I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 11 04:16:20 +14 2025 I: pbuilder-time-stamp: 1749564980 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [unifrac-tools_1.4-3.dsc] I: copying [./unifrac-tools_1.4.orig.tar.gz] I: copying [./unifrac-tools_1.4-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 3 12:28:53 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./unifrac-tools_1.4-3.dsc: no acceptable signature found dpkg-source: info: extracting unifrac-tools in unifrac-tools-1.4 dpkg-source: info: unpacking unifrac-tools_1.4.orig.tar.gz dpkg-source: info: unpacking unifrac-tools_1.4-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying remove_non-free_headers.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying soname.patch dpkg-source: info: applying baseline.patch dpkg-source: info: applying enable_linking_to_shared_hdf5_lib.patch dpkg-source: info: applying enable-debug-flag.patch dpkg-source: info: applying hardening dpkg-source: info: applying PR53.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/81194/tmp/hooks/D01_modify_environment starting debug: Running on infom02-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 10 14:16 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/81194/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/81194/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4778bfaad15442baaa6d460baf28ef4d LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=81194 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.TwiIdNaG/pbuilderrc_Kqzq --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.TwiIdNaG/b2 --logfile b2/build.log unifrac-tools_1.4-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/81194/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-exec, libhdf5-dev, hdf5-helpers, liblz4-dev, libblas-dev, liblapacke-dev, chrpath, gfortran, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19698 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on hdf5-helpers; however: Package hdf5-helpers is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on libblas-dev; however: Package libblas-dev is not installed. pbuilder-satisfydepends-dummy depends on liblapacke-dev; however: Package liblapacke-dev is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} chrpath{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} gfortran{a} gfortran-13{a} gfortran-13-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgssapi-krb5-2{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libldap-2.5-0{a} liblz4-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 57.0 MB of archives. After unpacking 236 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.2.0-24 [847 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-24 [10.7 MB] Get: 49 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.2.0-24 [12.2 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 gfortran-x86-64-linux-gnu amd64 4:13.2.0-7 [1280 B] Get: 51 http://deb.debian.org/debian trixie/main amd64 gfortran amd64 4:13.2.0-7 [1440 B] Get: 52 http://deb.debian.org/debian trixie/main amd64 hdf5-helpers amd64 1.10.10+repack-3.3 [23.4 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 55 http://deb.debian.org/debian trixie/main amd64 libaec-dev amd64 1.1.3-1 [21.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libblas-dev amd64 3.12.0-3 [159 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 63 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libcurl4-openssl-dev amd64 8.7.1-3 [547 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libhdf5-fortran-102t64 amd64 1.10.10+repack-3.3 [89.3 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-fortran-100t64 amd64 1.10.10+repack-3.3 [40.4 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-cpp-100t64 amd64 1.10.10+repack-3.3 [21.3 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3 [290 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libjpeg-dev amd64 1:2.1.5-3 [71.9 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libhdf5-dev amd64 1.10.10+repack-3.3 [2639 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 liblapack-dev amd64 3.12.0-3 [4880 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libtmglib3 amd64 3.12.0-3 [127 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 liblapacke amd64 3.12.0-3 [379 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libtmglib-dev amd64 3.12.0-3 [130 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 liblapacke-dev amd64 3.12.0-3 [348 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 liblz4-dev amd64 1.9.4-2 [82.8 kB] Fetched 57.0 MB in 2s (33.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19698 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20014 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... 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Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libgfortran-13-dev:amd64 (13.2.0-24) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up chrpath (0.16-2+b1) ... Setting up libblas-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.1.3-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libaec-dev:amd64 (1.1.3-1) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3) ... Setting up gfortran-13-x86-64-linux-gnu (13.2.0-24) ... Setting up libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:amd64 (3.12.0-3) ... Setting up gfortran-13 (13.2.0-24) ... Setting up liblapack-dev:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up liblapacke:amd64 (3.12.0-3) ... Setting up libtmglib-dev:amd64 (3.12.0-3) ... Setting up libcurl4t64:amd64 (8.7.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up liblapacke-dev:amd64 (3.12.0-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up gfortran-x86-64-linux-gnu (4:13.2.0-7) ... Setting up gfortran (4:13.2.0-7) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcurl4-openssl-dev:amd64 (8.7.1-3) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3.11 (3.11.9-1) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up libhdf5-fortran-102t64:amd64 (1.10.10+repack-3.3) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up dh-exec (0.29) ... Setting up libhdf5-hl-cpp-100t64:amd64 (1.10.10+repack-3.3) ... Setting up libhdf5-hl-fortran-100t64:amd64 (1.10.10+repack-3.3) ... Setting up libhdf5-dev (1.10.10+repack-3.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.38-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/81194/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/81194/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/unifrac-tools-1.