Fri Apr 19 20:30:58 UTC 2024 I: starting to build sortmerna/trixie/i386 on jenkins on '2024-04-19 20:30' Fri Apr 19 20:30:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/24541/console.log Fri Apr 19 20:30:58 UTC 2024 I: Downloading source for trixie/sortmerna=4.3.6-3 --2024-04-19 20:30:58-- http://deb.debian.org/debian/pool/main/s/sortmerna/sortmerna_4.3.6-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2270 (2.2K) [text/prs.lines.tag] Saving to: ‘sortmerna_4.3.6-3.dsc’ 0K .. 100% 271M=0s 2024-04-19 20:30:58 (271 MB/s) - ‘sortmerna_4.3.6-3.dsc’ saved [2270/2270] Fri Apr 19 20:30:58 UTC 2024 I: sortmerna_4.3.6-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sortmerna Binary: sortmerna Architecture: any-amd64 any-i386 Version: 4.3.6-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://bioinfo.lifl.fr/RNA/sortmerna/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/sortmerna Vcs-Git: https://salsa.debian.org/med-team/sortmerna.git Build-Depends: debhelper-compat (= 13), 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: 0f6105dd4b5709dfd6bf3d5f09bf9d6c112d3957 31269836 sortmerna_4.3.6.orig.tar.gz 902b77ea0ab4033b263c9885f88d04061beca8bf 12160 sortmerna_4.3.6-3.debian.tar.xz Checksums-Sha256: 1ddb7a9f50b63ab5b87c15855a4080949fb0ee0f33ecf0ea8dfb1c1c44cbe9da 31269836 sortmerna_4.3.6.orig.tar.gz 93c3de8bb8e9ae0ac862d51f7d053c0d18204e9e423efb08d8a553dcb7226e0b 12160 sortmerna_4.3.6-3.debian.tar.xz Files: 8ae18aa68af3810cff96733d2843cbe2 31269836 sortmerna_4.3.6.orig.tar.gz 425ccf55845af9716fdf37591fbc6e93 12160 sortmerna_4.3.6-3.debian.tar.xz Dgit: 71e9085ab1d89d28282bf46fe0f7cd779aa2a8af debian archive/debian/4.3.6-3 https://git.dgit.debian.org/sortmerna -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmT4vFgUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqgPA/+PKzx/jr2XILSHoXJsy3zhHaJvtVK IHiv8duLSQazPVHUq2AIdNjPPArtuWFPCg+tkVpybFHSfuyHbDQMCC8eO4gyn0Zp OYYHSUD5GhwRAAP7Dolcd6P/0rQLvZaBSFEAUTfgelsWuqCJzQXQQy/CGK7umZAJ nUongH/1Fvs99nw96ghcOXOHaeEvNOlw04Nh4olIuAFejWskMc9CC/rU2zI6KIho aHDhdima99JsGT5fRCJp0LdMsYfDqmwqXaIuS21pecO0Vp3WHwyHs4fTCEI1Q0aI VQycN7CUVVtyCDC5uGtiOcVZYWjMbWs6oyXkDSvtj2hUeFtbk6ajjz853YSjAjYF J0ceKDnd2tCjI+NhrMDxBWlEc0ZRwuPG9VQhNIJ/7xS3xS/uKUnryqwHDgqi3kX+ aNoMczYXUkD8oicLriZvmweBiXNzqWos2Znl9V0mHV9Cewt0qCx8Zu3SvQodmvVQ sp/U1Ffa5x6wIqXod2lAMTCefHKDd6Bqy+fHi8KxZz55SKvs/+Y7iL7MmKhpGBl4 BmVirCjvE7g0XJP+ry3AtqR5QqHi9M15D1Puxcb2fjwfTTjOadeqmTNjPRLVSNcv deKu7p5rCVahxXpzdBXHtPsiz4Wtq2bQMaTmK8WSoiRGRcmf7eiPHsXaIAmlndVc uWBL99qUJWFTq0Y= =C2nK -----END PGP SIGNATURE----- Fri Apr 19 20:30:58 UTC 2024 I: Checking whether the package is not for us Fri Apr 19 20:30:58 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Fri Apr 19 20:30:58 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Fri Apr 19 20:31:59 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 22 14:54:01 -12 2025 I: pbuilder-time-stamp: 1747968841 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_4.3.6-3.dsc] I: copying [./sortmerna_4.3.6.orig.tar.gz] I: copying [./sortmerna_4.3.6-3.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Sep 6 17:52:24 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sortmerna_4.3.6-3.dsc: no acceptable signature found dpkg-source: info: extracting sortmerna in sortmerna-4.3.6 dpkg-source: info: unpacking sortmerna_4.3.6.orig.tar.gz dpkg-source: info: unpacking sortmerna_4.3.6-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cmake_RocksDB.patch dpkg-source: info: applying rapidjson.patch dpkg-source: info: applying concurrentqueue.h.patch dpkg-source: info: applying no_static_linking.patch dpkg-source: info: applying typos.patch dpkg-source: info: applying gcc-13.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/83829/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=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='1a208ccafd114917b960086db08e423c' 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='83829' 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.PkR4KoW4/pbuilderrc_NmuK --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.PkR4KoW4/b1 --logfile b1/build.log sortmerna_4.3.6-3.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://85.184.249.68:3128' I: uname -a Linux ionos16-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 21 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/83829/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), 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 ... 19874 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 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-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbz2-dev{a} libconcurrentqueue-dev{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgflags-dev{a} libgflags2.2{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblz4-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librocksdb-dev{a} librocksdb8.9{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsnappy-dev{a} libsnappy1v5{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} po-debconf{a} procps{a} rapidjson-dev{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 47.2 MB of archives. After unpacking 182 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-4 [65.