Sat May 20 18:54:43 UTC 2023 I: starting to build unifrac-tools/bookworm/armhf on jenkins on '2023-05-20 18:54' Sat May 20 18:54:43 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_19/462/console.log Sat May 20 18:54:43 UTC 2023 I: Downloading source for bookworm/unifrac-tools=1.2-2 --2023-05-20 18:54:43-- http://cdn-fastly.deb.debian.org/debian/pool/main/u/unifrac-tools/unifrac-tools_1.2-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2269 (2.2K) [text/prs.lines.tag] Saving to: ‘unifrac-tools_1.2-2.dsc’ 0K .. 100% 73.6M=0s 2023-05-20 18:54:43 (73.6 MB/s) - ‘unifrac-tools_1.2-2.dsc’ saved [2269/2269] Sat May 20 18:54:43 UTC 2023 I: unifrac-tools_1.2-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: unifrac-tools Binary: unifrac-tools, libssu0, libssu-dev Architecture: any Version: 1.2-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/biocore/unifrac-binaries Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/unifrac-tools Vcs-Git: https://salsa.debian.org/med-team/unifrac-tools.git Testsuite: autopkgtest-pkg-python Build-Depends: debhelper-compat (= 13), dh-exec, libhdf5-dev, hdf5-helpers, liblz4-dev, libblas-dev, liblapacke-dev, chrpath, python3 Package-List: libssu-dev deb libdevel optional arch=any libssu0 deb libs optional arch=any unifrac-tools deb science optional arch=any Checksums-Sha1: 4dc502c9c738718d5ae01be095c5363e47cafee0 6571933 unifrac-tools_1.2.orig.tar.gz b155cb68612579bfe94b21bac9056e3bf891d1f2 7700 unifrac-tools_1.2-2.debian.tar.xz Checksums-Sha256: 321b2aa67d5c55241b15f5d53e79c6fca125c4f69fd5d26fd3dc2c811ef77b74 6571933 unifrac-tools_1.2.orig.tar.gz 5fc47081adcd4c5bb77665061630471e0ee23618fb1ffe7ed2d24b8f20b5d723 7700 unifrac-tools_1.2-2.debian.tar.xz Files: 714b1b6b89312049c4bbb60fd677d8e5 6571933 unifrac-tools_1.2.orig.tar.gz fe098c3647d46b5e1c265041a82e0846 7700 unifrac-tools_1.2-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmO7xmQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHQ+A/+N/ro+pu97hc25whonOC2iLycZL1kFthC N3EJwq8H2amS+RM/04XNlseGoT5LwvWXyv0qJaQLtXZ9t1kEOv/HfjC5Mct46T5y cVIE17S0+OI8PZb+epgi7fV5eA7NZMLOqW/oHmWamEhOAZfkbKDNJEeP59WLPstr L7Qvp3h35g5PiX2e6Nbb0jETaR1mSIumoi/3Zxd3TIcD+/I39NrBx0eDOQtNnkgO IRVMeLjx78EAYTT3GdKyXfmXDjUjayALI/5arGqdjJFpwuTmAFh2svwDaHTI3ihG sQ6QeSCKmmeQSVuQevcWAGug5S4Hs8ZW+Y47l4nDckTeg3Q17Eh6bux0vTxT96rV 2gytSyuOcUyaYHveeUpnKisBhjWSAH1wRXnaD43D9GW3c1fxQf78I0qm7y18FOPq 77bnC7lVkK5It0tnwn8inL0SkNCYNPRl2x471OP1ynyjum4tGVgyVwMAqPONhR3A YUPKO/X7M+NxlJie5LcKwgNaQVfYcw89r94YGz7rEl1TgrNjEA6S65NAD+q9Sx/T vyYdUgQ+rqJ9SdCU6k4JAVH7y91Z7+XSeLRyT+BXEpdVutjglO2fhHzNlD2fsvDo Hf6I0F66iHoRujseEhb1NPZKlkCB78ZLKqLiAE7xI5eh340mGuJfi6za3G1iVAHU CAZv/pRm9b0= =DKmb -----END PGP SIGNATURE----- Sat May 20 18:54:43 UTC 2023 I: Checking whether the package is not for us Sat May 20 18:54:43 UTC 2023 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Sat May 20 18:54:43 UTC 2023 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Sat May 20 18:59:31 UTC 2023 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 20 06:54:57 -12 2023 I: pbuilder-time-stamp: 1684608897 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 Sun Jan 8 19:46:44 2023 -12 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/2048/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='415ea96cad2046c3a7776c39b1d9ad4a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2048' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/pbuilderrc_Qqua --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/b1 --logfile b1/build.log unifrac-tools_1.2-2.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt64c 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/2048/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: armhf 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 ... 19329 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 37.4 MB of archives. After unpacking 144 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf chrpath armhf 0.16-2+b1 [15.9 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf dh-exec armhf 0.27 [26.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf hdf5-helpers armhf 1.10.8+repack1-1 [27.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf libaec0 armhf 1.0.6-1+b1 [19.8 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libsz2 armhf 1.0.6-1+b1 [7864 B] Get: 47 http://deb.debian.org/debian bookworm/main armhf libaec-dev armhf 1.0.6-1+b1 [18.1 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libblas-dev armhf 3.11.0-2 [115 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libcurl4-openssl-dev armhf 7.88.1-9 [453 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libhdf5-103-1 armhf 1.10.8+repack1-1 [1183 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf libhdf5-cpp-103-1 armhf 1.10.8+repack1-1 [119 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libhdf5-fortran-102 armhf 1.10.8+repack1-1 [82.1 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-100 armhf 1.10.8+repack1-1 [65.