Mon Jan 8 03:20:11 UTC 2024 I: starting to build hmmer/bullseye/amd64 on jenkins on '2024-01-08 03:19' Mon Jan 8 03:20:11 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/12516/console.log Mon Jan 8 03:20:11 UTC 2024 I: Downloading source for bullseye/hmmer=3.3.2+dfsg-1 --2024-01-08 03:20:12-- http://cdn-fastly.deb.debian.org/debian/pool/main/h/hmmer/hmmer_3.3.2%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2128 (2.1K) [text/prs.lines.tag] Saving to: ‘hmmer_3.3.2+dfsg-1.dsc’ 0K .. 100% 10.5M=0s 2024-01-08 03:20:12 (10.5 MB/s) - ‘hmmer_3.3.2+dfsg-1.dsc’ saved [2128/2128] Mon Jan 8 03:20:12 UTC 2024 I: hmmer_3.3.2+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hmmer Binary: hmmer, hmmer-doc, hmmer-examples Architecture: any-amd64 any-i386 powerpc ppc64 all Version: 3.3.2+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://hmmer.org/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/hmmer Vcs-Git: https://salsa.debian.org/med-team/hmmer.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libdivsufsort-dev, python3 Package-List: hmmer deb science optional arch=any-amd64,any-i386,powerpc,ppc64,x32 hmmer-doc deb doc optional arch=all hmmer-examples deb doc optional arch=all Checksums-Sha1: 9b796c84b7348c8520ba38c1c266becbf36a7520 12390556 hmmer_3.3.2+dfsg.orig.tar.xz 939de19e51fc3389d4ef003fe76ea52ba2329b97 14264 hmmer_3.3.2+dfsg-1.debian.tar.xz Checksums-Sha256: 32913d564890c0eac5a95af9cc0a4284e612138be4754212db316fff1d379803 12390556 hmmer_3.3.2+dfsg.orig.tar.xz 8d750af4414f6603cfa21387ae465057acf6990ded6f94da262cdc737c321d43 14264 hmmer_3.3.2+dfsg-1.debian.tar.xz Files: e04965f449d014e0f1ec30eb8e93680c 12390556 hmmer_3.3.2+dfsg.orig.tar.xz d2e5478082fd51a374751d254a9b3fbc 14264 hmmer_3.3.2+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl/trQUACgkQPCZ2P2xn 5uI4TRAAzD/nOH3fXRpAQj2p5hjrjJgKAueoVFpPoq852susxJ1Q+Pxt/XWRldyz BGC/pD3j02nbhLulk5+g/1jHpQEhWc7+tpeiwOEkyEl12sJxeFDnlTHb+3AMr9sL YzdxqrhaB+sSNd/XGmY7ZxYzz9HVQ1OW/6QHpLUK/5wXEAoL9oezSsLHVAMck0GQ s2+nSkHIricQRTrCoEFvViZPHDU1iP2mdeSz2l1t5uTHJLfHiN0qCp8MTJfa4ZaH ayONbN5MH/yeBHvhYSroJ3qT7CKYzfg/P56RK529VYmH1BASk2AoYHMX4wiuM6t9 7MxzUkJGjOxQ2C5x6QqPFakqucbHzvFYU9DAKjQALXS3thhd2yTeO77da6fpAlZP 4VSx+cz2zik7m11yslL4CCcOAsxHjBNMIxWGXncQgTUdiOcT+02Z/pLsWw6KMMWF Pz5TsMW3tJfp3QF+76nKY9qB57r8dajSn+cGTRPpPWnjbEAVUTxIsZtIcCwQPBHt SaEKr8GX1ve0GkmZPGB+89kXNRrFV3nxY5fXYTbWcEdbhdvrEWtb0+XufDhQTHrr +4Pm/7eTC2mhkXNpEVZ17ndAvVeiArwfFmVqQ5bXTetztCrdYxBcEJE4+0HLDWnx cXLXr/tJkcr93BDh6Zx1pMtdBmnR4y2oyK1GbUGu1P6hlAizSxE= =zakN -----END PGP SIGNATURE----- Mon Jan 8 03:20:12 UTC 2024 I: Checking whether the package is not for us Mon Jan 8 03:20:12 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Mon Jan 8 03:20:12 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Mon Jan 8 03:25:42 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Feb 8 21:43:21 -12 2025 I: pbuilder-time-stamp: 1739094201 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [hmmer_3.3.2+dfsg-1.dsc] I: copying [./hmmer_3.3.2+dfsg.orig.tar.xz] I: copying [./hmmer_3.3.2+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.VEjuLhPU/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 31 10:50:45 2020 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hmmer_3.3.2+dfsg-1.dsc dpkg-source: info: extracting hmmer in hmmer-3.3.2+dfsg dpkg-source: info: unpacking hmmer_3.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer_3.3.2+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_manpage_extension.patch dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch dpkg-source: info: applying verbose-easel dpkg-source: info: applying hardening dpkg-source: info: applying skip_threads_check dpkg-source: info: applying sub_make_parallel dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3693795/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9a35a2f3228b42439628c035f03b07b8' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3693795' 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.bmmNZzAk/pbuilderrc_Rzp6 --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bmmNZzAk/b1 --logfile b1/build.log hmmer_3.3.2+dfsg-1.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Feb 8 15:47 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3693795/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libdivsufsort-dev, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17743 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 libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} 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} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libpipeline1{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 24.1 MB of archives. After unpacking 92.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2021a-1+deb11u10 [286 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort-dev amd64 2.0.1-5 [19.1 kB] Fetched 24.1 MB in 0s (84.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17743 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2+deb11u5_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2+deb11u5) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18610 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... 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Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3+deb11u1) ... Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Feb 9 09:43:40 UTC 2025. Universal Time is now: Sun Feb 9 09:43:40 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libdivsufsort-dev:amd64 (2.0.1-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/hmmer-3.3.2+dfsg/ && 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 > ../hmmer_3.3.2+dfsg-1_source.changes dpkg-buildpackage: info: source package hmmer dpkg-buildpackage: info: source version 3.3.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from hmmer-3.3.2+dfsg/debian/source/options: --extend-diff-ignore=(^|/)config.(sub|guess)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_auto_clean rm -f testsuite/esltmp* rm -f easel/testsuite/esltmp* rm -f tutorial/MADE1.hmm.h3? rm -f config.log config.status configure find . -name Makefile -delete make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' AUTOHEADER=true dh_autoreconf make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2" dh_auto_configure -- --enable-threads --enable-sse ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-sse configure: Configuring HMMER3 for your system. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking whether to compile using MPI... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gcc option to accept ISO C99... none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking how to run the C preprocessor... gcc -E checking for a BSD-compatible install... /usr/bin/install -c checking for strip... strip checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether gcc can compile our SSE code... yes configure: Activating Intel/AMD SSE vector DP implementation checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes checking compiler support --start-group... yes checking for gzip... /bin/gzip checking for python3... yes checking for library containing clock_gettime... none required checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for sys/sysctl.h... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... yes checking whether byte ordering is bigendian... no checking for __attribute__((noreturn))... yes checking for __attribute__((format))... yes checking for mkstemp... yes checking for popen... yes checking for putenv... yes checking for strcasecmp... yes checking for strsep... yes checking for times... yes checking for getpid... yes checking for sysctl... yes checking for sysconf... yes checking for getcwd... yes checking for chmod... yes checking for stat... yes checking for fstat... yes checking for erfc... no checking for library containing ntohs... none required checking for library containing ntohl... none required checking for library containing htons... none required checking for library containing htonl... none required checking for library containing socket... none required checking for library containing inet_pton... none required checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating documentation/userguide/Makefile config.status: creating documentation/userguide/inclusions/Makefile config.status: creating easel/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/documentation/Makefile config.status: creating documentation/userguide/titlepage.tex config.status: creating documentation/userguide/titlepage_daemon.tex config.status: creating documentation/userguide/copyright.tex config.status: creating documentation/man/alimask.man config.status: creating documentation/man/hmmalign.man config.status: creating documentation/man/hmmbuild.man config.status: