Fri May 29 03:59:12 UTC 2020 I: starting to build hmmer2/buster/armhf on jenkins on '2020-05-29 03:58' Fri May 29 03:59:12 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_27/1784/console.log Fri May 29 03:59:12 UTC 2020 I: Downloading source for buster/hmmer2=2.3.2+dfsg-6 --2020-05-29 03:59:12-- http://deb.debian.org/debian/pool/main/h/hmmer2/hmmer2_2.3.2+dfsg-6.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2282 (2.2K) Saving to: ‘hmmer2_2.3.2+dfsg-6.dsc’ 0K .. 100% 243M=0s 2020-05-29 03:59:12 (243 MB/s) - ‘hmmer2_2.3.2+dfsg-6.dsc’ saved [2282/2282] Fri May 29 03:59:13 UTC 2020 I: hmmer2_2.3.2+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: hmmer2 Binary: hmmer2, hmmer2-pvm, hmmer2-doc, libhmmer2-dev Architecture: any all Version: 2.3.2+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Laszlo Kajan Homepage: http://hmmer.janelia.org/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/hmmer2 Vcs-Git: https://salsa.debian.org/med-team/hmmer2.git Testsuite: autopkgtest Testsuite-Triggers: libperl4-corelibs-perl Build-Depends: debhelper (>= 10), pvm-dev, libperl4-corelibs-perl, libsquid-dev, pkg-config, dh-exec, rename Package-List: hmmer2 deb science optional arch=any hmmer2-doc deb doc optional arch=all hmmer2-pvm deb science optional arch=any libhmmer2-dev deb libdevel optional arch=any Checksums-Sha1: 7467176def6174e90edd239558b6fcc2cb8033df 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 60124b87ea795111d002ee8f7aadb5263661db82 12844 hmmer2_2.3.2+dfsg-6.debian.tar.xz Checksums-Sha256: f9cd50acc23743648cb7de020c249bce396c3d07e0afe7e5418620cffa07bb44 331828 hmmer2_2.3.2+dfsg.orig.tar.xz dff2495a597ed3ea64790628cbbd93c5b55a564cd500e1d18ba27e5c279e6e08 12844 hmmer2_2.3.2+dfsg-6.debian.tar.xz Files: 4f8c9fd7c7de00fb8cfab499931ee4ba 331828 hmmer2_2.3.2+dfsg.orig.tar.xz 6985c0a0cadf2c51ae1191d2f83f39f6 12844 hmmer2_2.3.2+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluosDARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHrVQ/+LlXjYHLh4iZDNGWzCFr0Dk5zJghYCAhJ QTNcy87sG7iPmalhh/iugtNCh3CNRImdnowqWQQN/jSHNeHRD2c1gGzxfyTXtJ06 HF8LsfJms3Y63xHB0O3vawlqr7CBu6bXpZHjRqJZm7vOE+36RRT6TYFge6ZS5H9A DjSww6dtTt+/rgr88V9obnWf380zqKkcT80+56YidLuFxXSqUvd8UNw4SIjFQMfG ceXET4rlLKc5mwWY2WhJM51VnG9gco3Zafv23xvBqKM1KDrGm4zIqxyoBjed2Uf9 H1McS2jqeuNFV7GrpJ30c88n81x0+dNeaRmXFG+8RPeePc/TlXzzmjckw3bQcdFc chRCYXHBp5F+49qKAWnAJ5mz9AxJk6vQUxG0HQyLE3SkNjCp61/EXf0bJJDGjLdZ ph7XzX6JexnVybgMRSMveK3dl6Da31rF7BqWLKW7y/rVoEMa6EMFRmSZiWdJIW4F 70cbMMuHJrHhcLYGKFfEpl+xgFd8MiL5Cwd+CQQlgNr4faLCQE1c3pGc44cpQ0Lh 8pQ2BPlf8RE2ARur/JUnjgItWc26L2eM+jiAHlpZevoOKzDJEcrFEZhHEF9NvSV+ z7M5UUc+ubC6reNiEaJk9QoTNktQiWbRjk+zipBPg5fe6+J8VqGhtCb0/ia7qnA1 ZPdmUv0JWeU= =uq1n -----END PGP SIGNATURE----- Fri May 29 03:59:13 UTC 2020 I: Checking whether the package is not for us Fri May 29 03:59:13 UTC 2020 I: Starting 1st build on remote node odu3a-armhf-rb.debian.net. Fri May 29 03:59:13 UTC 2020 I: Preparing to do remote build '1' on odu3a-armhf-rb.debian.net. Fri May 29 04:01:40 UTC 2020 I: Deleting $TMPDIR on odu3a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 28 15:59:19 -12 2020 I: pbuilder-time-stamp: 1590724759 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [hmmer2_2.3.2+dfsg-6.dsc] I: copying [./hmmer2_2.3.2+dfsg.orig.tar.xz] I: copying [./hmmer2_2.3.2+dfsg-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Sep 23 21:36:48 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hmmer2_2.3.2+dfsg-6.dsc dpkg-source: info: extracting hmmer2 in hmmer2-2.3.2+dfsg dpkg-source: info: unpacking hmmer2_2.3.2+dfsg.orig.tar.xz dpkg-source: info: unpacking hmmer2_2.3.2+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying version2-manpage dpkg-source: info: applying userguidepdf dpkg-source: info: applying spelling.patch dpkg-source: info: applying use_debian_packaged_biosquid.patch dpkg-source: info: applying build_libhmmer.a_with-fPIC.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 10), pvm-dev, libperl4-corelibs-perl, libsquid-dev, pkg-config, dh-exec, rename dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 (>= 10); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on pvm-dev; however: Package pvm-dev is not installed. pbuilder-satisfydepends-dummy depends on libperl4-corelibs-perl; however: Package libperl4-corelibs-perl is not installed. pbuilder-satisfydepends-dummy depends on libsquid-dev; however: Package libsquid-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libperl4-corelibs-perl{a} libpipeline1{a} libpvm3{a} libreadline-dev{a} libreadline7{a} libsigsegv2{a} libsquid-dev{a} libsquid1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} openssh-client{a} pkg-config{a} po-debconf{a} pvm{a} pvm-dev{a} readline-common{a} rename{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 22.6 MB of archives. After unpacking 75.