I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 20 01:38:38 +14 2026 I: pbuilder-time-stamp: 1768822718 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sortmerna_4.3.7-2.dsc] I: copying [./sortmerna_4.3.7.orig.tar.gz] I: copying [./sortmerna_4.3.7-2.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Dec 11 17:21:38 2024 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 ./sortmerna_4.3.7-2.dsc: no acceptable signature found dpkg-source: info: extracting sortmerna in sortmerna-4.3.7 dpkg-source: info: unpacking sortmerna_4.3.7.orig.tar.gz dpkg-source: info: unpacking sortmerna_4.3.7-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying concurrentqueue.h.patch dpkg-source: info: applying gcc-13.patch dpkg-source: info: applying pyhon3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3617052/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jan 19 11:38 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3617052/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3617052/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=e439340cface43f2b5a68e243ffa4460 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3617052 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.EpGS2RSc/pbuilderrc_sT9D --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EpGS2RSc/b2 --logfile b2/build.log sortmerna_4.3.7-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3617052/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all, cmake, librocksdb-dev (>= 6.25.3), libgflags-dev, libsnappy-dev, libzstd-dev, rapidjson-dev, libconcurrentqueue-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on librocksdb-dev (>= 6.25.3); however: Package librocksdb-dev is not installed. pbuilder-satisfydepends-dummy depends on libgflags-dev; however: Package libgflags-dev is not installed. pbuilder-satisfydepends-dummy depends on libsnappy-dev; however: Package libsnappy-dev is not installed. pbuilder-satisfydepends-dummy depends on libzstd-dev; however: Package libzstd-dev is not installed. pbuilder-satisfydepends-dummy depends on rapidjson-dev; however: Package rapidjson-dev is not installed. pbuilder-satisfydepends-dummy depends on libconcurrentqueue-dev; however: Package libconcurrentqueue-dev 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libconcurrentqueue-dev{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgflags-dev{a} libgflags2.2{a} libgssapi-krb5-2{a} libicu72{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblz4-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnsl2{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librhash1{a} librocksdb-dev{a} librocksdb9.3{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsnappy-dev{a} libsnappy1v5{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} procps{a} python3{a} python3-all{a} python3-autocommand{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} rapidjson-dev{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 55.7 MB of archives. After unpacking 229 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.5-1 [2223 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.5-1 [11.4 MB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 63 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 75 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libconcurrentqueue-dev amd64 1.0.4+ds-1 [59.9 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libgflags2.2 amd64 2.2.2-2 [83.5 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libgflags-dev amd64 2.2.2-2 [100 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 liblz4-dev amd64 1.9.4-3+b1 [83.2 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 librocksdb9.3 amd64 9.3.1-1+b1 [3746 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libsnappy-dev amd64 1.2.1-1+b1 [44.1 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 librocksdb-dev amd64 9.3.1-1+b1 [5295 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 93 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Fetched 55.7 MB in 3s (20.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_amd64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:amd64 (3.12.8-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... 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 ... 20285 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_amd64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 19 11:39:14 UTC 2026. Universal Time is now: Mon Jan 19 11:39:14 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:amd64 (1.9.6-3) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up autopoint (0.22.5-2) ... Setting up liblz4-dev:amd64 (1.9.4-3+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up netbase (6.4) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:amd64 (1.4.5-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libgflags2.2 (2.2.2-2) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... 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 (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libsnappy-dev:amd64 (1.2.1-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up librocksdb9.3 (9.3.1-1+b1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libgflags-dev (2.2.2-2) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up librocksdb-dev (9.3.1-1+b1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up cmake (3.30.5-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up dh-python (6.20241024) ... Processing triggers for libc-bin (2.40-4) ... 