Tue Dec 17 06:46:18 UTC 2024 I: starting to build sortmerna/trixie/i386 on jenkins on '2024-12-17 06:46' Tue Dec 17 06:46:18 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_5/43477/console.log Tue Dec 17 06:46:18 UTC 2024 I: Downloading source for trixie/sortmerna=4.3.7-2 --2024-12-17 06:46:18-- http://deb.debian.org/debian/pool/main/s/sortmerna/sortmerna_4.3.7-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2208 (2.2K) [text/prs.lines.tag] Saving to: ‘sortmerna_4.3.7-2.dsc’ 0K .. 100% 49.5M=0s 2024-12-17 06:46:18 (49.5 MB/s) - ‘sortmerna_4.3.7-2.dsc’ saved [2208/2208] Tue Dec 17 06:46:18 UTC 2024 I: sortmerna_4.3.7-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sortmerna Binary: sortmerna Architecture: any-amd64 any-i386 Version: 4.3.7-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/sortmerna/sortmerna Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/sortmerna Vcs-Git: https://salsa.debian.org/med-team/sortmerna.git Testsuite: autopkgtest Build-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 Package-List: sortmerna deb science optional arch=any-amd64,any-i386,x32 Checksums-Sha1: 8e4a8ed95668fbda997df7fb09577b02a7184c2d 31353353 sortmerna_4.3.7.orig.tar.gz 9e0cc9324658f21be61ab8a9d90ae3f1a25404af 10960 sortmerna_4.3.7-2.debian.tar.xz Checksums-Sha256: 6b62def30704ea956e1de060b602f9bebc8f2ba68107c59329b332500997b1d2 31353353 sortmerna_4.3.7.orig.tar.gz 7582f67f4e98c71360d54e04528dcc357551fa66bb65d46173200abfe90c8c2d 10960 sortmerna_4.3.7-2.debian.tar.xz Files: bc312ee925efb6fc4a15c7d01db2526f 31353353 sortmerna_4.3.7.orig.tar.gz cbe78262b8e274ef793da9d58dc0b8aa 10960 sortmerna_4.3.7-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdZyiIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFC6A//SYunsh8iksWkQ3Td635yq2FyB92jKawA fn+UmPUUVegJzmsDKkpmJO/TiaDebWVB3S6X7xkT1HSGg6OzrKv+eNR7laaeo3HH l4CpIrr+PajTV0DcfrF+jX1lsBE8XvaoliPUhFmaR6YLVNakAWMovFpgr3vnlpdO DyPlrATmRuXqMIBpilLNrXPNmV52DyiZXLOCXwAf09mKyP9i6/+ZIHNZwmlF6cX0 rcm1fI7D0hLbah5thiLhUeJWGObrdqP2Rqa2PDJeK2MSh+tReTdIVAk/TQArOH0L Jnponk+Hjp9I7xALWVWQRFKSHfT2tBpmj2Dic6S0Pmiae8/US+GfgbqhOU7oYbb+ 1FAfQBjW/xgEneUxQOxTFYTjJzCvOiDbaNpgTD040dVcXcSK0htlAoo7Ibj/afxP QSUhACj7TN9sv83hVR0e7npv20WOUoB6yfp7qo3alkO6Qum0olpKHWCwKBsmYc9r 3aGWY+QY16xzu4upIVOQQ2JYyi0Wd4bSZ7Sy4iy3RTWCTj7XbMS9MwYXMu8YR783 Lp74fIGht/JOIjJksfXYGGo+fKZJ9RhwetSAqjxhE/YMCX/+IeGN77QXl3BE7tzJ b/niQuV/I7OLQ2A9Zs8t1sW12VGQBIfpPHwPXSG57YwZjaK6fY8sK1kNrruNhVN9 LGY4nahxrQo= =Im/5 -----END PGP SIGNATURE----- Tue Dec 17 06:46:18 UTC 2024 I: Checking whether the package is not for us Tue Dec 17 06:46:18 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Tue Dec 17 06:46:18 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Tue Dec 17 06:52:43 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 16 18:46:23 -12 2024 I: pbuilder-time-stamp: 1734417983 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [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/6115/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='9a3b574455e447e2a73e86a58c5d0699' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='6115' 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.iJvzrilG/pbuilderrc_7QBW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iJvzrilG/b1 --logfile b1/build.log sortmerna_4.3.7-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos12-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/6115/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-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 ... 19952 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 57.7 MB of archives. After unpacking 224 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpython3.12-minimal i386 3.12.8-3 [816 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 python3.12-minimal i386 3.12.8-3 [2239 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-5 [173 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 python3.12 i386 3.12.8-3 [677 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main i386 python3 i386 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.1-1 [393 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 57 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 63 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 75 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.2.0-1 [731 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20241024 [109 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libconcurrentqueue-dev i386 1.0.4+ds-1 [59.9 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libgflags2.2 i386 2.2.2-2 [84.1 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libgflags-dev i386 2.2.2-2 [102 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 liblz4-dev i386 1.9.4-3+b1 [84.8 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libsnappy1v5 i386 1.2.1-1+b1 [31.3 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 librocksdb9.3 i386 9.3.1-1 [3916 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libsnappy-dev i386 1.2.1-1+b1 [46.2 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 librocksdb-dev i386 9.3.1-1 [5532 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 python3-all i386 3.12.6-1 [1040 B] Get: 93 http://deb.debian.org/debian trixie/main i386 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Fetched 57.7 MB in 1s (39.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19952 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.8-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. 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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (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:i386. Preparing to unpack .../14-libreadline8t64_8.2-5_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_i386.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21335 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_i386.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libproc2-0:i386. 