creating documentation/man/hmmc2.man config.status: creating documentation/man/hmmconvert.man config.status: creating documentation/man/hmmemit.man config.status: creating documentation/man/hmmer.man config.status: creating documentation/man/hmmfetch.man config.status: creating documentation/man/hmmlogo.man config.status: creating documentation/man/hmmpgmd.man config.status: creating documentation/man/hmmpgmd_shard.man config.status: creating documentation/man/hmmpress.man config.status: creating documentation/man/hmmscan.man config.status: creating documentation/man/hmmsearch.man config.status: creating documentation/man/hmmsim.man config.status: creating documentation/man/hmmstat.man config.status: creating documentation/man/jackhmmer.man config.status: creating documentation/man/makehmmerdb.man config.status: creating documentation/man/nhmmer.man config.status: creating documentation/man/nhmmscan.man config.status: creating documentation/man/phmmer.man config.status: creating easel/miniapps/esl-afetch.man config.status: creating easel/miniapps/esl-alimanip.man config.status: creating easel/miniapps/esl-alimap.man config.status: creating easel/miniapps/esl-alimask.man config.status: creating easel/miniapps/esl-alimerge.man config.status: creating easel/miniapps/esl-alipid.man config.status: creating easel/miniapps/esl-alirev.man config.status: creating easel/miniapps/esl-alistat.man config.status: creating easel/miniapps/esl-compalign.man config.status: creating easel/miniapps/esl-compstruct.man config.status: creating easel/miniapps/esl-construct.man config.status: creating easel/miniapps/esl-histplot.man config.status: creating easel/miniapps/esl-mask.man config.status: creating easel/miniapps/esl-mixdchlet.man config.status: creating easel/miniapps/esl-reformat.man config.status: creating easel/miniapps/esl-selectn.man config.status: creating easel/miniapps/esl-seqrange.man config.status: creating easel/miniapps/esl-seqstat.man config.status: creating easel/miniapps/esl-sfetch.man config.status: creating easel/miniapps/esl-shuffle.man config.status: creating easel/miniapps/esl-ssdraw.man config.status: creating easel/miniapps/esl-translate.man config.status: creating easel/miniapps/esl-weight.man config.status: creating easel/decoy_config.h config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: linking src/impl_sse to src/impl HMMER configuration: compiler: gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread host: x86_64-pc-linux-gnu linker: -Wl,-z,relro -Wl,-z,now -flto libraries: DP implementation: sse Now do 'make' to build HMMER, and optionally: 'make check' to run self tests, 'make install' to install programs and man pages, '(cd easel; make install)' to install Easel tools. make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' export V=VERBOSE ; dh_auto_build make -j16 make[2]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' make -C easel all make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c easel.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_alloc.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_alphabet.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_arr2.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_arr3.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_bitfield.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_buffer.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_cluster.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_composition.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_cpu.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_dirichlet.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_distance.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_dmatrix.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_dsqdata.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_exponential.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_fileparser.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_gamma.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_gencode.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_getopts.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_gev.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_graph.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_gumbel.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_heap.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_histogram.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_hmm.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_huffman.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_hyperexp.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_json.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_keyhash.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_matrixops.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_mem.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_minimizer.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_mixdchlet.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_mixgev.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_mpi.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msa.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msacluster.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile2.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_a2m.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_afa.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_clustal.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_phylip.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_psiblast.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_selex.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msafile_stockholm.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msashuffle.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_msaweight.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_normal.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_paml.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_quicksort.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_random.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_rand64.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_randomseq.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_ratematrix.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_recorder.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_red_black.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_regexp.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_rootfinder.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_scorematrix.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_sq.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_sqio.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_sqio_ascii.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_sqio_ncbi.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_ssi.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_stack.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_stats.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_stopwatch.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_stretchexp.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_subcmd.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_threads.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_tree.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_varint.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_vectorops.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_weibull.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_workqueue.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_wuss.c In file included from esl_threads.c:24: /usr/include/x86_64-linux-gnu/sys/sysctl.h:21:2: warning: #warning "The header is deprecated and will be removed." [-Wcpp] 21 | #warning "The header is deprecated and will be removed." | ^~~~~~~ gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_sse.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_avx.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_avx512.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_neon.c gcc -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -c esl_vmx.c /usr/bin/ar -r libeasel.a easel.o esl_alloc.o esl_alphabet.o esl_arr2.o esl_arr3.o esl_bitfield.o esl_buffer.o esl_cluster.o esl_composition.o esl_cpu.o esl_dirichlet.o esl_distance.o esl_dmatrix.o esl_dsqdata.o esl_exponential.o esl_fileparser.o esl_gamma.o esl_gencode.o esl_getopts.o esl_gev.o esl_graph.o esl_gumbel.o esl_heap.o esl_histogram.o esl_hmm.o esl_huffman.o esl_hyperexp.o esl_json.o esl_keyhash.o esl_matrixops.o esl_mem.o esl_minimizer.o esl_mixdchlet.o esl_mixgev.o esl_mpi.o esl_msa.o esl_msacluster.o esl_msafile.o esl_msafile2.o esl_msafile_a2m.o esl_msafile_afa.o esl_msafile_clustal.o esl_msafile_phylip.o esl_msafile_psiblast.o esl_msafile_selex.o esl_msafile_stockholm.o esl_msashuffle.o esl_msaweight.o esl_normal.o esl_paml.o esl_quicksort.o esl_random.o esl_rand64.o esl_randomseq.o esl_ratematrix.o esl_recorder.o esl_red_black.o esl_regexp.o esl_rootfinder.o esl_scorematrix.o esl_sq.o esl_sqio.o esl_sqio_ascii.o esl_sqio_ncbi.o esl_ssi.o esl_stack.o esl_stats.o esl_stopwatch.o esl_stretchexp.o esl_subcmd.o esl_threads.o esl_tree.o esl_varint.o esl_vectorops.o esl_weibull.o esl_workqueue.o esl_wuss.o esl_sse.o esl_avx.o esl_avx512.o esl_neon.o esl_vmx.o > /dev/null 2>&1 make -C miniapps all make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/miniapps' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-afetch esl-afetch.