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-4 [876 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive13 i386 3.7.2-1 [386 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libcurl4 i386 8.5.0-2 [463 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libjsoncpp25 i386 1.9.5-6+b2 [89.2 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 librhash0 i386 1.4.3-3+b1 [143 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libuv1 i386 1.48.0-1 [156 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.28.3-1 [2128 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 cmake i386 3.28.3-1 [11.7 MB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-5.1 [31.4 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libconcurrentqueue-dev i386 1.0.4+ds-1 [59.9 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libgflags2.2 i386 2.2.2-2 [84.1 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libgflags-dev i386 2.2.2-2 [102 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 liblz4-dev i386 1.9.4-2 [85.5 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libsnappy1v5 i386 1.1.10-1+b1 [29.5 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 librocksdb8.9 i386 8.9.1-2 [3736 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libsnappy-dev i386 1.1.10-1+b1 [43.3 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.5+dfsg2-2 [346 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 librocksdb-dev i386 8.9.1-2 [5269 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB] Fetched 47.2 MB in 1s (46.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0: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 ... 19874 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-4_i386.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../04-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../10-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../17-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../18-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package libarchive13:i386. Preparing to unpack .../19-libarchive13_3.7.2-1_i386.deb ... Unpacking libarchive13:i386 (3.7.2-1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../20-libbrotli1_1.1.0-2+b3_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b3) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../21-libsasl2-modules-db_2.1.28+dfsg1-4+b1_i386.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/sortmerna-4.3.6/ && 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_4.3.6-3_source.changes dpkg-buildpackage: info: source package sortmerna dpkg-buildpackage: info: source version 4.3.6-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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 .. -- The CXX compiler identification is GNU 13.2.0 -- The C compiler identification is GNU 13.2.0 -- 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) CMAKE_CXX_COMPILER_ID = GNU CMAKE_CONFIGURATION_TYPES = CMAKE_HOST_SYSTEM_NAME = Linux CMAKE_HOST_SYSTEM_VERSION = 6.1.0-20-amd64 CMAKE_HOST_SYSTEM = Linux-6.1.0-20-amd64 PROJECT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu CMAKE_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu CMAKE_CURRENT_BINARY_DIR = /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu RUNTIME_OUTPUT_DIRECTORY_RELEASE = CMAKE_CURRENT_LIST_DIR: /build/reproducible-path/sortmerna-4.3.6 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") -- 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 package OK RocksDB::rocksdb-shared LOCATION: /usr/lib/i386-linux-gnu/librocksdb.so.8.9.1 RocksDB::rocksdb-shared LOCATION_DEBUG: /usr/lib/i386-linux-gnu/librocksdb.so.8.9.1 RocksDB::rocksdb-shared LOCATION_DEBUG: lib-NOTFOUND RocksDB::rocksdb-shared IMPORTED_CONFIGURATIONS: NONE RocksDB::rocksdb-shared IMPORTED_IMPLIB: lib-NOTFOUND RocksDB::rocksdb LIBRARY_OUTPUT_NAME: lib-NOTFOUND Using Shared RocksDB lib RocksDB::rocksdb-shared transitive link dependencies: rocksdb transitive link dependencies AFTER modification: /usr/lib/i386-linux-gnu/libz.so;Threads::Threads -- RapidJSON found. Headers: /usr/include SMR Objects transitive link dependencies: alp;RocksDB::rocksdb-shared;ZLIB::ZLIB SMR Objects COMPILE_OPT: COMPILE_OPT-NOTFOUND COMPILE_FLG: COMPILE_FLG-NOTFOUND package_config_destination: /usr/cmake/sortmerna -- Configuring done (0.9s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu dh_auto_build cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.6 -B/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu --check-build-system 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'/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' [ 1%] Building CXX object CMakeFiles/build_version.dir/build_version.cpp.o /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/obj-i686-linux-gnu/build_version.cpp [ 2%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o [ 4%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o [ 5%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o [ 7%] Building C object 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object 3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/bdz.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_dynprogproblim.cpp.o -MF CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o.d -o CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_dynprogproblim.cpp [ 16%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/bdz_ph.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 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3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/bmz8.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_ioutil.cpp.o -MF CMakeFiles/alp.dir/njn_ioutil.cpp.o.d -o CMakeFiles/alp.dir/njn_ioutil.