I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 9 03:28:19 +14 2024 I: pbuilder-time-stamp: 1704720499 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.2-2.dsc] I: copying [./unifrac-tools_1.2.orig.tar.gz] I: copying [./unifrac-tools_1.2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jan 9 07:46:44 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./unifrac-tools_1.2-2.dsc: no acceptable signature found dpkg-source: info: extracting unifrac-tools in unifrac-tools-1.2 dpkg-source: info: unpacking unifrac-tools_1.2.orig.tar.gz dpkg-source: info: unpacking unifrac-tools_1.2-2.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3998121/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. 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 Jan 8 13:28 /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/3998121/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3998121/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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=5372b3e06855406a8d179e75da46ec28 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=3998121 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.zw2AP5tI/pbuilderrc_vTPB --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zw2AP5tI/b2 --logfile b2/build.log unifrac-tools_1.2-2.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' http_proxy=http://192.168.101.104:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash -rwxr-xr-x 3 root root 67728 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67728 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67728 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67664 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 68536 Sep 20 2022 cat -rwxr-xr-x 1 root root 68616 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 68552 Sep 20 2022 chmod -rwxr-xr-x 1 root root 68632 Sep 20 2022 chown -rwxr-xr-x 1 root root 200264 Sep 20 2022 cp -rwxr-xr-x 1 root root 133640 Jan 5 2023 dash -rwxr-xr-x 1 root root 134144 Sep 20 2022 date -rwxr-xr-x 1 root root 134248 Sep 20 2022 dd -rwxr-xr-x 1 root root 134888 Sep 20 2022 df -rwxr-xr-x 1 root root 200440 Sep 20 2022 dir -rwxr-xr-x 1 root root 141720 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 68408 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 68384 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 134584 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 67744 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 198880 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 93752 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67592 Dec 19 2022 hostname -rwxr-xr-x 1 root root 68664 Sep 20 2022 ln -rwxr-xr-x 1 root root 69208 Mar 23 2023 login -rwxr-xr-x 1 root root 200440 Sep 20 2022 ls -rwxr-xr-x 1 root root 264360 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 134384 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 68768 Sep 20 2022 mknod -rwxr-xr-x 1 root root 68472 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 67752 Mar 23 2023 more -rwsr-xr-x 1 root root 67744 Mar 23 2023 mount -rwxr-xr-x 1 root root 67744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 134728 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 68496 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 68392 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed lrwxrwxrwx 1 root root 9 Jan 8 13:28 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar -rwxr-xr-x 1 root root 67904 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 67744 Mar 23 2023 umount -rwxr-xr-x 1 root root 68416 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 200440 Sep 20 2022 vdir -rwxr-xr-x 1 root root 133312 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3998121/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: arm64 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, 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 ... 18171 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 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} 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} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{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} libjpeg-dev{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} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{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} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{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, 79 newly installed, 0 to remove and 0 not upgraded. Need to get 39.5 MB of archives. After unpacking 185 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.3~deb12u1 [619 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 dh-exec arm64 0.27 [27.6 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 hdf5-helpers arm64 1.10.8+repack1-1 [27.