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimanip esl-alimanip.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimap esl-alimap.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimask esl-alimask.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alimerge esl-alimerge.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alipid esl-alipid.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alirev esl-alirev.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-alistat esl-alistat.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-compalign esl-compalign.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-compstruct esl-compstruct.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-construct esl-construct.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-histplot esl-histplot.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-mask esl-mask.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-mixdchlet esl-mixdchlet.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-reformat esl-reformat.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-selectn esl-selectn.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-seqrange esl-seqrange.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-seqstat esl-seqstat.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-sfetch esl-sfetch.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-shuffle esl-shuffle.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-ssdraw esl-ssdraw.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-translate esl-translate.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o esl-weight esl-weight.c -leasel -lm gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -c cmd_alistat.c gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -c cmd_downsample.c gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -c cmd_filter.c gcc -I. -I.. -I. -I./.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -c cmd_index.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L.. -I. -I.. -I. -I./.. -o easel easel.c cmd_alistat.o cmd_downsample.o cmd_filter.o cmd_index.o -leasel -lm make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/miniapps' make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' make -C src all make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o alimask.o -c alimask.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o build.o -c build.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o cachedb.o -c cachedb.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o cachedb_shard.o -c cachedb_shard.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o emit.o -c emit.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o errors.o -c errors.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o evalues.o -c evalues.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o eweight.o -c eweight.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_decoding.o -c generic_decoding.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_fwdback.o -c generic_fwdback.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_fwdback_chk.o -c generic_fwdback_chk.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_fwdback_banded.o -c generic_fwdback_banded.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_null2.o -c generic_null2.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_msv.o -c generic_msv.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_optacc.o -c generic_optacc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_stotrace.o -c generic_stotrace.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_viterbi.o -c generic_viterbi.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o generic_vtrace.o -c generic_vtrace.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o h2_io.o -c h2_io.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o heatmap.o -c heatmap.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmlogo.o -c hmmlogo.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdmstr.o -c hmmdmstr.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdmstr_shard.o -c hmmdmstr_shard.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmd_search_status.o -c hmmd_search_status.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdwrkr.o -c hmmdwrkr.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdwrkr_shard.o -c hmmdwrkr_shard.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmdutils.o -c hmmdutils.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmer.o -c hmmer.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o logsum.o -c logsum.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o modelconfig.o -c modelconfig.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o modelstats.o -c modelstats.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o mpisupport.o -c mpisupport.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o seqmodel.o -c seqmodel.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o tracealign.o -c tracealign.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_alidisplay.o -c p7_alidisplay.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_bg.o -c p7_bg.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_builder.o -c p7_builder.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_domain.o -c p7_domain.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_domaindef.o -c p7_domaindef.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gbands.o -c p7_gbands.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gmx.o -c p7_gmx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gmxb.o -c p7_gmxb.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_gmxchk.o -c p7_gmxchk.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hit.o -c p7_hit.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmm.o -c p7_hmm.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmcache.o -c p7_hmmcache.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmd_search_stats.o -c p7_hmmd_search_stats.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmfile.o -c p7_hmmfile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_hmmwindow.o -c p7_hmmwindow.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_pipeline.o -c p7_pipeline.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_prior.o -c p7_prior.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_profile.o -c p7_profile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_spensemble.o -c p7_spensemble.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_tophits.o -c p7_tophits.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_trace.o -c p7_trace.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o p7_scoredata.o -c p7_scoredata.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpgmd2msa.o -c hmmpgmd2msa.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_alphabet.o -c fm_alphabet.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_general.o -c fm_general.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_sse.o -c fm_sse.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o fm_ssv.o -c fm_ssv.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmalign.o -c hmmalign.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmbuild.o -c hmmbuild.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmconvert.o -c hmmconvert.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmemit.o -c hmmemit.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmfetch.o -c hmmfetch.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpgmd.o -c hmmpgmd.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpgmd_shard.o -c hmmpgmd_shard.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmpress.o -c hmmpress.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmscan.o -c hmmscan.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmsearch.o -c hmmsearch.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmsim.o -c hmmsim.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmstat.o -c hmmstat.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o jackhmmer.o -c jackhmmer.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o phmmer.o -c phmmer.