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_ioutil.cpp [ 22%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/brz.c [ 23%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_localmaxstat.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstat.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstat.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstat.cpp [ 25%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/buffer_entry.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_localmaxstatmatrix.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstatmatrix.cpp [ 26%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/buffer_manager.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_alignment_evaluer.cpp.o -MF CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alignment_evaluer.cpp [ 29%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o [ 29%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o [ 30%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o -MF CMakeFiles/cmph.dir/chd.c.o.d -o CMakeFiles/cmph.dir/chd.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/chd.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_random.cpp.o -MF CMakeFiles/alp.dir/njn_random.cpp.o.d -o CMakeFiles/alp.dir/njn_random.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_random.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o -MF CMakeFiles/cmph.dir/chd_ph.c.o.d -o CMakeFiles/cmph.dir/chd_ph.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/chd_ph.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o -MF CMakeFiles/cmph.dir/chm.c.o.d -o CMakeFiles/cmph.dir/chm.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/chm.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_localmaxstatutil.cpp.o -MF CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o.d -o CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/njn_localmaxstatutil.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o -MF CMakeFiles/cmph.dir/cmph.c.o.d -o CMakeFiles/cmph.dir/cmph.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/cmph.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_alp.cpp.o -MF CMakeFiles/alp.dir/sls_alp.cpp.o.d -o CMakeFiles/alp.dir/sls_alp.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alp.cpp /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/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-4.3.6/obj-i686-linux-gnu' [ 30%] Built target build_version [ 32%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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_alp_data.cpp.o -MF CMakeFiles/alp.dir/sls_alp_data.cpp.o.d -o CMakeFiles/alp.dir/sls_alp_data.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/alp/sls_alp_data.cpp [ 33%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 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/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o -MF CMakeFiles/cmph.dir/compressed_rank.c.o.d -o CMakeFiles/cmph.dir/compressed_rank.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/compressed_rank.c [ 39%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o [ 39%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time 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-I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/alp/sls_basic.cpp [ 42%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o -MF CMakeFiles/cmph.dir/fch.c.o.d -o CMakeFiles/cmph.dir/fch.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/fch.c [ 43%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o -MF CMakeFiles/cmph.dir/fch_buckets.c.o.d -o CMakeFiles/cmph.dir/fch_buckets.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/fch_buckets.c [ 45%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 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-ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/cmph/jenkins_hash.c [ 49%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o -MF CMakeFiles/cmph.dir/miller_rabin.c.o.d -o CMakeFiles/cmph.dir/miller_rabin.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/miller_rabin.c [ 50%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o -MF CMakeFiles/cmph.dir/select.c.o.d -o CMakeFiles/cmph.dir/select.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/select.c [ 52%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o [ 53%] Building CXX object 3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o -MF CMakeFiles/cmph.dir/vqueue.c.o.d -o CMakeFiles/cmph.dir/vqueue.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/vqueue.c cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/alp && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/3rdparty/alp/sls_pvalues.cpp [ 54%] Building C object 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/3rdparty/cmph && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT 3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o -MF CMakeFiles/cmph.dir/vstack.c.o.d -o CMakeFiles/cmph.dir/vstack.c.o -c /build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph/vstack.c make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' [ 54%] Built target cmph make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' [ 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-4.3.6/obj-i686-linux-gnu' cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.6 /build/reproducible-path/sortmerna-4.3.6/src/sortmerna 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/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/bitvector.cpp.o -MF CMakeFiles/smr_objs.dir/bitvector.cpp.o.d -o CMakeFiles/smr_objs.dir/bitvector.