I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 2 13:37:50 +14 2025 I: pbuilder-time-stamp: 1748821070 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: using eatmydata during job 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/107324/tmp/hooks/D01_modify_environment starting debug: Running on ionos6-i386. 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 1 23:38 /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/107324/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/107324/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]="i686-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=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=7fe593b3c5bd4249a29b7f64a4a39c09 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=107324 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.O47llR0w/pbuilderrc_7cXA --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.O47llR0w/b2 --logfile b2/build.log unifrac-tools_1.4-3.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/107324/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: i386 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 ... 19885 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-i686-linux-gnu{a} gfortran-i686-linux-gnu{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblz4-dev{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 48 newly installed, 0 to remove and 0 not upgraded. Need to get 39.9 MB of archives. After unpacking 164 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libhdf5-dev but it is not installable Depends: python3 but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) libaec-dev [1.1.3-1 (testing)] 4) libaec0 [1.1.3-1 (testing)] 5) libbrotli1 [1.1.0-2+b3 (testing)] 6) libcurl3t64-gnutls [8.7.1-3 (testing)] 7) libcurl4-gnutls-dev [8.7.1-3 (testing)] 8) libcurl4t64 [8.7.1-3 (testing)] 9) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 10) libexpat1 [2.6.2-1 (testing)] 11) libhdf5-103-1 [1.10.10+repack-3+b1 (testing)] 12) libhdf5-cpp-103-1 [1.10.10+repack-3+b1 (testing)] 13) libhdf5-dev [1.10.10+repack-3+b1 (testing)] 14) libhdf5-fortran-102 [1.10.10+repack-3+b1 (testing)] 15) libhdf5-hl-100 [1.10.10+repack-3+b1 (testing)] 16) libhdf5-hl-cpp-100 [1.10.10+repack-3+b1 (testing)] 17) libhdf5-hl-fortran-100 [1.10.10+repack-3+b1 (testing)] 18) libjpeg62-turbo [1:2.1.5-2+b2 (testing)] 19) libjpeg62-turbo-dev [1:2.1.5-2+b2 (testing)] 20) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 21) libnghttp2-14 [1.59.0-1 (testing)] 22) libpsl5t64 [0.21.2-1.1 (testing)] 23) libpython3-stdlib [3.11.8-1 (testing)] 24) libpython3.11-minimal [3.11.9-1 (testing)] 25) libpython3.11-stdlib [3.11.9-1 (testing)] 26) libreadline8t64 [8.2-4 (testing)] 27) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 28) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 29) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 30) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 31) libssl-dev [3.2.1-3 (testing)] 32) libssl3t64 [3.2.1-3 (testing)] 33) libsz2 [1.1.3-1 (testing)] 34) media-types [10.1.0 (testing)] 35) netbase [6.4 (testing)] 36) python3 [3.11.8-1 (testing)] 37) python3-minimal [3.11.8-1 (testing)] 38) python3.11 [3.11.9-1 (testing)] 39) python3.11-minimal [3.11.9-1 (testing)] 40) readline-common [8.2-4 (testing)] 41) tzdata [2024a-3 (testing)] 42) zlib1g-dev [1:1.3.dfsg-3.1 (testing)] 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-i686-linux-gnu{a} gfortran-i686-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} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdb5.3t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu72{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} libldap-2.5-0{a} liblz4-dev{a} libmagic-mgc{a} libmagic1{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} libssl3t64{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 will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 88 newly installed, 2 to remove and 0 not upgraded. Need to get 59.8 MB of archives. After unpacking 228 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libdb5.3t64 i386 5.3.28+dfsg2-7 [759 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libssl3t64 i386 3.2.1-3 [2234 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.9-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.9-1 [1918 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-4 [171 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.9-1 [1795 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.8-1 [9336 B] Get: 15 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3+b1 [1195 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 chrpath i386 0.16-2+b1 [17.5 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 dh-exec i386 0.29 [25.9 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14-20240330-1 [735 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libgfortran-13-dev i386 13.2.0-23 [783 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 gfortran-13-i686-linux-gnu i386 13.2.0-23 [11.1 MB] Get: 51 http://deb.debian.org/debian trixie/main i386 gfortran-13 i386 13.2.0-23 [11.2 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 gfortran-i686-linux-gnu i386 4:13.2.0-7 [1280 B] Get: 53 http://deb.debian.org/debian trixie/main i386 gfortran i386 4:13.2.0-7 [1432 B] Get: 54 http://deb.debian.org/debian trixie/main i386 hdf5-helpers i386 1.10.10+repack-3+b1 [23.5 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1 [24.5 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1 [7824 B] Get: 57 http://deb.debian.org/debian trixie/main i386 libaec-dev i386 1.1.3-1 [22.4 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3 [140 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3 [152 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.7.1-3 [467 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.7.1-3 [589 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.7.1-3 [477 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1 i386 1.10.10+repack-3+b1 [1177 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libhdf5-cpp-103-1 i386 1.10.10+repack-3+b1 [138 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libhdf5-fortran-102 i386 1.10.10+repack-3+b1 [97.9 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-100 i386 1.10.10+repack-3+b1 [74.3 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-fortran-100 i386 1.10.10+repack-3+b1 [41.8 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-cpp-100 i386 1.10.10+repack-3+b1 [21.7 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo-dev i386 1:2.1.5-2+b2 [303 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.2.1-3 [2744 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libhdf5-dev i386 1.10.10+repack-3+b1 [2773 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3 [2167 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-3 [4400 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libtmglib3 i386 3.12.0-3 [121 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 liblapacke i386 3.12.0-3 [374 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libtmglib-dev i386 3.12.0-3 [126 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 liblapacke-dev i386 3.12.0-3 [348 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 liblz4-dev i386 1.9.4-2 [85.5 kB] Fetched 59.8 MB in 1s (81.