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/3617052/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3617052/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/sortmerna-4.3.7/ && 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 > ../sortmerna_4.3.7-2_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.7-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: dh_auto_clean --buildsystem=cmake dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: dh_auto_configure --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build -- -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.12 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.12 -DPython_EXECUTABLE=/usr/bin/python3.12 -DPython_LIBRARY=/usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so -DPython_INCLUDE_DIR=/usr/include/python3.12 -DPython3_EXECUTABLE=/usr/bin/python3.12 -DPython3_LIBRARY=/usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so -DPython3_INCLUDE_DIR=/usr/include/python3.12 cd .pybuild/cpython3_3.12/build && PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.12 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.12 -DPython_EXECUTABLE=/usr/bin/python3.12 -DPython_LIBRARY=/usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so -DPython_INCLUDE_DIR=/usr/include/python3.12 -DPython3_EXECUTABLE=/usr/bin/python3.12 -DPython3_LIBRARY=/usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so -DPython3_INCLUDE_DIR=/usr/include/python3.12 ../../.. -- The CXX compiler identification is GNU 14.2.0 -- The C compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Could NOT find Git (missing: GIT_EXECUTABLE) parsing version file: include/version.h PROJECT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build CMAKE_CXX_COMPILER_ID = GNU CMAKE_CONFIGURATION_TYPES = CMAKE_HOST_SYSTEM_NAME = Linux CMAKE_HOST_SYSTEM_VERSION = 6.11.5+bpo-amd64 CMAKE_HOST_SYSTEM = Linux-6.11.5+bpo-amd64 CMAKE_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build CMAKE_CURRENT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build RUNTIME_OUTPUT_DIRECTORY_RELEASE = CMAKE_CXX_FLAGS_DEBUG: -g CMAKE_C_FLAGS_DEBUG: -g CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG EXTRA_CXX_FLAGS_RELEASE: -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") searching ZLIB in default locations ZLIB::ZLIB LOCATION: /usr/lib/x86_64-linux-gnu/libz.so ZLIB::ZLIB LOCATION_DEBUG: /usr/lib/x86_64-linux-gnu/libz.so searching RocksDB in default locations CMAKE_MODULE_PATH: /build/reproducible-path/sortmerna-4.3.7/cmake/modules/ -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found lz4: /usr/lib/x86_64-linux-gnu/liblz4.so -- Found zstd: /usr/lib/x86_64-linux-gnu/libzstd.so RocksDB found Using Shared RocksDB lib RocksDB::rocksdb-shared LOCATION: /usr/lib/x86_64-linux-gnu/librocksdb.so.9.3.1 RocksDB::rocksdb-shared LOCATION_DEBUG: /usr/lib/x86_64-linux-gnu/librocksdb.so.9.3.1 RocksDB::rocksdb-shared transitive link dependencies: rocksdb transitive link dependencies AFTER modification: /usr/lib/x86_64-linux-gnu/libz.so;Threads::Threads SMR Objects transitive link dependencies: alp;RocksDB::rocksdb-shared;ZLIB::ZLIB SMR Objects COMPILE_OPT: COMPILE_OPT-NOTFOUND COMPILE_FLG: COMPILE_FLG-NOTFOUND package_config_destination: /usr/cmake/sortmerna -- Configuring done (0.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED PYTHON_EXECUTABLE PYTHON_INCLUDE_DIR PYTHON_LIBRARY Python3_EXECUTABLE Python3_INCLUDE_DIR Python3_LIBRARY Python_EXECUTABLE Python_INCLUDE_DIR Python_LIBRARY -- Build files have been written to: /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: dh_auto_build --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build -- cd .pybuild/cpython3_3.12/build && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.7 -B/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/CMakeFiles /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/depend make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/depend make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/depend make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/CMakeFiles/build_version.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph/CMakeFiles/cmph.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp/CMakeFiles/alp.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f CMakeFiles/build_version.dir/build.make CMakeFiles/build_version.dir/build make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f 3rdparty/alp/CMakeFiles/alp.dir/build.make 3rdparty/alp/CMakeFiles/alp.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f 3rdparty/cmph/CMakeFiles/cmph.dir/build.make 3rdparty/cmph/CMakeFiles/cmph.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 1%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++17 -MD -MT CMakeFiles/build_version.dir/build_version.cpp.o -MF CMakeFiles/build_version.dir/build_version.cpp.o.d -o CMakeFiles/build_version.dir/build_version.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/build_version.cpp [ 2%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o [ 4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o [ 5%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o [ 7%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o [ 8%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogproblim.cpp [ 15%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o [ 15%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o [ 15%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o [ 15%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o [ 16%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o [ 16%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogprobproto.cpp [ 19%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o [ 19%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogprob.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogprob.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_dynprogprob.cpp [ 21%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o [ 22%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o -MF CMakeFiles/alp.dir/sls_alp_regression.