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../unifrac-tools_1.4-3_source.changes dpkg-buildpackage: info: source package unifrac-tools dpkg-buildpackage: info: source version 1.4-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' cd test && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/test' rm -f *.o capi_test make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/test' cd src && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f *.o ssu faithpd test_su test_ska test_api libssu.so make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' cd combined && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/combined' rm -f libssu.o libssu.so make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/combined' make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib dh_auto_build -- PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.4' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make clean && make api make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f *.o ssu_cpu_basic faithpd_cpu_basic test_su test_ska test_api libssu_cpu_basic.so make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c tree.cpp -o tree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ tree.cpp: In member function 'void su::BPTree::newick_to_bp(std::string)': tree.cpp:321:67: warning: 'last_structure' may be used uninitialized [-Wmaybe-uninitialized] 321 | if(potential_single_descendent || (last_structure == ',')) { | ~~~~~~~~~~~~~~~~^~~~~~~ tree.cpp:300:10: note: 'last_structure' was declared here 300 | char last_structure; | ^~~~~~~~~~~~~~ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom.cpp -o biom.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ biom.cpp: In constructor 'su::biom::biom(std::string)': biom.cpp:32:51: warning: implicitly-declared 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' is deprecated [-Wdeprecated-copy] 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:47, from biom.hpp:14, from biom.cpp:13: /usr/include/hdf5/serial/H5File.h:104:5: note: because 'H5::H5File' has user-provided 'H5::H5File::H5File(const H5::H5File&)' 104 | 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:24:17: warning: implicitly-declared 'H5::Group& H5::Group::operator=(const H5::Group&)' is deprecated [-Wdeprecated-copy] 24 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:46: /usr/include/hdf5/serial/H5Group.h:62:5: note: because 'H5::Group' has user-provided 'H5::Group::Group(const H5::Group&)' 62 | Group(const Group &original); | ^~~~~ biom.cpp: In constructor 'su::biom::biom(std::string)': biom.cpp:32:51: note: synthesized method 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' first required here 32 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp: In member function 'void su::biom::load_ids(const char*, std::vector >&)': biom.cpp:134:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 135 | 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:166:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function 'unsigned int su::biom::get_obs_data_direct(const std::string&, uint32_t*&, double*&)': biom.cpp:206:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In member function 'unsigned int su::biom::get_sample_data_direct(const std::string&, uint32_t*&, double*&)': biom.cpp:251:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c biom_inmem.cpp -o biom_inmem.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ biom_inmem.cpp: In constructor 'su::biom_inmem::biom_inmem(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int)': biom_inmem.cpp:328:30: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 328 | for(int i = 0; i < n_obs; i++) { | ~~^~~~~~~ biom_inmem.cpp:333:30: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 333 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ biom_inmem.cpp: In instantiation of 'void su::biom_inmem::get_obs_data_range_TT(uint32_t, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; uint32_t = unsigned int]': biom_inmem.cpp:427:34: required from 'void su::biom_inmem::get_obs_data_range_TT(const std::string&, unsigned int, unsigned int, bool, TFloat*) const [with TFloat = double; std::string = std::__cxx11::basic_string]' biom_inmem.cpp:431:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j]' biom_inmem.cpp:435:36: required from here biom_inmem.cpp:410:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] 410 | if ((j>=start)&&(j=start)&&(j::size_type' {aka 'long unsigned int'} [-Wsign-compare] 126 | for (int i=1; i< header_line.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~~ tsv.cpp:138:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 138 | for (int i=1; i< n_filter_els; i++) grouping[i] = n_filter_els; | ~^~~~~~~~~~~~~~ tsv.cpp:173:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 173 | for (int i=1; i< n_filter_els; i++) { | ~^~~~~~~~~~~~~~ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac.cpp -o unifrac.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from unifrac.cpp:13: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: 'int bind_to_core(int)' defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c cmd.cpp -o cmd.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ api.cpp: In function 'compute_status one_off_inmem_cpp(su::biom_interface&, su::BPTree&, const char*, bool, double, bool, unsigned int, mat_t**)': api.cpp:443:75: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 443 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld 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:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:97:62: note: in expansion of macro 'PARSE_TREE_TABLE' 97 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ | ^~~~~~~~~~~~~~~~ api.cpp:474:5: note: in expansion of macro 'PARSE_SYNC_TREE_TABLE' 474 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:485:75: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 485 | fprintf(stderr, "More threads were requested than stripes. Using %d threads.