-3+b1_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/unifrac-GAoX32 /tmp/unifrac-0.10.0-3+b1fe4y37ow I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.wwRr9BcSxP... I: success in 749.1779 seconds md5: libssu-dev_0.10.0-3+b1_amd64.deb: OK md5: libssu-tools-dbgsym_0.10.0-3+b1_amd64.deb: OK md5: libssu-tools_0.10.0-3+b1_amd64.deb: OK md5: libssu0-dbgsym_0.10.0-3+b1_amd64.deb: OK md5: libssu0_0.10.0-3+b1_amd64.deb: OK md5: python3-unifrac-dbgsym_0.10.0-3+b1_amd64.deb: OK md5: python3-unifrac_0.10.0-3+b1_amd64.deb: OK sha1: libssu-dev_0.10.0-3+b1_amd64.deb: OK sha1: libssu-tools-dbgsym_0.10.0-3+b1_amd64.deb: OK sha1: libssu-tools_0.10.0-3+b1_amd64.deb: OK sha1: libssu0-dbgsym_0.10.0-3+b1_amd64.deb: OK sha1: libssu0_0.10.0-3+b1_amd64.deb: OK sha1: python3-unifrac-dbgsym_0.10.0-3+b1_amd64.deb: OK sha1: python3-unifrac_0.10.0-3+b1_amd64.deb: OK sha256: libssu-dev_0.10.0-3+b1_amd64.deb: OK sha256: libssu-tools-dbgsym_0.10.0-3+b1_amd64.deb: OK sha256: libssu-tools_0.10.0-3+b1_amd64.deb: OK sha256: libssu0-dbgsym_0.10.0-3+b1_amd64.deb: OK sha256: libssu0_0.10.0-3+b1_amd64.deb: OK sha256: python3-unifrac-dbgsym_0.10.0-3+b1_amd64.deb: OK sha256: python3-unifrac_0.10.0-3+b1_amd64.deb: OK Checksums: OK