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Setting up libzstd-dev:i386 (1.5.6+dfsg-1+b1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libconcurrentqueue-dev (1.0.4+ds-1) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:i386 (1.1.0-2+b6) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:i386 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up rapidjson-dev (1.1.0+dfsg2-7.3) ... Setting up libsnappy1v5:i386 (1.2.1-1+b1) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Dec 17 06:47:52 UTC 2024. Universal Time is now: Tue Dec 17 06:47:52 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:i386 (1.9.6-3) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up autopoint (0.22.5-2) ... Setting up liblz4-dev:i386 (1.9.4-3+b1) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (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:i386 (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:i386 (1.4.5-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libgflags2.2 (2.2.2-2) ... Setting up libbz2-dev:i386 (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:i386 (1.2.1-1+b1) ... Setting up libldap-2.5-0:i386 (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) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up libgflags-dev (2.2.2-2) ... Setting up libreadline8t64:i386 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up libarchive13t64:i386 (3.7.4-1.1) ... Setting up librocksdb-dev (9.3.1-1) ... Setting up libcurl4t64:i386 (8.11.1-1) ... Setting up libtirpc3t64:i386 (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:i386 (1.3.0-3+b3) ... Setting up cmake (3.30.5-1) ... Setting up libpython3.12-stdlib:i386 (3.12.8-3) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.20) ... Setting up libpython3-stdlib:i386 (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: Running cd /build/reproducible-path/sortmerna-4.3.7/ && 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 > ../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 i386 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-i386-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-i386-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-i386-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/i386-linux-gnu -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3.12 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/python3.12/config-3.12-i386-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-i386-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-i386-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 = 6.1.0-28-amd64 CMAKE_HOST_SYSTEM = Linux-6.1.0-28-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/i386-linux-gnu/libz.so (found version "1.3.1") searching ZLIB in default locations ZLIB::ZLIB LOCATION: /usr/lib/i386-linux-gnu/libz.so ZLIB::ZLIB LOCATION_DEBUG: /usr/lib/i386-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/i386-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found lz4: /usr/lib/i386-linux-gnu/liblz4.so -- Found zstd: /usr/lib/i386-linux-gnu/libzstd.so RocksDB found Using Shared RocksDB lib RocksDB::rocksdb-shared LOCATION: /usr/lib/i386-linux-gnu/librocksdb.so.9.3.1 RocksDB::rocksdb-shared LOCATION_DEBUG: /usr/lib/i386-linux-gnu/librocksdb.so.9.3.1 RocksDB::rocksdb-shared transitive link dependencies: rocksdb transitive link dependencies AFTER modification: /usr/lib/i386-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 (7.0s) -- Generating done (0.1s) 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 -j11 "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 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/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]: 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' [ 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 -Wformat -Werror=format-security -msse2 -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 /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/build_version.cpp:4:44: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 4 | const char* sortmerna_build_compile_date = __DATE__; | ^~~~~~~~ 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]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 2%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o 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/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 -Wformat -Werror=format-security -msse2 -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 [ 4%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o [ 5%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o -MF CMakeFiles/cmph.dir/bdz.c.o.d -o CMakeFiles/cmph.dir/bdz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bdz.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o -MF 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 [ 7%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o [ 8%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.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 -Wformat -Werror=format-security -msse2 -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 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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o -MF CMakeFiles/cmph.dir/bmz.c.o.d -o CMakeFiles/cmph.dir/bmz.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/bmz.c [ 9%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o [ 11%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o -MF CMakeFiles/cmph.dir/buffer_manager.c.o.d -o CMakeFiles/cmph.dir/buffer_manager.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/buffer_manager.c 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 -Wformat -Werror=format-security -msse2 -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 [ 12%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o [ 12%] Built target build_version 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 -Wformat -Werror=format-security -msse2 -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 [ 14%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o cd 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33%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o -MF CMakeFiles/cmph.dir/jenkins_hash.c.o.d -o CMakeFiles/cmph.dir/jenkins_hash.c.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/cmph/jenkins_hash.c [ 35%] 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=. 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3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o -MF CMakeFiles/alp.dir/sls_alp_sim.