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/bitvector.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/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-4.3.6/src/sortmerna/cmd.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/izlib.cpp [ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/options.cpp.o [ 64%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/kseq_load.cpp.o [ 66%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/summary.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/index.cpp [ 67%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/indexdb.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/kvdb.cpp [ 69%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/output.cpp.o [ 70%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/processor.cpp.o [ 71%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o [ 73%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/read.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/indexdb.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/kseq_load.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/options.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/output.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/summary.cpp [ 74%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readfeed.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/paralleltraversal.cpp [ 76%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/alignment.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/processor.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/read.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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/alignment.cpp.o -MF CMakeFiles/smr_objs.dir/alignment.cpp.o.d -o CMakeFiles/smr_objs.dir/alignment.cpp.o -c /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/alignment.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/readfeed.cpp [ 77%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/readstats.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/readstats.cpp [ 78%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/references.cpp.o [ 80%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/refstats.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/references.cpp cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/refstats.cpp [ 81%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/traverse_bursttrie.cpp [ 83%] Building C object src/sortmerna/CMakeFiles/smr_objs.dir/ssw.c.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/cc -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/ssw.c [ 84%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/util.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/util.cpp [ 85%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/otumap.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/otumap.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/izlib.cpp: In member function 'int Izlib::inflatez(std::ifstream&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/izlib.cpp:244:17: note: here 244 | case Z_DATA_ERROR: | ^~~~ [ 87%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report.cpp [ 88%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fx_base.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fx_base.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In member function 'void Readfeed::init(std::vector >&, const int&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::loadReadByIdx(Read&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:187:37: warning: unused parameter 'read' [-Wunused-parameter] 187 | bool Readfeed::loadReadByIdx(Read & read) | ~~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::loadReadById(Read&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:271:35: warning: unused parameter 'read' [-Wunused-parameter] 271 | bool Readfeed::loadReadById(Read& read) | ~~~~~~^~~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In static member function 'static bool Readfeed::hasnext(std::ifstream&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp:553:39: warning: unused parameter 'ifs' [-Wunused-parameter] 553 | bool Readfeed::hasnext(std::ifstream& ifs) | ~~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readfeed.cpp: In member function 'bool Readfeed::define_format(const int&)': /build/reproducible-path/sortmerna-4.3.6/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) { [ 90%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_fastx.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/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-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_fx_other.