\n", dm_stripes.size()); | ~^ ~~~~~~~~~~~~~~~~~ | | | | int std::vector::size_type {aka long unsigned int} | %ld api.cpp: In function 'compute_status faith_pd_one_off(const char*, const char*, r_vec**)': api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:513:5: note: in expansion of macro 'PARSE_TREE_TABLE' 513 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)': api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:550:5: note: in expansion of macro 'PARSE_TREE_TABLE' 550 | PARSE_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'compute_status one_off_matrix_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp64_t**)': api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:628:5: note: in expansion of macro 'PARSE_TREE_TABLE' 628 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'compute_status one_off_matrix_fp32_v2(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, bool, const char*, mat_full_fp32_t**)': api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:650:5: note: in expansion of macro 'PARSE_TREE_TABLE' 650 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'IOStatus read_partial_header_fd(int, TPMat&)': api.cpp:1795:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp: In instantiation of 'compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = double; TMat = mat_full_fp64; hid_t = long int]': api.cpp:1400:59: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro 'PARSE_TREE_TABLE' 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of 'compute_status unifrac_multi_to_file_T(hid_t, bool, const char*, const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, unsigned int, unsigned int, bool, unsigned int, unsigned int, const char*, const char*, const char*) [with TReal = float; TMat = mat_full_fp32; hid_t = long int]': api.cpp:1408:58: required from here api.cpp:89:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 89 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:1281:5: note: in expansion of macro 'PARSE_TREE_TABLE' 1281 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In instantiation of 'IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': api.cpp:1963:48: required from here api.cpp:1795:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] 1795 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp:1821:15: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1821 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1827:14: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1827 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} | ~~~^~~~~~~~~~~~~~~~~~ api.cpp:1831:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1831 | for(int i = 0; i < n_samples; i++) { | ~~^~~~~~~~~~~ api.cpp: In instantiation of 'IOStatus read_partial_data_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': api.cpp:1965:49: required from here api.cpp:1864:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1864 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:1868:19: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1868 | if ( (i+1)n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In instantiation of 'MergeStatus check_partial(const TPMat* const*, int, bool) [with TPMat = partial_mat; MergeStatus = merge_status]': api.cpp:2109:36: required from here api.cpp:2042:39: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] 2042 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:2077:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 2077 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:2092:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 2092 | if(stripe_count != partial_mats[0]->stripe_total) { | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp: In function 'void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = double; TMat = mat_full_fp64]': api.cpp:257:18: warning: ignoring return value of 'int ftruncate(int, __off_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 257 | ftruncate(fd,msize); | ~~~~~~~~~^~~~~~~~~~ api.cpp: In function 'void initialize_mat_full_no_biom_T(TMat*&, const char* const*, unsigned int, const char*) [with TReal = float; TMat = mat_full_fp32]': api.cpp:257:18: warning: ignoring return value of 'int ftruncate(int, __off_t)' declared with attribute 'warn_unused_result' [-Wunused-result] h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from unifrac_internal.cpp:12: affinity.hpp:1: warning: "_GNU_SOURCE" redefined 1 | #define _GNU_SOURCE | : note: this is the location of the previous definition 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; | ^~~ affinity.hpp: At global scope: affinity.hpp:82:12: warning: 'int bind_to_core(int)' defined but not used [-Wunused-function] 82 | static int bind_to_core(int core) { | ^~~~~~~~~~~~ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from unifrac_cmp.cpp:19: unifrac_task.hpp:196: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 196 | #pragma acc enter data create(buf[:bsize]) | unifrac_task.hpp:357: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 357 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:395: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 395 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:438: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 438 | #pragma acc enter data create(zcheck[:n_samples],stripe_sums[:n_samples],sums[:bsize]) | In file included from unifrac_cmp.cpp:24: unifrac_task.cpp:41: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 41 | #pragma acc loop seq | unifrac_task.cpp:558: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 558 | #pragma acc loop seq | unifrac_task.cpp:1008: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1008 | #pragma acc loop seq | unifrac_task.cpp:1081: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1081 | #pragma acc loop seq | unifrac_task.cpp:1159: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1159 | #pragma acc loop seq | unifrac_task.cpp:1544: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1544 | #pragma acc loop vector | unifrac_task.cpp:1573: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1573 | #pragma acc loop vector | unifrac_task.cpp:1586: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 1586 | #pragma acc wait | unifrac_task.cpp:1700: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1700 | #pragma acc loop seq | unifrac_task.cpp:1710: warning: ignoring '#pragma acc loop' [-Wunknown-pragmas] 1710 | #pragma acc loop seq | unifrac_cmp.cpp:97: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 97 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:195: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 195 | #pragma acc wait | unifrac_cmp.cpp:204: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] 204 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:214: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] 214 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:282: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 282 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp:293: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 293 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:338: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 338 | #pragma acc wait | unifrac_cmp.cpp:339: warning: ignoring '#pragma acc update' [-Wunknown-pragmas] 339 | #pragma acc update device(lengths[:filled_emb]) | unifrac_cmp.cpp:347: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 347 | #pragma acc wait | unifrac_cmp.cpp:355: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] 355 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:366: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] 366 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:367: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] 367 | #pragma acc exit data delete(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = double]': unifrac_cmp.cpp:226:70: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = double]': unifrac_cmp.cpp:229:78: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = double]': unifrac_cmp.cpp:232:80: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = double]': unifrac_cmp.cpp:235:71: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnweightedTask; TFloat = float]': unifrac_cmp.cpp:238:69: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracNormalizedWeightedTask; TFloat = float]': unifrac_cmp.cpp:241:77: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracUnnormalizedWeightedTask; TFloat = float]': unifrac_cmp.cpp:244:79: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifracTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracGeneralizedTask; TFloat = float]': unifrac_cmp.cpp:247:70: required from here unifrac_cmp.cpp:94:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 94 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = double]': unifrac_cmp.cpp:380:77: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = double]': unifrac_cmp.cpp:383:85: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = double]': unifrac_cmp.cpp:386:87: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = double]': unifrac_cmp.cpp:389:78: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnweightedTask; TFloat = float]': unifrac_cmp.cpp:392:77: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawNormalizedWeightedTask; TFloat = float]': unifrac_cmp.cpp:395:85: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawUnnormalizedWeightedTask; TFloat = float]': unifrac_cmp.cpp:398:87: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_cmp.cpp: In instantiation of 'void unifrac_vawTT(const su::biom_interface&, const su::BPTree&, bool, std::vector&, std::vector&, const su::task_parameters*) [with TaskT = su_cpu::UnifracVawGeneralizedTask; TFloat = float]': unifrac_cmp.cpp:401:78: required from here unifrac_cmp.cpp:290:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 290 | fprintf(stderr, "posix_memalign(%d) failed: %d\n", sizeof(TFloat) * max_emb, err); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld unifrac_task.hpp: In constructor 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': unifrac_task.hpp:435:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor 'su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': unifrac_task.hpp:393:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor 'su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]': unifrac_task.hpp:355:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': unifrac_task.hpp:435:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 435 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:436:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 436 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:437:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 437 | posix_memalign((void **)&sums, 4096, sizeof(TFloat) * bsize); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor 'su_cpu::UnifracNormalizedWeightedTask::UnifracNormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': unifrac_task.hpp:393:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 393 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:394:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 394 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp: In constructor 'su_cpu::UnifracUnnormalizedWeightedTask::UnifracUnnormalizedWeightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]': unifrac_task.hpp:355:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 355 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:356:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 356 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5c++ -shared -fopenmp -shlib -o libssu_cpu_basic.so.0 tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu_cpu_basic.so.0 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 ln -sf libssu_cpu_basic.so.0 libssu_cpu_basic.so # FIXME: Should build static lib as well # h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make main make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib su.cpp -o ssu_cpu_basic tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++17 -pedantic -I. -Ofast -fPIC -L/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib faithpd.cpp -o faithpd_cpu_basic tree.o biom.o biom_inmem.o biom_subsampled.o tsv.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lgfortran -lpthread cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' export BUILD_VARIANT=cpu_basic ; export BUILD_FULL_OPTIMIZATION=False ; cd src && make install make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.4/src' rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib//libssu_cpu_basic.so; cp -a libssu_cpu_basic.so* /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/lib/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ssu_cpu_basic; cp ssu_cpu_basic /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/faithpd_cpu_basic; cp faithpd_cpu_basic /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/bin/ mkdir -p /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/task_parameters.hpp; cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/api.hpp; cp api.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ rm -f /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/status_enum.hpp; cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4/src' source ./setup_nv_h5.sh; export BUILD_VARIANT=nv_avx2 ; export BUILD_FULL_OPTIMIZATION=True ; cd src && make clean && make api /bin/sh: line 1: ./setup_nv_h5.sh: No such file or directory make[2]: *** [Makefile:43: api_nv_avx2] Error 1 make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.4/debian/tmp/usr returned exit code 2 make[1]: *** [debian/rules:15: override_dh_auto_build] Error 25 make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.4' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: user script /srv/workspace/pbuilder/81194/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Tue Jun 10 14:18:23 UTC 2025 Filesystem Size Used Avail Use% Mounted on tmpfs 12G 0 12G 0% /dev/shm I: user script /srv/workspace/pbuilder/81194/tmp/hooks/C01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/81194 and its subdirectories