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o nhmmer.o -c nhmmer.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o nhmmscan.o -c nhmmscan.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o makehmmerdb.o -c makehmmerdb.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmc2.o -c hmmc2.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o hmmerfm-exactmatch.o -c hmmerfm-exactmatch.c /usr/bin/ar -r libhmmer.a build.o cachedb.o cachedb_shard.o emit.o errors.o evalues.o eweight.o generic_decoding.o generic_fwdback.o generic_fwdback_chk.o generic_fwdback_banded.o generic_null2.o generic_msv.o generic_optacc.o generic_stotrace.o generic_viterbi.o generic_vtrace.o h2_io.o heatmap.o hmmlogo.o hmmdmstr.o hmmdmstr_shard.o hmmd_search_status.o hmmdwrkr.o hmmdwrkr_shard.o hmmdutils.o hmmer.o logsum.o modelconfig.o modelstats.o mpisupport.o seqmodel.o tracealign.o p7_alidisplay.o p7_bg.o p7_builder.o p7_domain.o p7_domaindef.o p7_gbands.o p7_gmx.o p7_gmxb.o p7_gmxchk.o p7_hit.o p7_hmm.o p7_hmmcache.o p7_hmmd_search_stats.o p7_hmmfile.o p7_hmmwindow.o p7_pipeline.o p7_prior.o p7_profile.o p7_spensemble.o p7_tophits.o p7_trace.o p7_scoredata.o hmmpgmd2msa.o fm_alphabet.o fm_general.o fm_sse.o fm_ssv.o > /dev/null 2>&1 make -C impl_sse libhmmer-impl.stamp make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src/impl_sse' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o decoding.o -c decoding.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o fwdback.o -c fwdback.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o io.o -c io.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o ssvfilter.o -c ssvfilter.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o msvfilter.o -c msvfilter.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o null2.o -c null2.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o optacc.o -c optacc.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o stotrace.o -c stotrace.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o vitfilter.o -c vitfilter.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o p7_omx.o -c p7_omx.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o p7_oprofile.o -c p7_oprofile.c gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -o mpi.o -c mpi.c /usr/bin/ar -r ../libhmmer.a decoding.o fwdback.o io.o ssvfilter.o msvfilter.o null2.o optacc.o stotrace.o vitfilter.o p7_omx.o p7_oprofile.o mpi.o > /dev/null 2>&1 make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src/impl_sse' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o alimask alimask.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmalign hmmalign.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmbuild hmmbuild.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmconvert hmmconvert.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmemit hmmemit.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmfetch hmmfetch.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmlogo hmmlogo.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmpgmd hmmpgmd.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmpgmd_shard hmmpgmd_shard.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmpress hmmpress.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmscan hmmscan.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmsearch hmmsearch.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmsim hmmsim.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmstat hmmstat.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o jackhmmer jackhmmer.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o phmmer phmmer.o -lhmmer -leasel -ldivsufsort -lm In function 'usual_master', inlined from 'main' at hmmbuild.c:463:7: hmmbuild.c:561:3: warning: argument 1 range [18446744022169944064, 18446744073709551592] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 561 | ESL_ALLOC(info, sizeof(*info) * infocnt); | ^ hmmbuild.c: In function 'main': /usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here 539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o nhmmer nhmmer.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o nhmmscan nhmmscan.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o makehmmerdb makehmmerdb.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmc2 hmmc2.o -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o hmmerfm-exactmatch hmmerfm-exactmatch.o -lhmmer -leasel -ldivsufsort -lm make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' make -C profmark all make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/profmark' gcc -I../easel -I../easel -I../src -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -o create-profmark.o -c create-profmark.c gcc -I../easel -I../easel -I../src -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -o rocplot.o -c rocplot.c gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L../easel -L../src -o rocplot rocplot.o -lhmmer -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -flto -L../easel -L../src -o create-profmark create-profmark.o -lhmmer -leasel -lm make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/profmark' make[2]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' export V=VERBOSE ; make check -j16 | tee debian/test_log make[2]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' make -C easel tests make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o easel_utest -I. -I. -L. -DeslEASEL_TESTDRIVE ./easel.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_alloc_utest -I. -I. -L. -DeslALLOC_TESTDRIVE ./esl_alloc.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_alphabet_utest -I. -I. -L. -DeslALPHABET_TESTDRIVE ./esl_alphabet.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_bitfield_utest -I. -I. -L. -DeslBITFIELD_TESTDRIVE ./esl_bitfield.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_cluster_utest -I. -I. -L. -DeslCLUSTER_TESTDRIVE ./esl_cluster.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_buffer_utest -I. -I. -L. -DeslBUFFER_TESTDRIVE ./esl_buffer.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_cpu_utest -I. -I. -L. -DeslCPU_TESTDRIVE ./esl_cpu.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_distance_utest -I. -I. -L. -DeslDISTANCE_TESTDRIVE ./esl_distance.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_dirichlet_utest -I. -I. -L. -DeslDIRICHLET_TESTDRIVE ./esl_dirichlet.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_dmatrix_utest -I. -I. -L. -DeslDMATRIX_TESTDRIVE ./esl_dmatrix.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_dsqdata_utest -I. -I. -L. -DeslDSQDATA_TESTDRIVE ./esl_dsqdata.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_fileparser_utest -I. -I. -L. -DeslFILEPARSER_TESTDRIVE ./esl_fileparser.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_exponential_utest -I. -I. -L. -DeslEXPONENTIAL_TESTDRIVE ./esl_exponential.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_gamma_utest -I. -I. -L. -DeslGAMMA_TESTDRIVE ./esl_gamma.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_gencode_utest -I. -I. -L. -DeslGENCODE_TESTDRIVE ./esl_gencode.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_getopts_utest -I. -I. -L. -DeslGETOPTS_TESTDRIVE ./esl_getopts.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_graph_utest -I. -I. -L. -DeslGRAPH_TESTDRIVE ./esl_graph.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_gumbel_utest -I. -I. -L. -DeslGUMBEL_TESTDRIVE ./esl_gumbel.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_heap_utest -I. -I. -L. -DeslHEAP_TESTDRIVE ./esl_heap.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_histogram_utest -I. -I. -L. -DeslHISTOGRAM_TESTDRIVE ./esl_histogram.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_hmm_utest -I. -I. -L. -DeslHMM_TESTDRIVE ./esl_hmm.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_huffman_utest -I. -I. -L. -DeslHUFFMAN_TESTDRIVE ./esl_huffman.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_hyperexp_utest -I. -I. -L. -DeslHYPEREXP_TESTDRIVE ./esl_hyperexp.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_json_utest -I. -I. -L. -DeslJSON_TESTDRIVE ./esl_json.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_keyhash_utest -I. -I. -L. -DeslKEYHASH_TESTDRIVE ./esl_keyhash.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_matrixops_utest -I. -I. -L. -DeslMATRIXOPS_TESTDRIVE ./esl_matrixops.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_mem_utest -I. -I. -L. -DeslMEM_TESTDRIVE ./esl_mem.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_minimizer_utest -I. -I. -L. -DeslMINIMIZER_TESTDRIVE ./esl_minimizer.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_mixdchlet_utest -I. -I. -L. -DeslMIXDCHLET_TESTDRIVE ./esl_mixdchlet.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msa_utest -I. -I. -L. -DeslMSA_TESTDRIVE ./esl_msa.