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libaec0 arm64 1.0.6-1+b1 [19.9 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libsz2 arm64 1.0.6-1+b1 [7740 B] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libaec-dev arm64 1.0.6-1+b1 [18.7 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libblas-dev arm64 3.11.0-2 [97.6 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1+deb12u1 [68.3 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-10+deb12u4 [366 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libcurl4-openssl-dev arm64 7.88.1-10+deb12u4 [475 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libhdf5-103-1 arm64 1.10.8+repack1-1 [1037 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libhdf5-cpp-103-1 arm64 1.10.8+repack1-1 [119 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libhdf5-fortran-102 arm64 1.10.8+repack1-1 [91.1 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-100 arm64 1.10.8+repack1-1 [64.0 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-fortran-100 arm64 1.10.8+repack1-1 [42.7 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-cpp-100 arm64 1.10.8+repack1-1 [25.4 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-2 [292 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libjpeg-dev arm64 1:2.1.5-2 [71.8 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libssl-dev arm64 3.0.11-1~deb12u2 [2302 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libhdf5-dev arm64 1.10.8+repack1-1 [2654 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libtmglib3 arm64 3.11.0-2 [95.3 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 liblapacke arm64 3.11.0-2 [330 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libtmglib-dev arm64 3.11.0-2 [99.0 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 liblapacke-dev arm64 3.11.0-2 [319 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 liblz4-dev arm64 1.9.4-1 [81.9 kB] Fetched 39.5 MB in 0s (118 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 18171 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 18487 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 18921 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../03-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package chrpath. Preparing to unpack .../16-chrpath_0.16-2+b1_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../24-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../26-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3~deb12u1_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3~deb12u1) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package dh-exec. Preparing to unpack .../32-dh-exec_0.27_arm64.deb ... Unpacking dh-exec (0.27) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../33-hdf5-helpers_1.10.8+repack1-1_arm64.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../34-libaec0_1.0.6-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.0.6-1+b1) ... Selecting previously unselected package libsz2:arm64. Preparing to unpack .../35-libsz2_1.0.6-1+b1_arm64.deb ... Unpacking libsz2:arm64 (1.0.6-1+b1) ... Selecting previously unselected package libaec-dev:arm64. Preparing to unpack .../36-libaec-dev_1.0.6-1+b1_arm64.deb ... Unpacking libaec-dev:arm64 (1.0.6-1+b1) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../37-libblas3_3.11.0-2_arm64.deb ... Unpacking libblas3:arm64 (3.11.0-2) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../38-libblas-dev_3.11.0-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../39-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../40-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../41-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../42-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../43-libnghttp2-14_1.52.0-1+deb12u1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.52.0-1+deb12u1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../44-libpsl5_0.21.2-1_arm64.deb ... Unpacking libpsl5:arm64 (0.21.2-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../46-libssh2-1_1.10.0-3+b1_arm64.deb ... Unpacking libssh2-1:arm64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../47-libcurl4_7.88.1-10+deb12u4_arm64.deb ... Unpacking libcurl4:arm64 (7.88.1-10+deb12u4) ... Selecting previously unselected package libcurl4-openssl-dev:arm64. Preparing to unpack .../48-libcurl4-openssl-dev_7.88.1-10+deb12u4_arm64.deb ... Unpacking libcurl4-openssl-dev:arm64 (7.88.1-10+deb12u4) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../49-libgfortran5_12.2.0-14_arm64.deb ... Unpacking libgfortran5:arm64 (12.2.0-14) ... Selecting previously unselected package libhdf5-103-1:arm64. Preparing to unpack .../50-libhdf5-103-1_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-cpp-103-1:arm64. Preparing to unpack .../51-libhdf5-cpp-103-1_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-cpp-103-1:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-fortran-102:arm64. Preparing to unpack .../52-libhdf5-fortran-102_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-fortran-102:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-100:arm64. Preparing to unpack .../53-libhdf5-hl-100_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-hl-100:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-fortran-100:arm64. Preparing to unpack .../54-libhdf5-hl-fortran-100_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-hl-fortran-100:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-cpp-100:arm64. Preparing to unpack .../55-libhdf5-hl-cpp-100_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-hl-cpp-100:arm64 (1.10.8+repack1-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../56-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../57-libjpeg62-turbo_1%3a2.1.5-2_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-2) ... Selecting previously unselected package libjpeg62-turbo-dev:arm64. Preparing to unpack .../58-libjpeg62-turbo-dev_1%3a2.1.5-2_arm64.deb ... Unpacking libjpeg62-turbo-dev:arm64 (1:2.1.5-2) ... Selecting previously unselected package libjpeg-dev:arm64. Preparing to unpack .../59-libjpeg-dev_1%3a2.1.5-2_arm64.deb ... Unpacking libjpeg-dev:arm64 (1:2.1.5-2) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../60-libssl-dev_3.0.11-1~deb12u2_arm64.deb ... Unpacking libssl-dev:arm64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../61-libhdf5-dev_1.10.8+repack1-1_arm64.deb ... Unpacking libhdf5-dev (1.10.8+repack1-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../62-liblapack3_3.11.0-2_arm64.deb ... Unpacking liblapack3:arm64 (3.11.0-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../63-liblapack-dev_3.11.0-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libtmglib3:arm64. Preparing to unpack .../64-libtmglib3_3.11.0-2_arm64.deb ... Unpacking libtmglib3:arm64 (3.11.0-2) ... Selecting previously unselected package liblapacke:arm64. Preparing to unpack .../65-liblapacke_3.11.0-2_arm64.deb ... Unpacking liblapacke:arm64 (3.11.0-2) ... Selecting previously unselected package libtmglib-dev:arm64. Preparing to unpack .../66-libtmglib-dev_3.11.0-2_arm64.deb ... Unpacking libtmglib-dev:arm64 (3.11.0-2) ... Selecting previously unselected package liblapacke-dev:arm64. Preparing to unpack .../67-liblapacke-dev_3.11.0-2_arm64.deb ... Unpacking liblapacke-dev:arm64 (3.11.0-2) ... Selecting previously unselected package liblz4-dev:arm64. Preparing to unpack .../68-liblz4-dev_1.9.4-1_arm64.deb ... Unpacking liblz4-dev:arm64 (1.9.4-1) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnghttp2-14:arm64 (1.52.0-1+deb12u1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libaec0:arm64 (1.0.6-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libssl-dev:arm64 (3.0.11-1~deb12u2) ... Setting up autopoint (0.21-12) ... Setting up liblz4-dev:arm64 (1.9.4-1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up chrpath (0.16-2+b1) ... Setting up libblas-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up libsz2:arm64 (1.0.6-1+b1) ... 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:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libaec-dev:arm64 (1.0.6-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-2) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtmglib3:arm64 (3.11.0-2) ... Setting up liblapack-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up liblapacke:arm64 (3.11.0-2) ... Setting up libcurl4:arm64 (7.88.1-10+deb12u4) ... Setting up libtmglib-dev:arm64 (3.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up liblapacke-dev:arm64 (3.11.0-2) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcurl4-openssl-dev:arm64 (7.88.1-10+deb12u4) ... Setting up libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.8+repack1-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up libhdf5-hl-100:arm64 (1.10.8+repack1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up dh-exec (0.27) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-fortran-102:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.36-9+deb12u3) ... 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/3998121/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bookworm I: user script /srv/workspace/pbuilder/3998121/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/unifrac-tools-1.2/ && 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_1.2-2_source.changes dpkg-buildpackage: info: source package unifrac-tools dpkg-buildpackage: info: source version 1.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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-1.2' cd test && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.2/test' rm -f *.o capi_test make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2/test' cd src && make clean make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.2/src' rm -f *.o ssu faithpd test_su test_ska test_api libssu.so make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2/src' make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' 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-1.2' mkdir -p /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/bin mkdir -p /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib dh_auto_build -- PREFIX=/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.2' cd src && make api make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.2/src' h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -c tree.cpp -o tree.o tree.cpp: In function 'std::string& rtrim(std::string&)': tree.cpp:374:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 374 | std::not1(std::ptr_fun(std::isspace))).base(), s.end()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from tree.hpp:13, from tree.cpp:1: /usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -c biom.cpp -o biom.o biom.cpp: In constructor 'su::biom::biom(std::string)': biom.cpp:30:51: warning: implicitly-declared 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' is deprecated [-Wdeprecated-copy] 30 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ In file included from /usr/include/hdf5/serial/H5Cpp.h:48, from biom.hpp:14, from biom.cpp:13: /usr/include/hdf5/serial/H5File.h:105:5: note: because 'H5::H5File' has user-provided 'H5::H5File::H5File(const H5::H5File&)' 105 | H5File(const H5File &original); | ^~~~~~ /usr/include/hdf5/serial/H5File.h: In member function 'H5::H5File& H5::H5File::operator=(const H5::H5File&)': /usr/include/hdf5/serial/H5File.h:25:17: warning: implicitly-declared 'H5::Group& H5::Group::operator=(const H5::Group&)' is deprecated [-Wdeprecated-copy] 25 | class H5_DLLCPP H5File : public Group { | ^~~~~~ In file included from /usr/include/hdf5/serial/H5Cpp.h:47: /usr/include/hdf5/serial/H5Group.h:63:5: note: because 'H5::Group' has user-provided 'H5::Group::Group(const