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_regression.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alp_regression.cpp [ 23%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/njn_random.cpp [ 25%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o -MF CMakeFiles/cmph.dir/bdz_ph.c.o.d -o CMakeFiles/cmph.dir/bdz_ph.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bdz_ph.c cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration 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CMakeFiles/cmph.dir/bmz8.c.o.d -o CMakeFiles/cmph.dir/bmz8.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bmz8.c [ 35%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o -MF CMakeFiles/cmph.dir/brz.c.o.d -o CMakeFiles/cmph.dir/brz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/brz.c [ 38%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o [ 38%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o -MF CMakeFiles/cmph.dir/buffer_entry.c.o.d -o CMakeFiles/cmph.dir/buffer_entry.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/buffer_entry.c [ 39%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD 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-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alp.cpp [ 42%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o [ 45%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o [ 45%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o -MF CMakeFiles/alp.dir/sls_pvalues.cpp.o.d -o CMakeFiles/alp.dir/sls_pvalues.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_pvalues.cpp [ 50%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o [ 50%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o [ 52%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc 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3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o -MF CMakeFiles/cmph.dir/compressed_seq.c.o.d -o CMakeFiles/cmph.dir/compressed_seq.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/compressed_seq.c [ 54%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o -MF CMakeFiles/cmph.dir/fch.c.o.d -o CMakeFiles/cmph.dir/fch.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/fch.c cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc 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macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4 | const char* sortmerna_build_compile_date = __DATE__; | ^~~~~~~~ cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o -MF CMakeFiles/cmph.dir/select.c.o.d -o CMakeFiles/cmph.dir/select.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/select.c cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o -MF CMakeFiles/cmph.dir/vqueue.c.o.d -o CMakeFiles/cmph.dir/vqueue.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/vqueue.c cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o -MF CMakeFiles/cmph.dir/vstack.c.o.d -o CMakeFiles/cmph.dir/vstack.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/vstack.c make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 54%] Built target build_version make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 54%] Built target cmph make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 54%] Built target alp make -f src/sortmerna/CMakeFiles/smr_objs.dir/build.make src/sortmerna/CMakeFiles/smr_objs.dir/depend make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/src/sortmerna /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna 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/usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o -MF CMakeFiles/smr_objs.dir/alignment.cpp.o.d -o CMakeFiles/smr_objs.dir/alignment.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/alignment.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong 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/build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp [ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o [ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/bitvector.cpp cd 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-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o -MF CMakeFiles/smr_objs.dir/indexdb.cpp.o.d -o CMakeFiles/smr_objs.dir/indexdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o -MF CMakeFiles/smr_objs.dir/kseq_load.cpp.o.d -o CMakeFiles/smr_objs.dir/kseq_load.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kseq_load.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/kvdb.cpp.o -MF CMakeFiles/smr_objs.dir/kvdb.cpp.o.d -o CMakeFiles/smr_objs.dir/kvdb.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o -MF CMakeFiles/smr_objs.dir/options.cpp.o.d -o CMakeFiles/smr_objs.dir/options.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp [ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o [ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o -MF CMakeFiles/smr_objs.dir/output.cpp.o.d -o CMakeFiles/smr_objs.dir/output.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/output.cpp [ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o -MF CMakeFiles/smr_objs.dir/summary.cpp.o.d -o CMakeFiles/smr_objs.dir/summary.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/summary.cpp [ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -MF CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o.d -o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp [ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall 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/usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o -MF CMakeFiles/smr_objs.dir/otumap.cpp.o.d -o CMakeFiles/smr_objs.dir/otumap.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/otumap.