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msacluster_utest -I. -I. -L. -DeslMSACLUSTER_TESTDRIVE ./esl_msacluster.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_utest -I. -I. -L. -DeslMSAFILE_TESTDRIVE ./esl_msafile.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile2_utest -I. -I. -L. -DeslMSAFILE2_TESTDRIVE ./esl_msafile2.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_a2m_utest -I. -I. -L. -DeslMSAFILE_A2M_TESTDRIVE ./esl_msafile_a2m.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_afa_utest -I. -I. -L. -DeslMSAFILE_AFA_TESTDRIVE ./esl_msafile_afa.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_clustal_utest -I. -I. -L. -DeslMSAFILE_CLUSTAL_TESTDRIVE ./esl_msafile_clustal.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_psiblast_utest -I. -I. -L. -DeslMSAFILE_PSIBLAST_TESTDRIVE ./esl_msafile_psiblast.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_phylip_utest -I. -I. -L. -DeslMSAFILE_PHYLIP_TESTDRIVE ./esl_msafile_phylip.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_selex_utest -I. -I. -L. -DeslMSAFILE_SELEX_TESTDRIVE ./esl_msafile_selex.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msafile_stockholm_utest -I. -I. -L. -DeslMSAFILE_STOCKHOLM_TESTDRIVE ./esl_msafile_stockholm.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_msaweight_utest -I. -I. -L. -DeslMSAWEIGHT_TESTDRIVE ./esl_msaweight.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_normal_utest -I. -I. -L. -DeslNORMAL_TESTDRIVE ./esl_normal.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_quicksort_utest -I. -I. -L. -DeslQUICKSORT_TESTDRIVE ./esl_quicksort.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_random_utest -I. -I. -L. -DeslRANDOM_TESTDRIVE ./esl_random.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_rand64_utest -I. -I. -L. -DeslRAND64_TESTDRIVE ./esl_rand64.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_randomseq_utest -I. -I. -L. -DeslRANDOMSEQ_TESTDRIVE ./esl_randomseq.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_ratematrix_utest -I. -I. -L. -DeslRATEMATRIX_TESTDRIVE ./esl_ratematrix.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_red_black_utest -I. -I. -L. -DeslRED_BLACK_TESTDRIVE ./esl_red_black.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_recorder_utest -I. -I. -L. -DeslRECORDER_TESTDRIVE ./esl_recorder.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_regexp_utest -I. -I. -L. -DeslREGEXP_TESTDRIVE ./esl_regexp.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_rootfinder_utest -I. -I. -L. -DeslROOTFINDER_TESTDRIVE ./esl_rootfinder.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_scorematrix_utest -I. -I. -L. -DeslSCOREMATRIX_TESTDRIVE ./esl_scorematrix.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_sq_utest -I. -I. -L. -DeslSQ_TESTDRIVE ./esl_sq.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_sqio_utest -I. -I. -L. -DeslSQIO_TESTDRIVE ./esl_sqio.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_ssi_utest -I. -I. -L. -DeslSSI_TESTDRIVE ./esl_ssi.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_stack_utest -I. -I. -L. -DeslSTACK_TESTDRIVE ./esl_stack.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_stats_utest -I. -I. -L. -DeslSTATS_TESTDRIVE ./esl_stats.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_stretchexp_utest -I. -I. -L. -DeslSTRETCHEXP_TESTDRIVE ./esl_stretchexp.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_tree_utest -I. -I. -L. -DeslTREE_TESTDRIVE ./esl_tree.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_varint_utest -I. -I. -L. -DeslVARINT_TESTDRIVE ./esl_varint.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_vectorops_utest -I. -I. -L. -DeslVECTOROPS_TESTDRIVE ./esl_vectorops.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_weibull_utest -I. -I. -L. -DeslWEIBULL_TESTDRIVE ./esl_weibull.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_wuss_utest -I. -I. -L. -DeslWUSS_TESTDRIVE ./esl_wuss.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_sse_utest -I. -I. -L. -DeslSSE_TESTDRIVE ./esl_sse.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_avx_utest -I. -I. -L. -DeslAVX_TESTDRIVE ./esl_avx.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_avx512_utest -I. -I. -L. -DeslAVX512_TESTDRIVE ./esl_avx512.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_neon_utest -I. -I. -L. -DeslNEON_TESTDRIVE ./esl_neon.c -leasel -lm gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wl,-z,relro -Wl,-z,now -flto -o esl_vmx_utest -I. -I. -L. -DeslVMX_TESTDRIVE ./esl_vmx.c -leasel -lm make -C miniapps tests make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/miniapps' make[4]: Nothing to be done for 'tests'. make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/miniapps' make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' make -C src tests make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' make -C impl_sse libhmmer-impl.stamp gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -I../easel -I../easel -I. -I. -o itest_brute.o -c itest_brute.c make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src/impl_sse' make[4]: 'libhmmer-impl.stamp' is up to date. make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src/impl_sse' {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_MSV_TESTDRIVE -o generic_msv_utest ./generic_msv.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7BUILD_TESTDRIVE -o build_utest ./build.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_FWDBACK_CHK_TESTDRIVE -o generic_fwdback_chk_utest ./generic_fwdback_chk.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_FWDBACK_TESTDRIVE -o generic_fwdback_utest ./generic_fwdback.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7MODELCONFIG_TESTDRIVE -o modelconfig_utest ./modelconfig.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7LOGSUM_TESTDRIVE -o logsum_utest ./logsum.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMER_TESTDRIVE -o hmmer_utest ./hmmer.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_VITERBI_TESTDRIVE -o generic_viterbi_utest ./generic_viterbi.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7SEQMODEL_TESTDRIVE -o seqmodel_utest ./seqmodel.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7ALIDISPLAY_TESTDRIVE -o p7_alidisplay_utest ./p7_alidisplay.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7DOMAIN_TESTDRIVE -o p7_domain_utest ./p7_domain.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GENERIC_STOTRACE_TESTDRIVE -o generic_stotrace_utest ./generic_stotrace.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7BG_TESTDRIVE -o p7_bg_utest ./p7_bg.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GMX_TESTDRIVE -o p7_gmx_utest ./p7_gmx.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7GMXCHK_TESTDRIVE -o p7_gmxchk_utest ./p7_gmxchk.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HIT_TESTDRIVE -o p7_hit_utest ./p7_hit.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMD_SEARCH_STATS_TESTDRIVE -o p7_hmmd_search_stats_utest ./p7_hmmd_search_stats.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMM_TESTDRIVE -o p7_hmm_utest ./p7_hmm.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMFILE_TESTDRIVE -o p7_hmmfile_utest ./p7_hmmfile.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7PROFILE_TESTDRIVE -o p7_profile_utest ./p7_profile.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7TOPHITS_TESTDRIVE -o p7_tophits_utest ./p7_tophits.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7TRACE_TESTDRIVE -o p7_trace_utest ./p7_trace.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7SCOREDATA_TESTDRIVE -o p7_scoredata_utest ./p7_scoredata.c -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMPGMD2MSA_TESTDRIVE -o hmmpgmd2msa_utest ./hmmpgmd2msa.c -lhmmer -leasel -ldivsufsort -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -DHAVE_CONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -L../easel -L./impl_sse -L. -o itest_brute itest_brute.o -lhmmer -leasel -ldivsufsort -lm {CC} -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../easel -L./impl_sse -L. -I../easel -I../easel -I. -I. -Dp7HMMD_SEARCH_STATUS_TESTDRIVE -o hmmd_search_status_utest ./hmmd_search_status.c -lhmmer -leasel -ldivsufsort -lm make -C impl_sse tests make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src/impl_sse' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7IO_TESTDRIVE -o io_utest ./io.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7MSVFILTER_TESTDRIVE -o msvfilter_utest ./msvfilter.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7DECODING_TESTDRIVE -o decoding_utest ./decoding.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7STOTRACE_TESTDRIVE -o stotrace_utest ./stotrace.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7NULL2_TESTDRIVE -o null2_utest ./null2.