H5::Group&)' 63 | Group(const Group &original); | ^~~~~ biom.cpp: In constructor 'su::biom::biom(std::string)': biom.cpp:30:51: note: synthesized method 'H5::H5File& H5::H5File::operator=(const H5::H5File&)' first required here 30 | file = H5File(filename.c_str(), H5F_ACC_RDONLY); | ^ biom.cpp: In constructor 'su::biom::biom(const char* const*, const char* const*, uint32_t*, uint32_t*, double*, int, int, int)': biom.cpp:176:31: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'const int' [-Wsign-compare] 176 | for(unsigned int i = 0; i < n_obs; i++) { | ~~^~~~~~~ biom.cpp: In member function 'void su::biom::load_ids(const char*, std::vector >&)': biom.cpp:224:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 224 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 225 | 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:256:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 256 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 257 | 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:305:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 305 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 306 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:311:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 311 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 312 | 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:412:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 412 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 413 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp:418:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 418 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | long int | %lld 419 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long long unsigned int biom.cpp: In instantiation of 'void su::biom::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.cpp:377:30: required from here biom.cpp:362:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] 362 | if ((j>=start)&&(j=start)&&(j]': biom.cpp:381:30: required from here biom.cpp:362:15: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'unsigned int' [-Wsign-compare] 362 | if ((j>=start)&&(j=start)&&(j: 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 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -c cmd.cpp -o cmd.o h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC api.cpp: In function 'compute_status one_off_inmem_cpp(su::biom&, su::BPTree&, const char*, bool, double, bool, unsigned int, mat_t**)': api.cpp:425:75: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 425 | 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:84:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 84 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:92:62: note: in expansion of macro 'PARSE_TREE_TABLE' 92 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ | ^~~~~~~~~~~~~~~~ api.cpp:456:5: note: in expansion of macro 'PARSE_SYNC_TREE_TABLE' 456 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp:467:75: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::vector::size_type' {aka 'long unsigned int'} [-Wformat=] 467 | 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:84:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 84 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:92:62: note: in expansion of macro 'PARSE_TREE_TABLE' 92 | #define PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) PARSE_TREE_TABLE(tree_filename, table_filename) \ | ^~~~~~~~~~~~~~~~ api.cpp:495:5: note: in expansion of macro 'PARSE_SYNC_TREE_TABLE' 495 | PARSE_SYNC_TREE_TABLE(tree_filename, table_filename) | ^~~~~~~~~~~~~~~~~~~~~ api.cpp: In function 'compute_status one_off(const char*, const char*, const char*, bool, double, bool, unsigned int, mat_t**)': api.cpp:84:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 84 | 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, table_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'compute_status one_off_matrix(const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, mat_full_fp64_t**)': api.cpp:84:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 84 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:591:5: note: in expansion of macro 'PARSE_TREE_TABLE' 591 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'compute_status one_off_matrix_fp32(const char*, const char*, const char*, bool, double, bool, unsigned int, const char*, mat_full_fp32_t**)': api.cpp:84:76: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses] 84 | if(table.n_samples <= 0 | table.n_obs <= 0) { \ | ~~~~~~~~~~~~~~~~^~~~ api.cpp:604:5: note: in expansion of macro 'PARSE_TREE_TABLE' 604 | PARSE_TREE_TABLE(tree_filename, biom_filename) | ^~~~~~~~~~~~~~~~ api.cpp: In function 'IOStatus read_partial_header_fd(int, TPMat&)': api.cpp:1166:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] 1166 | if(n_samples <= 0 || n_stripes <= 0 || stripe_total <= 0 || is_upper_triangle < 0) | ~~~~~~~~~~~~~~~~~~^~~ api.cpp: In instantiation of 'IOStatus read_partial_header_fd(int, TPMat&) [with TPMat = partial_mat; IOStatus = io_status]': api.cpp:1334:48: required from here api.cpp:1166:83: warning: comparison of constant '0' with boolean expression is always false [-Wbool-compare] api.cpp:1192:15: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1192 | if (cnt != sample_id_length_compressed) {free(cmp_buf); return magic_incompatible;} | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1198:14: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1198 | if (cnt!