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong 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-I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o -MF CMakeFiles/smr_objs.dir/report_biom.cpp.o.d -o CMakeFiles/smr_objs.dir/report_biom.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o -MF CMakeFiles/smr_objs.dir/report_sam.cpp.o.d -o CMakeFiles/smr_objs.dir/report_sam.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_sam.cpp /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp:243:29: warning: this statement may fall through [-Wimplicit-fallthrough=] 243 | ret = Z_DATA_ERROR; /* and fall through */ | ^ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp:244:17: note: here 244 | case Z_DATA_ERROR: | ^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function 'void Readfeed::init(std::vector >&, const int&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:105:69: warning: unused parameter 'dbg' [-Wunused-parameter] 105 | void Readfeed::init(std::vector& readfiles, const int& dbg) | ~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::loadReadByIdx(Read&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:187:37: warning: unused parameter 'read' [-Wunused-parameter] 187 | bool Readfeed::loadReadByIdx(Read & read) | ~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::loadReadById(Read&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:271:35: warning: unused parameter 'read' [-Wunused-parameter] 271 | bool Readfeed::loadReadById(Read& read) | ~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::hasnext(std::ifstream&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:553:39: warning: unused parameter 'ifs' [-Wunused-parameter] 553 | bool Readfeed::hasnext(std::ifstream& ifs) | ~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp: In member function 'bool Readfeed::define_format(const int&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp:857:36: warning: comparison is always false due to limited range of data type [-Wtype-limits] 857 | if (str[i] > 127 || str[i] < 0) { /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:33: warning: unused parameter 'readfeed' [-Wunused-parameter] 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) | ~~~~~~~~~~^~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_biom.cpp:41:52: warning: unused parameter 'opts' [-Wunused-parameter] 41 | void ReportBiom::init(Readfeed& readfeed, Runopts& opts) | ~~~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/indexdb.cpp:915:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] 915 | void help() | ^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp:39:25: warning: unused parameter 'opts' [-Wunused-parameter] 39 | Report::Report(Runopts& opts) : pid_str(std::to_string(getpid())), is_zip(false) {} | ~~~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_log(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:284:42: warning: unused parameter 'val' [-Wunused-parameter] 284 | void Runopts::opt_log(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_denovo_otu(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:290:49: warning: unused parameter 'val' [-Wunused-parameter] 290 | void Runopts::opt_denovo_otu(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_otu_map(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:295:46: warning: unused parameter 'val' [-Wunused-parameter] 295 | void Runopts::opt_otu_map(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_print_all_reads(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:300:54: warning: unused parameter 'val' [-Wunused-parameter] 300 | void Runopts::opt_print_all_reads(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_pid(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:305:42: warning: unused parameter 'val' [-Wunused-parameter] 305 | void Runopts::opt_pid(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:310:45: warning: unused parameter 'val' [-Wunused-parameter] 310 | void Runopts::opt_paired(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired_in(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:324:48: warning: unused parameter 'val' [-Wunused-parameter] 324 | void Runopts::opt_paired_in(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired_out(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:329:49: warning: unused parameter 'val' [-Wunused-parameter] 329 | void Runopts::opt_paired_out(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_out2(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:338:43: warning: unused parameter 'val' [-Wunused-parameter] 338 | void Runopts::opt_out2(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sout(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:343:43: warning: unused parameter 'val' [-Wunused-parameter] 343 | void Runopts::opt_sout(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_fastx(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:471:44: warning: unused parameter 'val' [-Wunused-parameter] 471 | void Runopts::opt_fastx(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sam(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:484:42: warning: unused parameter 'val' [-Wunused-parameter] 484 | void Runopts::opt_sam(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_no_best(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:593:46: warning: unused parameter 'val' [-Wunused-parameter] 593 | void Runopts::opt_no_best(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_edges(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:636:15: warning: unused variable 'end' [-Wunused-variable] 636 | char *end = 0; | ^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_full_search(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:651:50: warning: unused parameter 'val' [-Wunused-parameter] 651 | void Runopts::opt_full_search(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_SQ(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:661:41: warning: unused parameter 'val' [-Wunused-parameter] 661 | void Runopts::opt_SQ(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_version(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:740:46: warning: unused parameter 'val' [-Wunused-parameter] 740 | void Runopts::opt_version(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_unknown(char**, int&, char*)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:750:34: warning: unused parameter 'argv' [-Wunused-parameter] 750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt) | ~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:750:45: warning: unused parameter 'narg' [-Wunused-parameter] 750 | void Runopts::opt_unknown(char **argv, int &narg, char * opt) | ~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp: In member function 'void Index::load(uint32_t, uint32_t, std::vector, std::__cxx11::basic_string > >&, Refstats&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp:211:58: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 211 | ((NodeElement *&)dst) += 4; | ^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 257 | ((NodeElement *&)dst) += 4; | ^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_F(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:784:40: warning: unused parameter 'val' [-Wunused-parameter] 784 | void Runopts::opt_F(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_R(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:798:40: warning: unused parameter 'val' [-Wunused-parameter] 798 | void Runopts::opt_R(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_h(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:812:40: warning: unused parameter 'val' [-Wunused-parameter] 812 | void Runopts::opt_h(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_v(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:819:40: warning: unused parameter 'val' [-Wunused-parameter] 819 | void Runopts::opt_v(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_dbg_put_db(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:937:49: warning: unused parameter 'val' [-Wunused-parameter] 937 | void Runopts::opt_dbg_put_db(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_cmd(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:980:42: warning: unused parameter 'val' [-Wunused-parameter] 980 | void Runopts::opt_cmd(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_tmpdir(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1036:45: warning: unused parameter 'val' [-Wunused-parameter] 1036 | void Runopts::opt_tmpdir(const std::string &val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_align(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1193:44: warning: unused parameter 'val' [-Wunused-parameter] 1193 | void Runopts::opt_align(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::opt_filter(const std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1198:45: warning: unused parameter 'val' [-Wunused-parameter] 1198 | void Runopts::opt_filter(const std::string& val) | ~~~~~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/options.cpp:1368:50: warning: unused parameter 'dryrun' [-Wunused-parameter] 1368 | void Runopts::process(int argc, char**argv, bool dryrun) | ~~~~~^~~~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) | ~~~~~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] 58 | int KeyValueDatabase::clear(std::string dbpath) | ~~~~~~~~~~~~^~~~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:250:68: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 250 | if (index.positions_tbl[it->id].arr[i].seq == std::stoi(refid)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:36: warning: unused parameter 'opts' [-Wunused-parameter] 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) | ~~~~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter] 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) | ~~~~~~~~~~~~~~^~~ In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:47: /build/reproducible-path/sortmerna-4.3.7/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)': /build/reproducible-path/sortmerna-4.3.7/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter] 92 | void threadEntry(int i) | ~~~~^ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp: In member function 'void ReportFxBase::write_a_read(std::ostream&, Read&, Readstate&, Izlib&, bool, const int&)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp:201:123: warning: unused parameter 'dbg' [-Wunused-parameter] 201 | void ReportFxBase::write_a_read(std::ostream& strm, Read& read, Readstate& rstate, Izlib& izlib, bool is_last, const int& dbg) | ~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)': /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:292:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 292 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:40, from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp:52: /build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 171 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' 221 | __KSEQ_READ | ^~~~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' 43 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ In file included from /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/paralleltraversal.cpp:41: /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp: At global scope: /build/reproducible-path/sortmerna-4.3.7/include/kseq.h:171:20: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function] 171 | static int kseq_read(kseq_t *seq) \ | ^~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' 221 | __KSEQ_READ | ^~~~~~~~~~~ /build/reproducible-path/sortmerna-4.3.7/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' 43 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 97%] Built target smr_objs make -f src/sortmerna/CMakeFiles/sortmerna.dir/build.make src/sortmerna/CMakeFiles/sortmerna.dir/depend make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.7 /build/reproducible-path/sortmerna-4.3.7/src/sortmerna /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna/CMakeFiles/sortmerna.