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-fortran-100 armhf 1.10.8+repack1-1 [38.8 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libhdf5-hl-cpp-100 armhf 1.10.8+repack1-1 [25.2 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [260 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libssl-dev armhf 3.0.8-1 [2132 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libhdf5-dev armhf 1.10.8+repack1-1 [2573 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf liblapack-dev armhf 3.11.0-2 [1798 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libtmglib3 armhf 3.11.0-2 [92.3 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf liblapacke armhf 3.11.0-2 [300 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libtmglib-dev armhf 3.11.0-2 [95.8 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf liblapacke-dev armhf 3.11.0-2 [286 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf liblz4-dev armhf 1.9.4-1 [76.6 kB] Fetched 37.4 MB in 1s (35.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19329 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (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 ... 19645 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.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:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (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 ... 20079 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../06-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../09-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-3_armhf.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_armhf.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:armhf. Preparing to unpack .../24-libelf1_0.188-2.1_armhf.deb ... Unpacking libelf1:armhf (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_armhf.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../26-libicu72_72.1-3_armhf.deb ... Unpacking libicu72:armhf (72.1-3) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.2_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-12_armhf.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_armhf.deb ... Unpacking dh-exec (0.27) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../33-hdf5-helpers_1.10.8+repack1-1_armhf.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1) ... Selecting previously unselected package libaec0:armhf. Preparing to unpack .../34-libaec0_1.0.6-1+b1_armhf.deb ... Unpacking libaec0:armhf (1.0.6-1+b1) ... Selecting previously unselected package libsz2:armhf. Preparing to unpack .../35-libsz2_1.0.6-1+b1_armhf.deb ... Unpacking libsz2:armhf (1.0.6-1+b1) ... Selecting previously unselected package libaec-dev:armhf. Preparing to unpack .../36-libaec-dev_1.0.6-1+b1_armhf.deb ... Unpacking libaec-dev:armhf (1.0.6-1+b1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../37-libblas3_3.11.0-2_armhf.deb ... Unpacking libblas3:armhf (3.11.0-2) ... Selecting previously unselected package libblas-dev:armhf. Preparing to unpack .../38-libblas-dev_3.11.0-2_armhf.deb ... Unpacking libblas-dev:armhf (3.11.0-2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../39-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../40-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../41-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../42-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../43-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../44-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../46-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../47-libcurl4_7.88.1-9_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-9) ... Selecting previously unselected package libcurl4-openssl-dev:armhf. Preparing to unpack .../48-libcurl4-openssl-dev_7.88.1-9_armhf.deb ... Unpacking libcurl4-openssl-dev:armhf (7.88.1-9) ... Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../49-libgfortran5_12.2.0-14_armhf.deb ... Unpacking libgfortran5:armhf (12.2.0-14) ... Selecting previously unselected package libhdf5-103-1:armhf. Preparing to unpack .../50-libhdf5-103-1_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-103-1:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-cpp-103-1:armhf. Preparing to unpack .../51-libhdf5-cpp-103-1_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-cpp-103-1:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-fortran-102:armhf. Preparing to unpack .../52-libhdf5-fortran-102_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-fortran-102:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-100:armhf. Preparing to unpack .../53-libhdf5-hl-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-fortran-100:armhf. Preparing to unpack .../54-libhdf5-hl-fortran-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-fortran-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package libhdf5-hl-cpp-100:armhf. Preparing to unpack .../55-libhdf5-hl-cpp-100_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-hl-cpp-100:armhf (1.10.8+repack1-1) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../56-zlib1g-dev_1%3a1.2.13.dfsg-1_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Selecting previously unselected package libjpeg62-turbo:armhf. Preparing to unpack .../57-libjpeg62-turbo_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg62-turbo:armhf (1:2.1.5-2) ... Selecting previously unselected package libjpeg62-turbo-dev:armhf. Preparing to unpack .../58-libjpeg62-turbo-dev_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg62-turbo-dev:armhf (1:2.1.5-2) ... Selecting previously unselected package libjpeg-dev:armhf. Preparing to unpack .../59-libjpeg-dev_1%3a2.1.5-2_armhf.deb ... Unpacking libjpeg-dev:armhf (1:2.1.5-2) ... Selecting previously unselected package libssl-dev:armhf. Preparing to unpack .../60-libssl-dev_3.0.8-1_armhf.deb ... Unpacking libssl-dev:armhf (3.0.8-1) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../61-libhdf5-dev_1.10.8+repack1-1_armhf.deb ... Unpacking libhdf5-dev (1.10.8+repack1-1) ... Selecting previously unselected package liblapack3:armhf. Preparing to unpack .../62-liblapack3_3.11.0-2_armhf.deb ... Unpacking liblapack3:armhf (3.11.0-2) ... Selecting previously unselected package liblapack-dev:armhf. Preparing to unpack .../63-liblapack-dev_3.11.0-2_armhf.deb ... Unpacking liblapack-dev:armhf (3.11.0-2) ... Selecting previously unselected package libtmglib3:armhf. Preparing to unpack .../64-libtmglib3_3.11.0-2_armhf.deb ... Unpacking libtmglib3:armhf (3.11.0-2) ... Selecting previously unselected package liblapacke:armhf. Preparing to unpack .../65-liblapacke_3.11.0-2_armhf.deb ... Unpacking liblapacke:armhf (3.11.0-2) ... Selecting previously unselected package libtmglib-dev:armhf. Preparing to unpack .../66-libtmglib-dev_3.11.0-2_armhf.deb ... Unpacking libtmglib-dev:armhf (3.11.0-2) ... Selecting previously unselected package liblapacke-dev:armhf. Preparing to unpack .../67-liblapacke-dev_3.11.0-2_armhf.deb ... Unpacking liblapacke-dev:armhf (3.11.0-2) ... Selecting previously unselected package liblz4-dev:armhf. Preparing to unpack .../68-liblz4-dev_1.9.4-1_armhf.deb ... Unpacking liblz4-dev:armhf (1.9.4-1) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libicu72:armhf (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:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (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:armhf (1.0.6-1+b1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ... Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libssl-dev:armhf (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up liblz4-dev:armhf (1.9.4-1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... 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Not building database; man-db/auto-update is not 'true'. Setting up libcurl4-openssl-dev:armhf (7.88.1-9) ... Setting up libhdf5-103-1:armhf (1.10.8+repack1-1) ... Setting up libhdf5-cpp-103-1:armhf (1.10.8+repack1-1) ... Setting up libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up libhdf5-hl-100:armhf (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:armhf (1.10.8+repack1-1) ... Setting up libhdf5-fortran-102:armhf (1.10.8+repack1-1) ... Setting up libhdf5-hl-fortran-100:armhf (1.10.8+repack1-1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Processing triggers for libc-bin (2.36-9) ... 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: Running cd /build/unifrac-tools-1.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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 armhf debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/build/unifrac-tools-1.2' cd test && make clean make[2]: Entering directory '/build/unifrac-tools-1.2/test' rm -f *.o capi_test make[2]: Leaving directory '/build/unifrac-tools-1.2/test' cd src && make clean make[2]: Entering directory '/build/unifrac-tools-1.2/src' rm -f *.o ssu faithpd test_su test_ska test_api libssu.so make[2]: Leaving directory '/build/unifrac-tools-1.2/src' make[1]: Leaving directory '/build/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/unifrac-tools-1.2' mkdir -p /build/unifrac-tools-1.2/debian/tmp/usr/bin mkdir -p /build/unifrac-tools-1.2/debian/tmp/usr/lib dh_auto_build -- PREFIX=/build/unifrac-tools-1.2/debian/tmp/usr make -j1 "INSTALL=install --strip-program=true" PREFIX=/build/unifrac-tools-1.2/debian/tmp/usr make[2]: Entering directory '/build/unifrac-tools-1.2' cd src && make api make[3]: Entering directory '/build/unifrac-tools-1.2/src' h5c++ -g -O2 -ffile-prefix-map=/build/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/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/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/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 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 224 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 225 | 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:256:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 256 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 257 | 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:305:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 305 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 306 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:311:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 311 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 312 | 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:412:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 412 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 413 | sizeof(uint32_t) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka long long unsigned int} biom.cpp:418:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'hsize_t' {aka 'long long unsigned int'} [-Wformat=] 418 | fprintf(stderr, "Failed to allocate %zd bytes; [%s]:%d\n", | ~~^ | | | int | %lld 419 | sizeof(double) * count[0], __FILE__, __LINE__); | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | hsize_t {aka 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/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/unifrac-tools-1.2/debian/tmp/usr/lib -c cmd.cpp -o cmd.o h5c++ -g -O2 -ffile-prefix-map=/build/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/unifrac-tools-1.2/debian/tmp/usr/lib -c skbio_alt.cpp -o skbio_alt.o h5c++ -g -O2 -ffile-prefix-map=/build/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/unifrac-tools-1.2/debian/tmp/usr/lib api.cpp -c -o api.o -fPIC api.cpp: In function 'compute_status partial(const char*, const char*, const char*, bool, double, bool, unsigned int, unsigned int, unsigned int, partial_mat_t**)': api.cpp: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: 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, __off64_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, __off64_t)' declared with attribute 'warn_unused_result' [-Wunused-result] h5c++ -g -O2 -ffile-prefix-map=/build/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/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/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/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 initialize_sample_counts(TFloat*&, const su::task_parameters*, const su::biom_interface&) [with TFloat = double]': unifrac_cmp.cpp:267:29: 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:366:77: required from here unifrac_cmp.cpp:36:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 36 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 37 | 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:267:29: 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:378:77: required from here unifrac_cmp.cpp:36:47: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 36 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 37 | 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:530:78: 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:608:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' unifrac_cmp.cpp:271:11: 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:366:77: required from here unifrac_task.hpp:190:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 191 | 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:530:78: 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:608:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' unifrac_cmp.cpp:271:11: 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:378:77: required from here unifrac_task.hpp:190:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 191 | 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:142:51: 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:318:90: 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:426:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = double]' unifrac_cmp.cpp:75:11: 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:212:70: required from here unifrac_task.hpp:190:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 191 | 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:142:51: 