=sample_id_length) {free(samples_buf); free(cmp_buf); return magic_incompatible;} | ~~~^~~~~~~~~~~~~~~~~~ api.cpp:1202:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1202 | 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:1336:49: required from here api.cpp:1235:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1235 | for(int i = 0; i < n_stripes; i++) { | ~~^~~~~~~~~~~ api.cpp:1239:19: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1239 | if ( (i+1)n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:1448:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1448 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1463:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1463 | 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:1480:36: required from here api.cpp:1413:39: warning: comparison of integer expressions of different signedness: 'const uint32_t' {aka 'const unsigned int'} and 'int' [-Wsign-compare] 1413 | if(partial_mats[i]->n_samples != n_samples) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ api.cpp:1448:54: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1448 | for(int j = partial_mats[i]->stripe_start; j < partial_mats[i]->stripe_stop; j++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ api.cpp:1463:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 1463 | 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:240:18: warning: ignoring return value of 'int ftruncate(int, __off_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 240 | 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:240:18: warning: ignoring return value of 'int ftruncate(int, __off_t)' declared with attribute 'warn_unused_result' [-Wunused-result] h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -c unifrac_internal.cpp -o unifrac_internal.o 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 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -c unifrac_cmp.cpp -o unifrac_cmp_cpu.o In file included from unifrac_cmp.cpp:19: unifrac_task.hpp:194: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 194 | #pragma acc enter data create(buf[:bsize]) | unifrac_task.hpp:355: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 355 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:393: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 393 | #pragma acc enter data create(zcheck[:n_samples],sums[:n_samples]) | unifrac_task.hpp:436: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 436 | #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:83: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 83 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:181: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 181 | #pragma acc wait | unifrac_cmp.cpp:190: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] 190 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:200: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] 200 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:268: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 268 | #pragma acc enter data copyin(sample_total_counts[:n_samples_r]) | unifrac_cmp.cpp:279: warning: ignoring '#pragma acc enter' [-Wunknown-pragmas] 279 | #pragma acc enter data create(lengths[:max_emb]) | unifrac_cmp.cpp:324: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 324 | #pragma acc wait | unifrac_cmp.cpp:325: warning: ignoring '#pragma acc update' [-Wunknown-pragmas] 325 | #pragma acc update device(lengths[:filled_emb]) | unifrac_cmp.cpp:333: warning: ignoring '#pragma acc wait' [-Wunknown-pragmas] 333 | #pragma acc wait | unifrac_cmp.cpp:341: warning: ignoring '#pragma acc parallel' [-Wunknown-pragmas] 341 | #pragma acc parallel loop collapse(2) present(dm_stripes_buf,dm_stripes_total_buf) | unifrac_cmp.cpp:352: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] 352 | #pragma acc exit data delete(lengths[:max_emb]) | unifrac_cmp.cpp:353: warning: ignoring '#pragma acc exit' [-Wunknown-pragmas] 353 | #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:212:70: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:215:78: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:218:80: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:221:71: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:224:69: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:227:77: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:230:79: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:233:70: required from here unifrac_cmp.cpp:80:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 80 | 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:366:77: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:369:85: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:372:87: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:375:78: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:378:77: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:381:85: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:384:87: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:387:78: required from here unifrac_cmp.cpp:276:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=] 276 | 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:433:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 433 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:434:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 434 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 **)&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:391:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:392:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 