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/indexdb.cpp:916:14: warning: 'void {anonymous}::help()' defined but not used [-Wunused-function] 916 | void help() | ^~~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.cpp: In member function 'int KeyValueDatabase::clear(std::string)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/kvdb.cpp:58:41: warning: unused parameter 'dbpath' [-Wunused-parameter] 58 | int KeyValueDatabase::clear(std::string dbpath) | ~~~~~~~~~~~~^~~~~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_log(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_denovo_otu(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_otu_map(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_print_all_reads(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_pid(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired_in(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_paired_out(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_out2(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sout(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_fastx(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_sam(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_no_best(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_edges(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:636:15: warning: unused variable 'end' [-Wunused-variable] 636 | char *end = 0; | ^~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_full_search(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_SQ(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_version(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_unknown(char**, int&, char*)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_F(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_R(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_h(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_v(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_dbg_put_db(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_cmd(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_tmpdir(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_align(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::opt_filter(const std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/options.cpp: In member function 'void Runopts::process(int, char**, bool)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/options.cpp:1368:50: warning: unused parameter 'dryrun' [-Wunused-parameter] 1368 | void Runopts::process(int argc, char**argv, bool dryrun) | ~~~~~^~~~~~ /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdIndex(Runopts&, std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/cmd.cpp: In member function 'void CmdSession::cmdTest(Runopts&, std::string&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/cmd.cpp:317:56: warning: unused parameter 'cmd' [-Wunused-parameter] 317 | void CmdSession::cmdTest(Runopts & opts, std::string & cmd) | ~~~~~~~~~~~~~~^~~ /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/src/sortmerna/index.cpp:257:82: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 257 | ((NodeElement *&)dst) += 4; | ^~~ In file included from /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:47: /build/reproducible-path/sortmerna-4.3.6/include/ThreadPool.hpp: In member function 'void ThreadPool::threadEntry(int)': /build/reproducible-path/sortmerna-4.3.6/include/ThreadPool.hpp:92:38: warning: unused parameter 'i' [-Wunused-parameter] 92 | void threadEntry(int i) | ~~~~^ [ 92%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_blast.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_blast.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report.cpp: In constructor 'Report::Report(Runopts&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/src/sortmerna/paralleltraversal.cpp: In function 'void traverse(Runopts&, Index&, References&, Readstats&, Refstats&, Read&, bool)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:289:99: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 289 | bool is_last_idx = (index.index_num == opts.indexfiles.size() - 1) && (index.part == refstats.num_index_parts[index.index_num] - 1); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 94%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_denovo.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_denovo.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp: In member function 'void Read::unmarshallJson(KeyValueDatabase&)': /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/read.cpp:540:46: warning: unused parameter 'kvdb' [-Wunused-parameter] 540 | void Read::unmarshallJson(KeyValueDatabase & kvdb) | ~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:40, from /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/readstats.cpp:52: /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' 221 | __KSEQ_READ | ^~~~~~~~~~~ /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' 43 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ [ 95%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_biom.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_biom.cpp In file included from /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/paralleltraversal.cpp:41: /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp: At global scope: /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/include/kseq.h:221:9: note: in expansion of macro '__KSEQ_READ' 221 | __KSEQ_READ | ^~~~~~~~~~~ /build/reproducible-path/sortmerna-4.3.6/include/kseq_load.hpp:43:1: note: in expansion of macro 'KSEQ_INIT' 43 | KSEQ_INIT(gzFile, gzread) | ^~~~~~~~~ /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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) | ~~~~~~~~~~~^~~ [ 97%] Building CXX object src/sortmerna/CMakeFiles/smr_objs.dir/report_sam.