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_sim.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_alp_sim.cpp make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 52%] Built target cmph [ 53%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_basic.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -MD -MT 3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o -MF CMakeFiles/alp.dir/sls_basic.cpp.o.d -o CMakeFiles/alp.dir/sls_basic.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/3rdparty/alp/sls_basic.cpp [ 54%] 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/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 -Wformat -Werror=format-security -msse2 -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 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 /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna/CMakeFiles/smr_objs.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/smr_objs.dir/build.make src/sortmerna/CMakeFiles/smr_objs.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build' [ 56%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.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 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src/sortmerna/CMakeFiles/smr_objs.dir/cmd.cpp.o -MF CMakeFiles/smr_objs.dir/cmd.cpp.o.d -o CMakeFiles/smr_objs.dir/cmd.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/cmd.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/izlib.cpp.o -MF CMakeFiles/smr_objs.dir/izlib.cpp.o.d -o CMakeFiles/smr_objs.dir/izlib.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/izlib.cpp [ 61%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o [ 63%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/index.cpp.o -MF CMakeFiles/smr_objs.dir/index.cpp.o.d -o CMakeFiles/smr_objs.dir/index.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/index.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 -Wformat -Werror=format-security -msse2 -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 [ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.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 -Wformat -Werror=format-security -msse2 -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 [ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o [ 67%] 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 -Wformat -Werror=format-security -msse2 -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 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 -Wformat -Werror=format-security -msse2 -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 [ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.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 -Wformat -Werror=format-security -msse2 -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 [ 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 -Wformat -Werror=format-security -msse2 -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 /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: | ^~~~ [ 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 -Wformat -Werror=format-security -msse2 -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 /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_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/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/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/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) | ~~~~~^~~~~~ [ 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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o -MF CMakeFiles/smr_objs.dir/processor.cpp.o.d -o CMakeFiles/smr_objs.dir/processor.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/processor.cpp /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) | ~~~~~~~~~~~~^~~~~~ [ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o -MF CMakeFiles/smr_objs.dir/read.cpp.o.d -o CMakeFiles/smr_objs.dir/read.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/read.cpp /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/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/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) | ^~~~~~~~~ [ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o -MF CMakeFiles/smr_objs.dir/readfeed.cpp.o.d -o CMakeFiles/smr_objs.dir/readfeed.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readfeed.cpp /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/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) { [ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o -MF CMakeFiles/smr_objs.dir/readstats.cpp.o.d -o CMakeFiles/smr_objs.dir/readstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/readstats.cpp [ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o -MF CMakeFiles/smr_objs.dir/references.cpp.o.d -o CMakeFiles/smr_objs.dir/references.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/references.cpp [ 80%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o cd /build/reproducible-path/sortmerna-4.3.7/.pybuild/cpython3_3.12/build/src/sortmerna && /usr/bin/cc -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.7=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o -MF CMakeFiles/smr_objs.dir/ssw.c.o.d -o CMakeFiles/smr_objs.dir/ssw.c.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/ssw.c [ 81%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o -MF CMakeFiles/smr_objs.dir/refstats.cpp.o.d -o CMakeFiles/smr_objs.dir/refstats.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/refstats.cpp [ 83%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o 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) | ^~~~~~~~~ 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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -MF CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o.d -o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/traverse_bursttrie.cpp [ 84%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o -MF CMakeFiles/smr_objs.dir/util.cpp.o.d -o CMakeFiles/smr_objs.dir/util.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/util.cpp [ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.