392 | 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:353:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 353 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:354:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 354 | 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:433:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 433 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:434:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 434 | posix_memalign((void **)&stripe_sums, 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 **)&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:391:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:392:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 392 | 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:353:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 353 | posix_memalign((void **)&zcheck, 4096, sizeof(bool) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unifrac_task.hpp:354:25: warning: ignoring return value of 'int posix_memalign(void**, size_t, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 354 | posix_memalign((void **)&sums , 4096, sizeof(TFloat) * n_samples); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ h5c++ -shared -fopenmp -shlib -o libssu.so.0 tree.o biom.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 -shlib -Wl,-soname,libssu.so.0 -llapacke -lblas -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5 ln -sf libssu.so.0 libssu.so # FIXME: Should build static lib as well # h5c++ -shared -fopenmp -shlib -o libssu.a tree.o biom.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 -llapacke -lblas -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2/src' cd src && make main make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.2/src' h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib su.cpp -o ssu tree.o biom.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lpthread h5c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/unifrac-tools-1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wextra -Wno-unused-parameter -g -Wall -std=c++14 -pedantic -I. -O4 -fPIC -L/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib faithpd.cpp -o faithpd tree.o biom.o unifrac_internal.o unifrac_cmp_cpu.o unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 -llapacke -lblas -lpthread make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2/src' cd src && make install make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.2/src' cp -a libssu.so* /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib/ cp ssu faithpd /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/bin/ mkdir -p /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp api.hpp /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2/src' make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' chmod +x /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/bin/* make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.2' export PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/bin ; \ cd ci ; \ ./crawford_test.sh All tests succeeded make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.2' mkdir -p /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/bin mkdir -p /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib dh_auto_install -- PREFIX=/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr make -j1 install DESTDIR=/build/reproducible-path/unifrac-tools-1.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr make[2]: Entering directory '/build/reproducible-path/unifrac-tools-1.2' cd src && make install make[3]: Entering directory '/build/reproducible-path/unifrac-tools-1.2/src' cp -a libssu.so* /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/lib/ cp ssu faithpd /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/bin/ mkdir -p /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac cp task_parameters.hpp /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp api.hpp /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp status_enum.hpp /build/reproducible-path/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2/src' make[2]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/unifrac-tools-1.2' chrpath -d debian/tmp/usr/bin/ssu chrpath -d debian/tmp/usr/bin/faithpd chrpath -d debian/tmp/usr/lib/libssu.so* dh_install make[1]: Leaving directory '/build/reproducible-path/unifrac-tools-1.2' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installman -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dpkg-gencontrol: warning: Depends field of package libssu-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'unifrac-tools-dbgsym' in '../unifrac-tools-dbgsym_1.2-2_arm64.deb'. dpkg-deb: building package 'libssu0' in '../libssu0_1.2-2_arm64.deb'. dpkg-deb: building package 'unifrac-tools' in '../unifrac-tools_1.2-2_arm64.deb'. dpkg-deb: building package 'libssu0-dbgsym' in '../libssu0-dbgsym_1.2-2_arm64.deb'. dpkg-deb: building package 'libssu-dev' in '../libssu-dev_1.2-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../unifrac-tools_1.2-2_arm64.buildinfo dpkg-genchanges --build=binary -O../unifrac-tools_1.2-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3998121/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3998121/tmp/hooks/B01_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/3998121 and its subdirectories I: Current time: Tue Jan 9 03:29:26 +14 2024 I: pbuilder-time-stamp: 1704720566