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/report_sam.cpp /build/reproducible-path/sortmerna-4.3.6/src/sortmerna/report_biom.cpp: In member function 'virtual void ReportBiom::init(Readfeed&, Runopts&)': /build/reproducible-path/sortmerna-4.3.6/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-4.3.6/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-4.3.6/obj-i686-linux-gnu' [ 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-4.3.6/obj-i686-linux-gnu' cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sortmerna-4.3.6 /build/reproducible-path/sortmerna-4.3.6/src/sortmerna /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna/CMakeFiles/sortmerna.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' make -f src/sortmerna/CMakeFiles/sortmerna.dir/build.make src/sortmerna/CMakeFiles/sortmerna.dir/build make[3]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' [ 98%] Building CXX object src/sortmerna/CMakeFiles/sortmerna.dir/main.cpp.o cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/src/sortmerna && /usr/bin/c++ -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/concurrentqueue -I/build/reproducible-path/sortmerna-4.3.6/include -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/cmph -I/build/reproducible-path/sortmerna-4.3.6/3rdparty/alp -g -O2 -ffile-prefix-map=/build/reproducible-path/sortmerna-4.3.6=. -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-4.3.6/src/sortmerna/main.cpp [100%] Linking CXX executable sortmerna cd /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/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-4.3.6=. -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 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/usr/lib/gcc/i686-linux-gnu/13/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/13/crtbeginS.o -L/usr/lib/gcc/i686-linux-gnu/13 -L/usr/lib/gcc/i686-linux-gnu/13/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/13/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/13/../../.. -v -z relro -z now CMakeFiles/sortmerna.dir/main.cpp.o ../../CMakeFiles/build_version.dir/build_version.cpp.o CMakeFiles/smr_objs.dir/alignment.cpp.o CMakeFiles/smr_objs.dir/bitvector.cpp.o CMakeFiles/smr_objs.dir/cmd.cpp.o CMakeFiles/smr_objs.dir/izlib.cpp.o CMakeFiles/smr_objs.dir/index.cpp.o CMakeFiles/smr_objs.dir/indexdb.cpp.o CMakeFiles/smr_objs.dir/kseq_load.cpp.o CMakeFiles/smr_objs.dir/kvdb.cpp.o CMakeFiles/smr_objs.dir/options.cpp.o CMakeFiles/smr_objs.dir/output.cpp.o CMakeFiles/smr_objs.dir/summary.cpp.o CMakeFiles/smr_objs.dir/paralleltraversal.cpp.o CMakeFiles/smr_objs.dir/processor.cpp.o CMakeFiles/smr_objs.dir/read.cpp.o CMakeFiles/smr_objs.dir/readfeed.cpp.o CMakeFiles/smr_objs.dir/readstats.cpp.o CMakeFiles/smr_objs.dir/references.cpp.o CMakeFiles/smr_objs.dir/refstats.cpp.o CMakeFiles/smr_objs.dir/ssw.c.o CMakeFiles/smr_objs.dir/traverse_bursttrie.cpp.o CMakeFiles/smr_objs.dir/util.cpp.o CMakeFiles/smr_objs.dir/otumap.cpp.o CMakeFiles/smr_objs.dir/report.cpp.o CMakeFiles/smr_objs.dir/report_fx_base.cpp.o CMakeFiles/smr_objs.dir/report_fastx.cpp.o CMakeFiles/smr_objs.dir/report_fx_other.cpp.o CMakeFiles/smr_objs.dir/report_blast.cpp.o CMakeFiles/smr_objs.dir/report_denovo.cpp.o CMakeFiles/smr_objs.dir/report_biom.cpp.o CMakeFiles/smr_objs.dir/report_sam.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprob.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogproblim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_dynprogprobproto.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_ioutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstat.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatmatrix.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_localmaxstatutil.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/njn_random.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alignment_evaluer.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_data.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_regression.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_alp_sim.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_basic.cpp.o ../../3rdparty/alp/CMakeFiles/alp.dir/sls_pvalues.cpp.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bdz_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/bmz8.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/brz.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_entry.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/buffer_manager.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chd_ph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/chm.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/cmph_structs.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_rank.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/compressed_seq.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/fch_buckets.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/graph.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/jenkins_hash.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/miller_rabin.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/select.