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:318:90: 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:426:88: required from 'su_cpu::UnifracUnweightedTask::UnifracUnweightedTask(std::vector&, std::vector&, unsigned int, const su::task_parameters*) [with TFloat = float]' unifrac_cmp.cpp:75:11: 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:224:69: required from here unifrac_task.hpp:190:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 191 | 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:142:51: 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:530:161: 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:608:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = double]' unifrac_cmp.cpp:271:11: 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:366:77: required from here unifrac_task.hpp:190:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 191 | 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:142:51: 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:530:161: 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:608:111: required from 'su_cpu::UnifracVawUnweightedTask::UnifracVawUnweightedTask(std::vector&, std::vector&, const TFloat*, unsigned int, const su::task_parameters*) [with TFloat = float]' unifrac_cmp.cpp:271:11: 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:378:77: required from here unifrac_task.hpp:190:51: warning: format '%zd' expects argument of type 'signed size_t', but argument 3 has type 'long long unsigned int' [-Wformat=] 190 | fprintf(stderr, "Failed to allocate %zd bytes, err %d; [%s]:%d\n", | ~~^ | | | int | %lld 191 | 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: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/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/unifrac-tools-1.2/debian/tmp/usr/lib make[3]: Leaving directory '/build/unifrac-tools-1.2/src' cd src && make main make[3]: Entering directory '/build/unifrac-tools-1.2/src' h5c++ -g -O2 -ffile-prefix-map=/build/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/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/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/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/unifrac-tools-1.2/src' cd src && make install make[3]: Entering directory '/build/unifrac-tools-1.2/src' cp -a libssu.so* /build/unifrac-tools-1.2/debian/tmp/usr/lib/ cp ssu faithpd /build/unifrac-tools-1.2/debian/tmp/usr/bin/ mkdir -p /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac cp task_parameters.hpp /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp api.hpp /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp status_enum.hpp /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/unifrac-tools-1.2/src' make[2]: Leaving directory '/build/unifrac-tools-1.2' chmod +x /build/unifrac-tools-1.2/debian/tmp/usr/bin/* make[1]: Leaving directory '/build/unifrac-tools-1.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/unifrac-tools-1.2' export PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/unifrac-tools-1.2/debian/tmp/usr/bin ; \ cd ci ; \ ./crawford_test.sh All tests succeeded make[1]: Leaving directory '/build/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/unifrac-tools-1.2' mkdir -p /build/unifrac-tools-1.2/debian/tmp/usr/bin mkdir -p /build/unifrac-tools-1.2/debian/tmp/usr/lib dh_auto_install -- PREFIX=/build/unifrac-tools-1.2/debian/tmp/usr make -j1 install DESTDIR=/build/unifrac-tools-1.2/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/build/unifrac-tools-1.2/debian/tmp/usr make[2]: Entering directory '/build/unifrac-tools-1.2' cd src && make install make[3]: Entering directory '/build/unifrac-tools-1.2/src' cp -a libssu.so* /build/unifrac-tools-1.2/debian/tmp/usr/lib/ cp ssu faithpd /build/unifrac-tools-1.2/debian/tmp/usr/bin/ mkdir -p /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac cp task_parameters.hpp /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp api.hpp /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ cp status_enum.hpp /build/unifrac-tools-1.2/debian/tmp/usr/include/unifrac/ make[3]: Leaving directory '/build/unifrac-tools-1.2/src' make[2]: Leaving directory '/build/unifrac-tools-1.2' make[1]: Leaving directory '/build/unifrac-tools-1.2' debian/rules override_dh_install make[1]: Entering directory '/build/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/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 dpkg-shlibdeps: warning: debian/unifrac-tools/usr/bin/ssu contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/unifrac-tools/usr/bin/faithpd contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libssu0/usr/lib/arm-linux-gnueabihf/libssu.so.0 found in none of the libraries 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' in '../unifrac-tools_1.2-2_armhf.deb'. dpkg-deb: building package 'libssu-dev' in '../libssu-dev_1.2-2_armhf.deb'. dpkg-deb: building package 'libssu0' in '../libssu0_1.2-2_armhf.deb'. dpkg-deb: building package 'libssu0-dbgsym' in '../libssu0-dbgsym_1.2-2_armhf.deb'. dpkg-deb: building package 'unifrac-tools-dbgsym' in '../unifrac-tools-dbgsym_1.2-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../unifrac-tools_1.2-2_armhf.buildinfo dpkg-genchanges --build=binary -O../unifrac-tools_1.2-2_armhf.