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7FWDBACK_TESTDRIVE -o fwdback_utest ./fwdback.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7OPTACC_TESTDRIVE -o optacc_utest ./optacc.c -lhmmer -leasel -lm gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/hmmer-3.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -flto -DHAVE_CONFIG_H -L../../easel -L.. -I../../easel -I../../easel -I. -I.. -I. -I../../src -I./.. -Dp7VITFILTER_TESTDRIVE -o vitfilter_utest ./vitfilter.c -lhmmer -leasel -lm make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src/impl_sse' make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' make -C easel check make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' make -C miniapps check make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/miniapps' make[4]: Nothing to be done for 'check'. make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/miniapps' make -C testsuite check make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/testsuite' Running Easel test suite... exercise 1 [ easel-utest] ... ok. exercise 2 [ alloc-utest] ... ok. exercise 3 [ alphabet-utest] ... ok. exercise 4 [ avx-utest] ... ok. exercise 5 [ avx512-utest] ... ok. exercise 6 [ bitfield-utest] ... ok. exercise 7 [ buffer-utest] ... ok. exercise 8 [ cluster-utest] ... ok. exercise 9 [ cpu-utest] ... ok. exercise 10 [ dirichlet-utest] ... ok. exercise 11 [ distance-utest] ... ok. exercise 12 [ dmatrix-utest] ... ok. exercise 13 [ dsqdata-utest] ... ok. exercise 14 [ exponential-utest] ... ok. exercise 15 [ fileparser-utest] ... ok. exercise 16 [ gamma-utest] ... ok. exercise 17 [ gencode-utest] ... ok. exercise 18 [ getopts-utest] ... ok. exercise 19 [ graph-utest] ... ok. exercise 20 [ gumbel-utest] ... ok. exercise 21 [ heap-utest] ... ok. exercise 22 [ histogram-utest] ... ok. exercise 23 [ huffman-utest] ... ok. exercise 24 [ hyperexp-utest] ... ok. exercise 25 [ json-utest] ... ok. exercise 26 [ keyhash-utest] ... ok. exercise 27 [ matrixops-utest] ... ok. exercise 28 [ mem-utest] ... ok. exercise 29 [ minimizer-utest] ... ok. exercise 30 [ mixdchlet-utest] ... ok. exercise 31 [ msa-utest] ... ok. exercise 32 [ msacluster-utest] ... ok. exercise 33 [ msafile] ... ok. exercise 34 [ msafile2] ... ok. exercise 35 [ msafile-a2m] ... ok. exercise 36 [ msafile-afa] ... ok. exercise 37 [ msafile-clustal] ... ok. exercise 38 [ msafile-phylip] ... ok. exercise 39 [ msafile-psiblast] ... ok. exercise 40 [ msafile-selex] ... ok. exercise 41 [ msafile-stockholm] ... ok. exercise 42 [ msaweight-utest] ... ok. exercise 43 [ neon-utest] ... ok. exercise 44 [ normal-utest] ... ok. exercise 45 [ quicksort-utest] ... ok. exercise 46 [ random-utest] ... ok. exercise 47 [ rand64-utest] ... ok. exercise 48 [ randomseq-utest] ... ok. exercise 49 [ ratematrix-utest] ... ok. exercise 50 [ recorder-utest] ... ok. exercise 51 [ red_black-utest] ... ok. exercise 52 [ regexp-utest] ... ok. exercise 53 [ rootfinder-utest] ... ok. exercise 54 [ scorematrix-utest] ... ok. exercise 55 [ sq-utest] ... ok. exercise 56 [ sqio-utest] ... ok. exercise 57 [ sse-utest] ... ok. exercise 58 [ ssi-utest] ... ok. exercise 59 [ stack-utest] ... ok. exercise 60 [ stats-utest] ... ok. exercise 61 [ stretchexp-utest] ... ok. exercise 62 [ tree-utest] ... ok. exercise 63 [ varint-utest] ... ok. exercise 64 [ vectorops-utest] ... ok. exercise 65 [ vmx-utest] ... ok. exercise 66 [ weibull-utest] ... ok. exercise 67 [ wuss-utest] ... ok. exercise 68 [ e2] ... ok. exercise 69 [ degen-residues] ... ok. exercise 70 [ ncbi-indices] ... ok. exercise 71 [ blank-gf] ... ok. exercise 72 [ esl-translate] ... ok. exercise 73 [ esl-afetch] ... ok. exercise 74 [ esl-alimanip] ... ok. exercise 75 [ esl-alimap] ... ok. exercise 76 [ esl-alimask] ... ok. exercise 77 [ esl-alimerge] ... ok. exercise 78 [ esl-alistat] ... ok. exercise 79 [ esl-compalign] ... ok. exercise 80 [ esl-construct] ... ok. exercise 81 [ esl-mask] ... ok. exercise 82 [ esl-seqrange] ... ok. exercise 83 [ esl-shuffle] ... ok. exercise 84 [ esl-ssdraw] ... ok. All 84 exercises at level <= 2 passed. System information: Sat Feb 8 21:47:23 -12 2025 Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel/testsuite' make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' make -C testsuite check make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/testsuite' Running HMMER test suite... exercise 1 [ hmmer] ... ok. exercise 2 [ build] ... ok. exercise 3 [ generic_fwdback] ... ok. exercise 4 [ generic_msv] ... ok. exercise 5 [ generic_stotrace] ... ok. exercise 6 [ generic_viterbi] ... ok. exercise 7 [ hmmd_search_status] ... ok. exercise 8 [ logsum] ... ok. exercise 9 [ modelconfig] ... ok. exercise 10 [ seqmodel] ... ok. exercise 11 [ p7_alidisplay] ... ok. exercise 12 [ p7_bg] ... ok. exercise 13 [ p7_domain] ... ok. exercise 14 [ p7_gmx] ... ok. exercise 15 [ p7_hit] ... ok. exercise 16 [ p7_hmm] ... ok. exercise 17 [ p7_hmmfile] ... ok. exercise 18 [ p7_hmmd_search_stats] ... ok. exercise 19 [ p7_profile] ... ok. exercise 20 [ p7_tophits] ... ok. exercise 21 [ p7_trace] ... ok. exercise 22 [ p7_scoredata] ... ok. exercise 23 [ decoding] ... ok. exercise 24 [ fwdback] ... ok. exercise 25 [ io] ... ok. exercise 26 [ msvfilter] ... ok. exercise 27 [ null2] ... ok. exercise 28 [ optacc] ... ok. exercise 29 [ stotrace] ... ok. exercise 30 [ vitfilter] ... ok. exercise 31 [ hmmpgmd2msa] ... ok. exercise 32 [ hmmalign] ... ok. exercise 33 [ hmmalign/-h] ... ok. exercise 34 [ hmmalign/-o] ... ok. exercise 35 [ hmmalign/--mapali] ... ok. exercise 36 [ hmmalign/--trim] ... ok. exercise 37 [ hmmalign/--amino] ... ok. exercise 38 [ hmmalign/--informat] ... ok. exercise 39 [ hmmalign/--outformat] ... ok. exercise 40 [ hmmbuild] ... ok. exercise 41 [ build/-h] ... ok. exercise 42 [ build/-n] ... ok. exercise 43 [ build/-o] ... ok. exercise 44 [ build/-O] ... ok. exercise 45 [ build/--amino] ... ok. exercise 46 [ build/--dna] ... ok. exercise 47 [ build/--rna] ... ok. exercise 48 [ build/--fast] ... ok. exercise 49 [ build/--hand] ... ok. exercise 50 [ build/--symfrac] ... ok. exercise 51 [ build/--fragthresh] ... ok. exercise 52 [ build/--wpb] ... ok. exercise 53 [ build/--wgsc] ... ok. exercise 54 [ build/--wblosum] ... ok. exercise 55 [ build/--wnone] ... ok. exercise 56 [ build/--wid] ... ok. exercise 57 [ build/--eent] ... ok. exercise 58 [ build/--eclust] ... ok. exercise 59 [ build/--enone] ... ok. exercise 60 [ build/--eset] ... ok. exercise 61 [ build/--ere] ... ok. exercise 62 [ build/--esigma] ... ok. exercise 63 [ build/--eid] ... ok. exercise 64 [ build/--pnone] ... ok. exercise 65 [ build/--plaplace] ... ok. exercise 66 [ build/--EmL] ... ok. exercise 67 [ build/--EmN] ... ok. exercise 68 [ build/--EvL] ... ok. exercise 69 [ build/--EvN] ... ok. exercise 70 [ build/--EfL] ... ok. exercise 71 [ build/--EfN] ... ok. exercise 72 [ build/--Eft] ... ok. exercise 73 [ build/--informat] ... ok. exercise 74 [ build/--seed] ... ok. exercise 75 [ search] ... ok. exercise 76 [ search/-h] ... ok. exercise 77 [ search/-o] ... ok. exercise 78 [ search/-A] ... ok. exercise 79 [ search/--tblout] ... ok. exercise 80 [ search/--domtblout] ... ok. exercise 81 [ search/--pfamtblout] ... ok. exercise 82 [ search/--acc] ... ok. exercise 83 [ search/--noali] ... ok. exercise 84 [ search/--notextw] ... ok. exercise 85 [ search/--textw] ... ok. exercise 86 [ search/-E] ... ok. exercise 87 [ search/-T] ... ok. exercise 88 [ search/--domE] ... ok. exercise 89 [ search/--domT] ... ok. exercise 90 [ search/--incE] ... ok. exercise 91 [ search/--incT] ... ok. exercise 92 [ search/--incdomE] ... ok. exercise 93 [ search/--incdomT] ... ok. exercise 94 [ search/--cut_ga] ... ok. exercise 95 [ search/--cut_nc] ... ok. exercise 96 [ search/--cut_tc] ... ok. exercise 97 [ search/--max] ... ok. exercise 98 [ search/--F1] ... ok. exercise 99 [ search/--F2] ... ok. exercise 100 [ search/--F3] ... ok. exercise 101 [ search/--nobias] ... ok. exercise 102 [ search/--nonull2] ... ok. exercise 103 [ search/-Z] ... ok. exercise 104 [ search/--domZ] ... ok. exercise 105 [ search/--seed] ... ok. exercise 106 [ search/--tformat] ... ok. exercise 107 [ hmmscan] ... ok. exercise 108 [ scan/-h] ... ok. exercise 109 [ scan/-o] ... ok. exercise 110 [ scan/--tblout] ... ok. exercise 111 [ scan/--domtblout] ... ok. exercise 112 [ scan/--pfamtblout] ... ok. exercise 113 [ scan/--acc] ... ok. exercise 114 [ scan/--noali] ... ok. exercise 115 [ scan/--notextw] ... ok. exercise 116 [ scan/--textw] ... ok. exercise 117 [ scan/-E] ... ok. exercise 118 [ scan/-T] ... ok. exercise 119 [ scan/--domE] ... ok. exercise 120 [ scan/--domT] ... ok. exercise 121 [ scan/--incE] ... ok. exercise 122 [ scan/--incT] ... ok. exercise 123 [ scan/--incdomE] ... ok. exercise 124 [ scan/--incdomT] ... ok. exercise 125 [ scan/--incdomT] ... ok. exercise 126 [ scan/--cut_ga] ... ok. exercise 127 [ scan/--cut_nc] ... ok. exercise 128 [ scan/--cut_tc] ... ok. exercise 129 [ scan/--max] ... ok. exercise 130 [ scan/--F1] ... ok. exercise 131 [ scan/--F2] ... ok. exercise 132 [ scan/--F3] ... ok. exercise 133 [ scan/--nobias] ... ok. exercise 134 [ scan/--nonull2] ... ok. exercise 135 [ scan/-Z] ... ok. exercise 136 [ scan/--domZ] ... ok. exercise 137 [ scan/--seed] ... ok. exercise 138 [ scan/--qformat] ... ok. exercise 139 [ scan/--cpu] ... ok. exercise 140 [ jackhmmer] ... ok. exercise 141 [ j/-h] ... ok. exercise 142 [ j/-N] ... ok. exercise 143 [ j/-o] ... ok. exercise 144 [ j/-A] ... ok. exercise 145 [ j/--tblout] ... ok. exercise 146 [ j/--domtblout] ... ok. exercise 147 [ j/--chkhmm] ... ok. exercise 148 [ j/--chkali] ... ok. exercise 149 [ j/--acc] ... ok. exercise 150 [ j/--noali] ... ok. exercise 151 [ j/--notextw] ... ok. exercise 152 [ j/--textw] ... ok. exercise 153 [ j/--popen] ... ok. exercise 154 [ j/--pextend] ... ok. exercise 155 [ j/--mxfile] ... ok. exercise 156 [ j/-E] ... ok. exercise 157 [ j/-T] ... ok. exercise 158 [ j/--domE] ... ok. exercise 159 [ j/--domT] ... ok. exercise 160 [ j/--incE] ... ok. exercise 161 [ j/--incT] ... ok. exercise 162 [ j/--incdomE] ... ok. exercise 163 [ j/--incdomT] ... ok. exercise 164 [ j/--max] ... ok. exercise 165 [ j/--F1] ... ok. exercise 166 [ j/--F2] ... ok. exercise 167 [ j/--F3] ... ok. exercise 168 [ j/--nobias] ... ok. exercise 169 [ j/--EmL] ... ok. exercise 170 [ j/--EmN] ... ok. exercise 171 [ j/--EvL] ... ok. exercise 172 [ j/--EvN] ... ok. exercise 173 [ j/--EfL] ... ok. exercise 174 [ j/--EfN] ... ok. exercise 175 [ j/--Eft] ... ok. exercise 176 [ j/--nonull2] ... ok. exercise 177 [ j/-Z] ... ok. exercise 178 [ j/--domZ] ... ok. exercise 179 [ j/--seed] ... ok. exercise 180 [ j/--qformat] ... ok. exercise 181 [ j/--tformat] ... ok. exercise 182 [ phmmer] ... ok. exercise 183 [ phmmer/-h] ... ok. exercise 184 [ phmmer/-o] ... ok. exercise 185 [ phmmer/-A] ... ok. exercise 186 [ phmmer/--tblout] ... ok. exercise 187 [ phmmer/--domtblout] ... ok. exercise 188 [ phmmer/--pfamtblout] ... ok. exercise 189 [ phmmer/--acc] ... ok. exercise 190 [ phmmer/--noali] ... ok. exercise 191 [ phmmer/--notextw] ... ok. exercise 192 [ phmmer/--textw] ... ok. exercise 193 [ phmmer/--popen] ... ok. exercise 194 [ phmmer/--pextend] ... ok. exercise 195 [ phmmer/--mxfile] ... ok. exercise 196 [ phmmer/-E] ... ok. exercise 197 [ phmmer/-T] ... ok. exercise 198 [ phmmer/--domE] ... ok. exercise 199 [ phmmer/--domT] ... ok. exercise 200 [ phmmer/--incE] ... ok. exercise 201 [ phmmer/--incT] ... ok. exercise 202 [ phmmer/--incdomE] ... ok. exercise 203 [ phmmer/--incdomT] ... ok. exercise 204 [ phmmer/--max] ... ok. exercise 205 [ phmmer/--F1] ... ok. exercise 206 [ phmmer/--F2] ... ok. exercise 207 [ phmmer/--F3] ... ok. exercise 208 [ phmmer/--nobias] ... ok. exercise 209 [ phmmer/--EmL] ... ok. exercise 210 [ phmmer/--EmN] ... ok. exercise 211 [ phmmer/--EvL] ... ok. exercise 212 [ phmmer/--EvN] ... ok. exercise 213 [ phmmer/--EfL] ... ok. exercise 214 [ phmmer/--EfN] ... ok. exercise 215 [ phmmer/--Eft] ... ok. exercise 216 [ phmmer/--nonull2] ... ok. exercise 217 [ phmmer/-Z] ... ok. exercise 218 [ phmmer/--domZ] ... ok. exercise 219 [ phmmer/--seed] ... ok. exercise 220 [ phmmer/--qformat] ... ok. exercise 221 [ phmmer/--tformat] ... ok. exercise 222 [ nhmmer] ... ok. exercise 223 [ nhmmer/-h] ... ok. exercise 224 [ nhmmer/-o] ... ok. exercise 225 [ nhmmer/-A] ... ok. exercise 226 [ nhmmer/--tblout] ... ok. exercise 227 [ nhmmer/--dfamtblout] ... ok. exercise 228 [ nhmmer/--acc] ... ok. exercise 229 [ nhmmer/--noali] ... ok. exercise 230 [ nhmmer/--notextw] ... ok. exercise 231 [ nhmmer/--textw] ... ok. exercise 232 [ nhmmer/-E] ... ok. exercise 233 [ nhmmer/-T] ... ok. exercise 234 [ nhmmer/--incE] ... ok. exercise 235 [ nhmmer/--incT] ... ok. exercise 236 [ nhmmer/--max] ... ok. exercise 237 [ nhmmer/--F1] ... ok. exercise 238 [ nhmmer/--F2] ... ok. exercise 239 [ nhmmer/--F3] ... ok. exercise 240 [ nhmmer/--nobias] ... ok. exercise 241 [ nhmmer/--nonull2] ... ok. exercise 242 [ nhmmer/-Z] ... ok. exercise 243 [ nhmmer/--seed] ... ok. exercise 244 [ nhmmscan] ... ok. exercise 245 [ nhmmscan/-h] ... ok. exercise 246 [ nhmmscan/-o] ... ok. exercise 247 [ nhmmscan/--tblout] ... ok. exercise 248 [nhmmscan/--dfamtblout] ... ok. exercise 249 [ nhmmscan/--acc] ... ok. exercise 250 [ nhmmscan/--noali] ... ok. exercise 251 [ nhmmscan/--notextw] ... ok. exercise 252 [ nhmmscan/--textw] ... ok. exercise 253 [ nhmmscan/-E] ... ok. exercise 254 [ nhmmscan/-T] ... ok. exercise 255 [ nhmmscan/--incE] ... ok. exercise 256 [ nhmmscan/--incT] ... ok. exercise 257 [ nhmmscan/--max] ... ok. exercise 258 [ nhmmscan/--F1] ... ok. exercise 259 [ nhmmscan/--F2] ... ok. exercise 260 [ nhmmscan/--F3] ... ok. exercise 261 [ nhmmscan/--nobias] ... ok. exercise 262 [ nhmmscan/--nonull2] ... ok. exercise 263 [ nhmmscan/-Z] ... ok. exercise 264 [ nhmmscan/--seed] ... ok. exercise 265 [ hmmemit] ... ok. exercise 266 [ hmmemit/-h] ... ok. exercise 267 [ hmmemit/-c] ... ok. exercise 268 [ hmmemit/-o] ... ok. exercise 269 [ hmmemit/-p] ... ok. exercise 270 [ hmmemit/-N] ... ok. exercise 271 [ hmmemit/-L] ... ok. exercise 272 [ hmmemit/--local] ... ok. exercise 273 [ hmmemit/--unilocal] ... ok. exercise 274 [ hmmemit/--glocal] ... ok. exercise 275 [ hmmemit/--uniglocal] ... ok. exercise 276 [ hmmfetch] ... ok. exercise 277 [ hmmstat] ... ok. exercise 278 [ hmmlogo] ... ok. exercise 279 [ hmmconvert] ... ok. exercise 280 [ hmmsim] ... ok. exercise 281 [ hmmbuild_variation] ... ok. exercise 282 [ hmmscan_variation] ... ok. exercise 283 [ hmmsearch_variation] ... ok. exercise 284 [ phmmer_variation] ... ok. exercise 285 [ mapali] ... ok. exercise 286 [ fragments] ... ok. exercise 287 [ nonresidues] ... ok. exercise 288 [ opt-annotation] ... ok. exercise 289 [ dup-names] ... ok. exercise 290 [ mapali-again] ... ok. exercise 291 [ delete-corruption] ... ok. exercise 292 [ msa-integrity] ... ok. exercise 293 [ hmmemit-consensus] ... ok. exercise 294 [ hmmconvert] ... ok. exercise 295 [ stdin_pipes] ... ok. exercise 296 [ nhmmer_generic] ... ok. exercise 297 [ hmmpgmd_ga] ... ok. exercise 298 [ rewind] ... ok. exercise 299 [ hmmpgmd_shard_ga] ... ok. exercise 300 [ bad-fasta] ... ok. exercise 301 [ brute-itest] ... ok. exercise 302 [ hmmpress-itest] ... ok. exercise 303 [ h39] ... ok. exercise 304 [ h45] ... ok. exercise 305 [ h50] ... ok. exercise 306 [ h82] ... ok. exercise 307 [ iss159] ... ok. All 307 exercises at level <= 2 passed. System information: Sat Feb 8 21:47:43 -12 2025 Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/testsuite' make[2]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' if tail -n 6 debian/test_log | head -n 1 | grep -q FAILED ; then false ; fi make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_auto_install make -j16 install DESTDIR=/build/reproducible-path/hmmer-3.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' SUBDIR easel make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' SUBDIR miniapps make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/easel' SUBDIR src make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' SUBDIR impl_sse make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' SUBDIR profmark /usr/bin/install -c -d /build/reproducible-path/hmmer-3.3.2+dfsg/debian/tmp/usr/bin /usr/bin/install -c -d /build/reproducible-path/hmmer-3.3.2+dfsg/debian/tmp/usr/share/man/man1 make -C src install make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \ /usr/bin/install -c -m 0755 $file /build/reproducible-path/hmmer-3.3.2+dfsg/debian/tmp/usr/bin/ ;\ done make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/src' make -C documentation install make[3]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/documentation' make -C man install make[4]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg/documentation/man' for file in hmmer hmmalign hmmbuild hmmc2 hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /usr/bin/install -c -m 0664 $file.man /build/reproducible-path/hmmer-3.3.2+dfsg/debian/tmp/usr/share/man/man1/${file}.1 ;\ done make[4]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/documentation/man' make[3]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg/documentation' make[2]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' mkdir -p /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer/usr/lib/x86_64-linux-gnu/hmmer/ cp src/hmmc2 /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer/usr/lib/x86_64-linux-gnu/hmmer/ make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_installexamples mkdir -p /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/impl find src/ -maxdepth 1 -name "*_utest" -exec cp \{\} /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/ \; find src/impl_sse -name "*_utest" -exec cp \{\} /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src/impl \; cp src/itest_brute /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src cp src/hmmpress.itest.pl /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples/src cp -aR testsuite /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples find easel -name "*.o" -delete cp -aR easel /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples cp -aR tutorial /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples find /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples -name 'Makefile' | xargs sed -i "s^/build/reproducible-path/hmmer-3.3.2+dfsg^.