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vqueue.c.o ../../3rdparty/cmph/CMakeFiles/cmph.dir/vstack.c.o /usr/lib/i386-linux-gnu/librocksdb.so.8.9.1 -ldl /usr/lib/i386-linux-gnu/libz.so -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/13/crtendS.o /usr/lib/gcc/i686-linux-gnu/13/../../../i386-linux-gnu/crtn.o GNU ld (GNU Binutils for Debian) 2.42 make[3]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' [100%] Built target sortmerna make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/sortmerna/ cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/sortmerna-4.3.6/debian/sortmerna AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sortmerna-4.3.6 -B/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/sortmerna-4.3.6/debian/sortmerna/usr/bin/sortmerna -- Installing: /build/reproducible-path/sortmerna-4.3.6/debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake -- Installing: /build/reproducible-path/sortmerna-4.3.6/debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6/obj-i686-linux-gnu' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6' find debian -name cmake -type d | xargs rm -rvf removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfigVersion.cmake' removed 'debian/sortmerna/usr/cmake/sortmerna/sortmernaConfig.cmake' removed directory 'debian/sortmerna/usr/cmake/sortmerna' removed directory 'debian/sortmerna/usr/cmake' make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6' dh_installdocs dh_installchangelogs dh_installexamples debian/rules execute_after_dh_installexamples make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6' # Convert example files to Unicode. set -e \ ; cd /build/reproducible-path/sortmerna-4.3.6/tests/sortmerna/ \ ; for cxxfile in *.cpp \ ; do iconv -f ISO-8859-15 -t UTF-8 \ < ${cxxfile} \ > /build/reproducible-path/sortmerna-4.3.6/debian/sortmerna/usr/share/doc/sortmerna/examples/${cxxfile} \ ; done make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6' dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/sortmerna-4.3.6' 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/build.py' retained as 0644 (rw-r--r--) mode of 'debian/sortmerna/usr/share/sortmerna/scripts/run.py' retained as 0644 (rw-r--r--) make[1]: Leaving directory '/build/reproducible-path/sortmerna-4.3.6' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'sortmerna-dbgsym' in '../sortmerna-dbgsym_4.3.6-3_i386.deb'. dpkg-deb: building package 'sortmerna' in '../sortmerna_4.3.6-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../sortmerna_4.3.6-3_i386.buildinfo dpkg-genchanges --build=binary -O../sortmerna_4.3.6-3_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/83829 and its subdirectories I: Current time: Thu May 22 14:54:58 -12 2025 I: pbuilder-time-stamp: 1747968898 Fri Apr 19 20:31:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Fri Apr 19 20:31:59 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Fri Apr 19 20:37:00 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Fri Apr 19 20:37:01 UTC 2024 I: sortmerna_4.3.6-3_i386.changes: Format: 1.8 Date: Wed, 06 Sep 2023 19:43:10 +0200 Source: sortmerna Binary: sortmerna sortmerna-dbgsym Architecture: i386 Version: 4.3.6-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: sortmerna - tool for filtering, mapping and OTU-picking NGS reads Closes: 1051325 Changes: sortmerna (4.3.6-3) unstable; urgency=medium . * d/rules: convert example files to Unicode per lintian flag. * typos.patch: add; fix typos caught by lintian. * d/copyright: update copyright year. * concurrentqueue.h.patch: update concurrentqueue.h location. (Closes: #1051325) * gcc-13.patch: new: fix ftbfs with gcc-13. Checksums-Sha1: 622c9721d868bde44c267742688fd0f5de10952b 7058868 sortmerna-dbgsym_4.3.6-3_i386.deb 8a0c426fbb0d7d595e8e15ec34cce20176241a40 6504 sortmerna_4.3.6-3_i386.buildinfo 865e93e306723677c936ad4e0c2af89b9c9c4190 590636 sortmerna_4.3.6-3_i386.deb Checksums-Sha256: 03a9629db6b9373ef2e60ad2f06ca43288451664b035ec807bf9fe28396fcc32 7058868 sortmerna-dbgsym_4.3.6-3_i386.deb 1186710f0ce34595c1d1b3440a698407a7f13d1ca3a2e12e2677de7db1ddb6b5 6504 sortmerna_4.3.6-3_i386.buildinfo 717fc376fbb1d3db1d4bb2fe3762adb0d5f3b27abc9509d2b203e95de3fbb3d1 590636 sortmerna_4.3.6-3_i386.deb Files: b5d8d537b404bff2f2645bbf44a9667a 7058868 debug optional sortmerna-dbgsym_4.3.6-3_i386.deb 3b70a746a01021aebf995b16fcceefad 6504 science optional sortmerna_4.3.6-3_i386.buildinfo 215d500c975a8d73314be826195c02b5 590636 science optional sortmerna_4.3.6-3_i386.deb Fri Apr 19 20:37:02 UTC 2024 I: diffoscope 264 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_8-24541.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.PkR4KoW4/sortmerna_4.3.6-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.PkR4KoW4/sortmerna_4.3.6-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.PkR4KoW4/sortmerna_4.3.6-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.PkR4KoW4/b1/sortmerna_4.3.6-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.PkR4KoW4/b2/sortmerna_4.3.6-3_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: 0.427s) 0.427s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.105s) 0.105s 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: 773ms CPU time consumed: 774ms Fri Apr 19 20:37:03 UTC 2024 I: diffoscope 264 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 19 20:37:03 UTC 2024 I: sortmerna from trixie built successfully and reproducibly on i386. Fri Apr 19 20:37:05 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Apr 19 20:37:05 UTC 2024 I: Submitting 8.0K b1/sortmerna_4.3.6-3_i386.buildinfo.asc Fri Apr 19 20:37:06 UTC 2024 I: Submitting 8.0K b2/sortmerna_4.3.6-3_i386.buildinfo.asc Fri Apr 19 20:37:07 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 19 20:37:07 UTC 2024 I: Done submitting .buildinfo files. Fri Apr 19 20:37:07 UTC 2024 I: Removing signed sortmerna_4.3.6-3_i386.buildinfo.asc files: removed './b1/sortmerna_4.3.6-3_i386.buildinfo.asc' removed './b2/sortmerna_4.3.6-3_i386.buildinfo.asc'