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:i386: dependency problems, but removing anyway as you requested: libperl5.38:i386 depends on libdb5.3. libpam-modules:i386 depends on libdb5.3. (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 ... 19885 files and directories currently installed.) Removing libdb5.3:i386 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:i386. (Reading database ... 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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_i386.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:i386. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/107324/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/107324/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 i386 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 134 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 135 | sizeof(char*) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 166 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 167 | sizeof(uint32_t) * dims[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 206 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 207 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:212:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 212 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 213 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 251 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 252 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:257:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 257 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 258 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} h5c++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.4=. -fstack-protector-strong -Wformat -Werror=format-security -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 'TData* malloc_wcheck(unsigned int) [with TData = double]': biom_inmem.cpp:99:60: required from here biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int]': biom_inmem.cpp:100:62: required from here biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = unsigned int*]': biom_inmem.cpp:177:55: required from here biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} biom_inmem.cpp: In instantiation of 'TData* malloc_wcheck(unsigned int) [with TData = double*]': biom_inmem.cpp:178:55: required from here biom_inmem.cpp:23:47: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 23 | fprintf(stderr, "Failed to allocate %ld bytes; [%s]:%d\n", | ~~^ | | | long int | %d 24 | bufsize, __FILE__, __LINE__); | ~~~~~~~ | | | size_t {aka unsigned int} 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 '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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 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: 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 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 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, __off64_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, __off64_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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': unifrac_cmp.cpp:281:29: required from '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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_cmp.cpp: In instantiation of 'void initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = float]': unifrac_cmp.cpp:281:29: required from '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:50:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 50 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 51 | sizeof(TFloat) * n_samples_r, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = double; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' unifrac_cmp.cpp:285:11: required from '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_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = float; uint64_t = long long unsigned int]': unifrac_task.hpp:532:78: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' unifrac_cmp.cpp:285:11: required from '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_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = long long unsigned int]' unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' unifrac_cmp.cpp:89:11: required from '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_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = long long unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' unifrac_task.hpp:320:90: required from 'su_cpu::UnifracTask::UnifracTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = long long unsigned int]' unifrac_task.hpp:428:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' unifrac_cmp.cpp:89:11: required from '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_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = double; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double; TEmb = unsigned int]' unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' unifrac_cmp.cpp:285:11: required from '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_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int unifrac_task.hpp: In instantiation of 'static TEmb* su_cpu::UnifracTaskBase::initialize_embedded(uint64_t, unsigned int) [with TFloat = float; TEmb = unsigned int; uint64_t = long long unsigned int]': unifrac_task.hpp:144:51: required from 'su_cpu::UnifracTaskBase::UnifracTaskBase(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' unifrac_task.hpp:532:161: required from 'su_cpu::UnifracVawTask::UnifracVawTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float; TEmb = unsigned int]' unifrac_task.hpp:610:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' unifrac_cmp.cpp:285:11: required from '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_task.hpp:192:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 192 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 193 | sizeof(TEmb) * bsize, err, __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int 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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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/107324/tmp/hooks/C01_cleanup starting debug output: disk usage on i-capture-the-hostname at Sun Jun 1 23:39:08 UTC 2025 Filesystem Size Used Avail Use% Mounted on tmpfs 3.9G 0 3.9G 0% /dev/shm I: user script /srv/workspace/pbuilder/107324/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/107324 and its subdirectories