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: 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/2048 and its subdirectories I: Current time: Sat May 20 06:59:18 -12 2023 I: pbuilder-time-stamp: 1684609158 Sat May 20 18:59:34 UTC 2023 I: 1st build successful. Starting 2nd build on remote node cbxi4a-armhf-rb.debian.net. Sat May 20 18:59:34 UTC 2023 I: Preparing to do remote build '2' on cbxi4a-armhf-rb.debian.net. Sat May 20 19:19:26 UTC 2023 I: Deleting $TMPDIR on cbxi4a-armhf-rb.debian.net. Sat May 20 19:19:28 UTC 2023 I: unifrac-tools_1.2-2_armhf.changes: Format: 1.8 Date: Mon, 09 Jan 2023 08:31:31 +0100 Source: unifrac-tools Binary: libssu-dev libssu0 libssu0-dbgsym unifrac-tools unifrac-tools-dbgsym Architecture: armhf Version: 1.2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libssu-dev - high-performance phylogenetic diversity calculations (dev) libssu0 - high-performance phylogenetic diversity calculations (lib) unifrac-tools - high-performance phylogenetic diversity calculations (binaries) Closes: 1028051 Changes: unifrac-tools (1.2-2) unstable; urgency=medium . * Sneak in CFLAGS via CPPFLAGS to work around missing support of CLFAGS in upstream Makefile Closes: #1028051 Checksums-Sha1: 5ae51b54c78b2ae2953fd421cb52b4b484625bc9 8236 libssu-dev_1.2-2_armhf.deb bcd4a6f797902802b4ca4c4e549a208514fa4826 1037088 libssu0-dbgsym_1.2-2_armhf.deb 6c522b6668433616e98b517affe81dd7dd5a43db 91564 libssu0_1.2-2_armhf.deb 178f2b98b950668a3e0538bbb37790f1154823ed 2010936 unifrac-tools-dbgsym_1.2-2_armhf.deb c119743ca97770772efec2be8763e952a964648c 7525 unifrac-tools_1.2-2_armhf.buildinfo 3987aebf6395330648b55828080539e990e23685 1396760 unifrac-tools_1.2-2_armhf.deb Checksums-Sha256: 0d54210382c7876512847d1d4a8585ec2d0c8cd61d09ac62faa66ee5ee87dc65 8236 libssu-dev_1.2-2_armhf.deb f32e55666b819eeb9daab7d10fef198e6778c44040080f72f521e1f3f40e5cb1 1037088 libssu0-dbgsym_1.2-2_armhf.deb fa7d73773fc5683ddcdefe3672b1f545ed7d8d7d49fd5f53a4c6590ae22150a7 91564 libssu0_1.2-2_armhf.deb faac5677cbd19e8e27fe8c16acaa7baeb7b888f061fe0ac798826f2a80afba97 2010936 unifrac-tools-dbgsym_1.2-2_armhf.deb fa8f7f5a5cb5e08935508d3b3b66225bdb24cb9f57735fe4177979eb6f5a4fa4 7525 unifrac-tools_1.2-2_armhf.buildinfo 5fceef4d05bb32cc0a1332167a53e4f7a82eab849b6d3917ca82c022f12ca474 1396760 unifrac-tools_1.2-2_armhf.deb Files: 90558be26403e04a8171a05540f2f2ed 8236 libdevel optional libssu-dev_1.2-2_armhf.deb 957661e42e1c99770516e07469a3df36 1037088 debug optional libssu0-dbgsym_1.2-2_armhf.deb 4da649d4aa4efe34e344da6c624ae6ac 91564 libs optional libssu0_1.2-2_armhf.deb 9fdc756029fb4d26d2f170f2056a6063 2010936 debug optional unifrac-tools-dbgsym_1.2-2_armhf.deb 7a1b4bc9ee7d19691de7abc913b98bac 7525 science optional unifrac-tools_1.2-2_armhf.buildinfo 1fa79e221fc51358e00a67d99344ac90 1396760 science optional unifrac-tools_1.2-2_armhf.deb Sat May 20 19:19:33 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/unifrac-tools_1.2-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/unifrac-tools_1.2-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/unifrac-tools_1.2-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/b1/unifrac-tools_1.2-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.kmo5k8vN/b2/unifrac-tools_1.2-2_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 6.461s) 6.461s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.788s) 0.787s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sat May 20 19:21:03 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Sat May 20 19:21:03 UTC 2023 I: unifrac-tools from bookworm built successfully and reproducibly on armhf. Sat May 20 19:21:05 UTC 2023 I: Submitting .buildinfo files to external archives: Sat May 20 19:21:05 UTC 2023 I: Submitting 12K b1/unifrac-tools_1.2-2_armhf.buildinfo.asc Sat May 20 19:21:07 UTC 2023 I: Submitting 12K b2/unifrac-tools_1.2-2_armhf.buildinfo.asc Sat May 20 19:21:11 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 20 19:21:11 UTC 2023 I: Done submitting .buildinfo files. Sat May 20 19:21:11 UTC 2023 I: Removing signed unifrac-tools_1.2-2_armhf.buildinfo.asc files: removed './b1/unifrac-tools_1.2-2_armhf.buildinfo.asc' removed './b2/unifrac-tools_1.2-2_armhf.buildinfo.asc'