^g" find /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples -name "esltmp*" -delete make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_compress -Xtutorial/ make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/hmmer-3.3.2+dfsg' dh_fixperms find debian -name .dropbox.attr -delete find debian -name "*.fa" -executable -exec chmod -x \{\} \; find /build/reproducible-path/hmmer-3.3.2+dfsg/debian/hmmer-examples/usr/share/doc/hmmer/examples -name "*.man" -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/hmmer-3.3.2+dfsg' 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 'hmmer' in '../hmmer_3.3.2+dfsg-1_amd64.deb'. dpkg-deb: building package 'hmmer-dbgsym' in '../hmmer-dbgsym_3.3.2+dfsg-1_amd64.deb'. dpkg-deb: building package 'hmmer-doc' in '../hmmer-doc_3.3.2+dfsg-1_all.deb'. dpkg-deb: building package 'hmmer-examples' in '../hmmer-examples_3.3.2+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hmmer_3.3.2+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from hmmer-3.3.2+dfsg/debian/source/options: --extend-diff-ignore=(^|/)config.(sub|guess)$ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/3693795 and its subdirectories I: Current time: Sat Feb 8 21:48:48 -12 2025 I: pbuilder-time-stamp: 1739094528 Mon Jan 8 03:25:43 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Mon Jan 8 03:25:43 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Mon Jan 8 04:53:38 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Mon Jan 8 04:53:39 UTC 2024 I: hmmer_3.3.2+dfsg-1_amd64.changes: Format: 1.8 Date: Thu, 31 Dec 2020 11:50:25 +0100 Source: hmmer Binary: hmmer hmmer-dbgsym hmmer-doc hmmer-examples Architecture: amd64 all Version: 3.3.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: hmmer - profile hidden Markov models for protein sequence analysis hmmer-doc - profile hidden Markov models for protein sequence analysis (docs) hmmer-examples - profile hidden Markov models for protein sequence analysis (examp Changes: hmmer (3.3.2+dfsg-1) unstable; urgency=medium . * Team upload. * debian/watch: fix version matching * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * debian/control: mark the '-doc' package as Multi-Arch: foreign * Refresh the patches. * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * debian/upstream/metadata: document their GitHub repo Checksums-Sha1: 03372d245019d172dc4e8a825c859a33be0653f7 11788004 hmmer-dbgsym_3.3.2+dfsg-1_amd64.deb 5a7df7dd144e14eec436c3cc48533e3ff84a3db4 771480 hmmer-doc_3.3.2+dfsg-1_all.deb 3e680bd15daff008a56bf4238e8fceba1f986975 32306668 hmmer-examples_3.3.2+dfsg-1_all.deb 24f7722524ecef9c952352190937e49659d6ac63 6388 hmmer_3.3.2+dfsg-1_amd64.buildinfo b4a799d2dd656912ddd469eceefb22d9456a55a9 1153244 hmmer_3.3.2+dfsg-1_amd64.deb Checksums-Sha256: ef462cc0f422b2db64a552e4b1db2f722c6e0029c2aee35b0aa088f4ca5b5bbb 11788004 hmmer-dbgsym_3.3.2+dfsg-1_amd64.deb 6dfd02da3c06228e52df393f7999056b025bff93fb795b9847f32430ddbd531c 771480 hmmer-doc_3.3.2+dfsg-1_all.deb f0266909f2e1ad0d8020ccb0f4119efa9e5f7f47ee526f3b8f4ed9a02b29a4b6 32306668 hmmer-examples_3.3.2+dfsg-1_all.deb a3243068f35ee4ab4b33f6b15fe4a4997cb726465bff2ab2536e043c5f6ff5ce 6388 hmmer_3.3.2+dfsg-1_amd64.buildinfo 70190f5dff154cd9d6e35b0168891f75ab2328a5ff77d1e1ae2d8a61638ff7b4 1153244 hmmer_3.3.2+dfsg-1_amd64.deb Files: 63922c5339784089182e674a08a3504e 11788004 debug optional hmmer-dbgsym_3.3.2+dfsg-1_amd64.deb 3e9bd4215ad06542e947522cea983378 771480 doc optional hmmer-doc_3.3.2+dfsg-1_all.deb c457a7293b5dcafd90c1c47261940cc7 32306668 doc optional hmmer-examples_3.3.2+dfsg-1_all.deb 8dabc136b2a61d95e17f94105f70e19b 6388 science optional hmmer_3.3.2+dfsg-1_amd64.buildinfo 4aa1d1c3ababfcdbe467ce4bba52dda2 1153244 science optional hmmer_3.3.2+dfsg-1_amd64.deb Mon Jan 8 04:53:40 UTC 2024 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bmmNZzAk/hmmer_3.3.2+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bmmNZzAk/hmmer_3.3.2+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bmmNZzAk/hmmer_3.3.2+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bmmNZzAk/b1/hmmer_3.3.2+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bmmNZzAk/b2/hmmer_3.3.2+dfsg-1_amd64.changes ## close_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer 0.000s 2 calls diffoscope.comparators.gzip.GzipContainer ## command (total time: 22.550s) 11.686s 3041 calls diff 4.964s 30832 calls readelf 4.580s 6 calls xz 0.764s 902 calls strings 0.143s 11 calls nm 0.110s 1804 calls objdump 0.098s 26 calls cmp 0.097s 26 calls cmp (external) 0.096s 2 calls gzip 0.008s 85 calls cmp (internal) 0.005s 164 calls objcopy ## compare_files (cumulative) (total time: 303.640s) 45.097s 1 call abc.DotChangesFile 45.008s 1 call abc.DebFile 44.729s 2 calls abc.XzFile 40.038s 1 call abc.DebDataTarFile 38.118s 1 call abc.GzipFile 38.009s 1 call abc.ArFile 37.362s 82 calls abc.ElfFile 8.409s 738 calls diffoscope.comparators.elf.ElfSection 4.827s 82 calls diffoscope.comparators.elf.ElfCodeSection 1.936s 164 calls diffoscope.comparators.elf.ElfStringSection 0.075s 1 call abc.TarFile 0.032s 1 call abc.Md5sumsFile ## container_extract (total time: 5.772s) 4.580s 6 calls diffoscope.comparators.xz.XzContainer 0.760s 1476 calls diffoscope.comparators.deb.DebTarContainer 0.241s 8 calls diffoscope.comparators.deb.DebContainer 0.096s 2 calls diffoscope.comparators.gzip.GzipContainer 0.086s 164 calls diffoscope.comparators.ar.ArContainer 0.008s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 16.078s) 16.078s 10220 calls linediff ## has_same_content_as (total time: 0.120s) 0.059s 82 calls abc.ElfFile 0.030s 4 calls abc.DebFile 0.024s 1 call abc.DebDataTarFile 0.004s 738 calls diffoscope.comparators.elf.ElfSection 0.001s 164 calls diffoscope.comparators.elf.ElfStringSection 0.001s 2 calls abc.Md5sumsFile 0.001s 82 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 2 calls abc.TextFile 0.000s 2 calls abc.XzFile 0.000s 1 call abc.TarFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.GzipFile 0.000s 1 call abc.ArFile ## main (total time: 224.982s) 224.978s 2 calls outputs 0.004s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 6 calls diffoscope.comparators.xz.XzContainer 0.000s 4 calls diffoscope.comparators.tar.TarContainer 0.000s 2 calls diffoscope.comparators.deb.DebTarContainer 0.000s 2 calls diffoscope.comparators.deb.DebContainer 0.000s 2 calls diffoscope.comparators.ar.ArContainer 0.000s 2 calls diffoscope.comparators.gzip.GzipContainer ## output (total time: 178.203s) 178.141s 1 call html 0.038s 1 call text 0.024s 1 call json ## recognizes (total time: 2.799s) 1.197s 12 calls diffoscope.comparators.binary.FilesystemFile 0.958s 16236 calls diffoscope.comparators.elf.ElfSection 0.246s 5498 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.202s 3608 calls diffoscope.comparators.elf.ElfStringSection 0.112s 1804 calls diffoscope.comparators.elf.ElfCodeSection 0.042s 216 calls diffoscope.comparators.debian.DebControlMember 0.042s 372 calls diffoscope.comparators.utils.archive.ArchiveMember 0.000s 10 calls abc.DotChangesFile 0.000s 16 calls abc.Md5sumsFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink ## specialize (total time: 1.797s) 1.797s 1082 calls specialize Mon Jan 8 04:57:26 UTC 2024 E: hmmer failed to build reproducibly in bullseye on amd64. Mon Jan 8 04:57:26 UTC 2024 E: diffoscope 240 found issues, please check https://tests.reproducible-builds.org/debian/dbd/bullseye/amd64/hmmer_3.3.2+dfsg-1.diffoscope.html Mon Jan 8 04:57:29 UTC 2024 I: Submitting .buildinfo files to external archives: Mon Jan 8 04:57:29 UTC 2024 I: Submitting 8.0K b1/hmmer_3.3.2+dfsg-1_amd64.buildinfo.asc Mon Jan 8 04:57:30 UTC 2024 I: Submitting 8.0K b2/hmmer_3.3.2+dfsg-1_amd64.buildinfo.asc Mon Jan 8 04:57:31 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 8 04:57:31 UTC 2024 I: Done submitting .buildinfo files. Mon Jan 8 04:57:31 UTC 2024 I: Removing signed hmmer_3.3.2+dfsg-1_amd64.buildinfo.asc files: removed './b1/hmmer_3.3.2+dfsg-1_amd64.buildinfo.asc' removed './b2/hmmer_3.3.2+dfsg-1_amd64.buildinfo.asc'