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 -Wformat -Werror=format-security -msse2 -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 [ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o -MF CMakeFiles/smr_objs.dir/report.cpp.o.d -o CMakeFiles/smr_objs.dir/report.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report.cpp [ 88%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_base.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_base.cpp [ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o -MF CMakeFiles/smr_objs.dir/report_fastx.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fastx.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fastx.cpp [ 91%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -MF CMakeFiles/smr_objs.dir/report_fx_other.cpp.o.d -o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_fx_other.cpp [ 92%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o -MF CMakeFiles/smr_objs.dir/report_blast.cpp.o.d -o CMakeFiles/smr_objs.dir/report_blast.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_blast.cpp [ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -std=gnu++17 -MD -MT src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o -MF CMakeFiles/smr_objs.dir/report_denovo.cpp.o.d -o CMakeFiles/smr_objs.dir/report_denovo.cpp.o -c /build/reproducible-path/sortmerna-4.3.7/src/sortmerna/report_denovo.cpp /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/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) | ~~~~~~~~~~~^~~ [ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.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 -Wformat -Werror=format-security -msse2 -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 [ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.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 -Wformat -Werror=format-security -msse2 -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/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) | ~~~~~~~~~^~~~ 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 -Wformat -Werror=format-security -msse2 -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 -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wextra -Wall -Xlinker -v -Wl,-z,relro -Wl,-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 -o sortmerna ../../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 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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/i386-linux-gnu/librocksdb.so.9.3.1 -ldl /usr/lib/i386-linux-gnu/libz.so -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/14/crtendS.o /usr/lib/gcc/i686-linux-gnu/14/../../../i386-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 -j11 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/sortmernaConfig.cmake' removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.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_i386.deb'. dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_4.3.7-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../sortmerna_4.3.7-2_i386.buildinfo dpkg-genchanges --build=binary -O../sortmerna_4.3.7-2_i386.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/6115 and its subdirectories I: Current time: Mon Dec 16 18:52:41 -12 2024 I: pbuilder-time-stamp: 1734418361 Tue Dec 17 06:52:43 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos6-i386.debian.net. Tue Dec 17 06:52:43 UTC 2024 I: Preparing to do remote build '2' on ionos6-i386.debian.net. Tue Dec 17 06:54:42 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. Tue Dec 17 06:54:42 UTC 2024 I: sortmerna_4.3.7-2_i386.changes: Format: 1.8 Date: Wed, 11 Dec 2024 17:38:13 +0100 Source: sortmerna Binary: sortmerna sortmerna-dbgsym Architecture: i386 Version: 4.3.7-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: sortmerna - tool for filtering, mapping and OTU-picking NGS reads Closes: 1087092 Changes: sortmerna (4.3.7-2) unstable; urgency=medium . * Fix Python3.12 string syntax Closes: #1087092 * d/copyright: Fixes thanks to lrc Checksums-Sha1: af898b6173e534cc607113b05ef07131f016a1bc 7243356 sortmerna-dbgsym_4.3.7-2_i386.deb b7aa25897b8ccf129becc0240de41e1ddf0b5c43 7229 sortmerna_4.3.7-2_i386.buildinfo 986ef11546226460b9ede42ac96753f011dd972c 599888 sortmerna_4.3.7-2_i386.deb Checksums-Sha256: 261827dcfe5056da40bba00134f2ebf95619cfcc1870671d1cbcd567950bf8fa 7243356 sortmerna-dbgsym_4.3.7-2_i386.deb dcb6f48c1aaddb95e76878e757241a865686b149f5215a6164f0a264990f9f0c 7229 sortmerna_4.3.7-2_i386.buildinfo 797e53fb7c198ea04ff62d8850f04e7afa5dcd10a7f4645d7093477c2c5e3825 599888 sortmerna_4.3.7-2_i386.deb Files: c1b78b369e8a8664292becbd7285bfa8 7243356 debug optional sortmerna-dbgsym_4.3.7-2_i386.deb 5ce59187fb0f9fc21d04081bacf2e00a 7229 science optional sortmerna_4.3.7-2_i386.buildinfo a2a9208b915ce72ad7c819a9096ebf2c 599888 science optional sortmerna_4.3.7-2_i386.deb Tue Dec 17 06:54:43 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_5-43477.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.iJvzrilG/sortmerna_4.3.7-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.iJvzrilG/sortmerna_4.3.7-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.iJvzrilG/sortmerna_4.3.7-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.iJvzrilG/b1/sortmerna_4.3.7-2_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.iJvzrilG/b2/sortmerna_4.3.7-2_i386.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: 0.415s) 0.415s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.083s) 0.083s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 747ms CPU time consumed: 745ms Tue Dec 17 06:54:44 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Tue Dec 17 06:54:44 UTC 2024 I: sortmerna from trixie built successfully and reproducibly on i386. Tue Dec 17 06:54:46 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Dec 17 06:54:46 UTC 2024 I: Submitting 8.0K b1/sortmerna_4.3.7-2_i386.buildinfo.asc Tue Dec 17 06:54:46 UTC 2024 I: Submitting 8.0K b2/sortmerna_4.3.7-2_i386.buildinfo.asc Tue Dec 17 06:54:47 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Dec 17 06:54:47 UTC 2024 I: Done submitting .buildinfo files. Tue Dec 17 06:54:47 UTC 2024 I: Removing signed sortmerna_4.3.7-2_i386.buildinfo.asc files: removed './b1/sortmerna_4.3.7-2_i386.buildinfo.asc' removed './b2/sortmerna_4.3.7-2_i386.buildinfo.asc'