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make -f src/sortmerna/CMakeFiles/sortmerna.dir/build.make src/sortmerna/CMakeFiles/sortmerna.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 98%] Building CXX object src/sortmerna/CMakeFiles/sortmerna.dir/main.cpp.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.7/include -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.7/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/sortmerna.dir/main.cpp.o -MF CMakeFiles/sortmerna.dir/main.cpp.o.d -o CMakeFiles/sortmerna.dir/main.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/main.cpp [100%] Linking CXX executable sortmerna cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/cmake -E cmake_link_script CMakeFiles/sortmerna.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall 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--eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o sortmerna /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -v -z relro -z now CMakeFiles/sortmerna.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o CMakeFiles/smr_objs.dir/alignment.cpp.o CMakeFiles/smr_objs.dir/bitvector.cpp.o CMakeFiles/smr_objs.dir/cmd.cpp.o CMakeFiles/smr_objs.dir/izlib.cpp.o CMakeFiles/smr_objs.dir/index.cpp.o CMakeFiles/smr_objs.dir/indexdb.cpp.o CMakeFiles/smr_objs.dir/kseq_load.cpp.o CMakeFiles/smr_objs.dir/kvdb.cpp.o CMakeFiles/smr_objs.dir/options.cpp.o CMakeFiles/smr_objs.dir/output.cpp.o CMakeFiles/smr_objs.dir/summary.cpp.o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o CMakeFiles/smr_objs.dir/processor.cpp.o CMakeFiles/smr_objs.dir/read.cpp.o CMakeFiles/smr_objs.dir/readfeed.cpp.o CMakeFiles/smr_objs.dir/readstats.cpp.o CMakeFiles/smr_objs.dir/references.cpp.o CMakeFiles/smr_objs.dir/refstats.cpp.o CMakeFiles/smr_objs.dir/ssw.c.o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o CMakeFiles/smr_objs.dir/util.cpp.o CMakeFiles/smr_objs.dir/otumap.cpp.o CMakeFiles/smr_objs.dir/report.cpp.o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o CMakeFiles/smr_objs.dir/report_fastx.cpp.o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o CMakeFiles/smr_objs.dir/report_blast.cpp.o CMakeFiles/smr_objs.dir/report_denovo.cpp.o CMakeFiles/smr_objs.dir/report_biom.cpp.o CMakeFiles/smr_objs.dir/report_sam.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /usr/lib/x86_64-linux-gnu/librocksdb.so.9.3.1 -ldl /usr/lib/x86_64-linux-gnu/libz.so -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o GNU ld (GNU Binutils for Debian) 2.43.50.20241210 make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [100%] Built target sortmerna make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: dh_auto_test --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build -- create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/sortmerna/ -O--buildsystem=pybuild I: pybuild base:311: dh_auto_install --buildsystem=cmake --builddirectory=/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build --destdir=/build/reproducible-path/sortmerna-4.3.7/debian/sortmerna -- cd .pybuild/cpython3_3.12/build && make -j42 install DESTDIR=/build/reproducible-path/sortmerna-4.3.7/debian/sortmerna AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.7 -B/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/bin/sortmerna -- Installing: /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake -- Installing: /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' dh_install -O--buildsystem=pybuild debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7' find debian -name cmake -type d | xargs rm -rvf removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake' removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake' removed directory 'debian/sortmerna/usr/cmake/sortmerna' removed directory 'debian/sortmerna/usr/cmake' make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7' # Convert example files to Unicode. set -e \ ; cd /build/reproducible-path/sortmerna-4.3.7/tests/sortmerna/ \ ; for cxxfile in *.cpp \ ; do iconv -f ISO-8859-15 -t UTF-8 \ < ${cxxfile} \ > /build/reproducible-path/sortmerna-4.3.7/debian/sortmerna/usr/share/doc/sortmerna/examples/${cxxfile} \ ; done make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7' dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.7' find debian/sortmerna -name '*.sh' -exec chmod -v +x '{}' ';' mode of 'debian/sortmerna/usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) find debian/sortmerna -name '*.py' -exec chmod -v -x '{}' ';' mode of 'debian/sortmerna/usr/share/sortmerna/scripts/run.py' retained as 0644 (rw-r--r--) make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'sortmerna' in '../sortmerna_4.3.7-2_amd64.deb'. dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_4.3.7-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../sortmerna_4.3.7-2_amd64.buildinfo dpkg-genchanges --build=binary -O../sortmerna_4.3.7-2_amd64.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/3617052/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3617052/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/3617052 and its subdirectories I: Current time: Tue Jan 20 01:39:58 +14 2026 I: pbuilder-time-stamp: 1768822798