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 11 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 12 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 14 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 17 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 20 http://deb.debian.org/debian buster/main armhf openssh-client armhf 1:7.9p1-10+deb10u2 [704 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 22 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 23 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 24 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 26 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 28 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 33 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 39 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 40 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 41 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 42 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 43 http://deb.debian.org/debian buster/main armhf dh-exec armhf 0.23.1 [24.9 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libncurses-dev armhf 6.1+20181013-2+deb10u2 [295 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libperl4-corelibs-perl all 0.004-1+deb10u1 [38.4 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libpvm3 armhf 3.4.6-2 [76.3 kB] Get: 47 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libreadline-dev armhf 7.0-5 [121 kB] Get: 49 http://deb.debian.org/debian buster/main armhf libsquid1 armhf 1.9g+cvs20050121-11 [63.4 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libsquid-dev armhf 1.9g+cvs20050121-11 [375 kB] Get: 51 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB] Get: 52 http://deb.debian.org/debian buster/main armhf pvm armhf 3.4.6-2 [149 kB] Get: 53 http://deb.debian.org/debian buster/main armhf pvm-dev armhf 3.4.6-2 [262 kB] Get: 54 http://deb.debian.org/debian buster/main armhf rename all 1.10-1 [17.2 kB] Fetched 22.6 MB in 4s (5503 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../06-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../09-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../12-libedit2_3.1-20181209-1_armhf.deb ... Unpacking libedit2:armhf (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../13-libkeyutils1_1.6-6_armhf.deb ... Unpacking libkeyutils1:armhf (1.6-6) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../14-libkrb5support0_1.17-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.17-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../15-libk5crypto3_1.17-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.17-3) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../16-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../17-libkrb5-3_1.17-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.17-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../18-libgssapi-krb5-2_1.17-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.17-3) ... Selecting previously unselected package openssh-client. Preparing to unpack .../19-openssh-client_1%3a7.9p1-10+deb10u2_armhf.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../20-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../21-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../22-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../23-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../24-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../25-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../26-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. 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I: Building the package I: Running cd /build/hmmer2-2.3.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package hmmer2 dpkg-buildpackage: info: source version 2.3.2+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg' dh_auto_configure -- --enable-threads --enable-lfs --enable-pvm ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --enable-threads --enable-lfs --enable-pvm configure: configuring HMMER for your system. configure: This is a full source distribution - using full config checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... 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 ANSI C... none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking whether your make is GNU make... yes, it is. configure: configured for optional LFS, large file support configure: enabled optional PVM (Parallel Virtual Machine) support configure: enabled POSIX multithreading support checking for pthread_setconcurrency... no checking for pthread_attr_setscope... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes configure: creating ./config.status config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating Makefile config.status: creating src/config.h # avoid duplicated definition of PACKAGE_NAME (basically conflicting with biosquid when used together) sed -i -e '/^#define PACKAGE_NAME /i #ifndef PACKAGE_NAME' \ -e '/^#define PACKAGE_NAME /a #endif' \ -e '/^#define PACKAGE_VERSION /i #ifndef PACKAGE_VERSION' \ -e '/^#define PACKAGE_VERSION /a #endif' \ -e '/^#define _LARGEFILE_SOURCE /i #ifndef _LARGEFILE_SOURCE' \ -e '/^#define _LARGEFILE_SOURCE /a #endif' \ -e '/^#define _LARGEFILE64_SOURCE /i #ifndef _LARGEFILE64_SOURCE' \ -e '/^#define _LARGEFILE64_SOURCE /a #endif' \ -e '/^#define VERSION /i #ifndef VERSION' \ -e '/^#define VERSION /a #endif' \ src/config.h make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' dh_auto_build make -j3 make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg' make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg/src' gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmalign.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c alphabet.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c core_algorithms.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c debug.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c display.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c emit.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c emulation.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c fast_algorithms.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c histogram.c histogram.c: In function 'ExtremeValueSetHistogram': histogram.c:725:23: warning: implicit declaration of function 'IncompleteGamma'; did you mean 'SampleGamma'? [-Wimplicit-function-declaration] h->chip = (float) IncompleteGamma((double)(nbins-1-ndegrees)/2., ^~~~~~~~~~~~~~~ SampleGamma gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmio.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c mathsupport.c mathsupport.c: In function 'Logp_cvec': mathsupport.c:229:15: warning: implicit declaration of function 'Gammln'; did you mean 'daemon'? [-Wimplicit-function-declaration] lnp += Gammln(alpha[x] + cvec[x]); ^~~~~~ daemon gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c masks.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c misc.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c modelmakers.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c plan7.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c plan9.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c postprob.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c prior.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c pvm.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c threads.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c tophits.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c trace.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmbuild.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmcalibrate.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmconvert.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmemit.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmfetch.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmindex.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmpfam.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmsearch.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmcalibrate-pvm.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmpfam-pvm.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H -pthread `pkg-config --cflags libsquid` -I/include -c hmmsearch-pvm.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmalign hmmalign.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmbuild hmmbuild.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmcalibrate hmmcalibrate.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmconvert hmmconvert.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmemit hmmemit.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmfetch hmmfetch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmindex hmmindex.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmpfam hmmpfam.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmsearch hmmsearch.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmcalibrate-pvm hmmcalibrate-pvm.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmpfam-pvm hmmpfam-pvm.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -pthread -DHAVE_CONFIG_H -Wl,-z,relro -Wl,-z,now -L/lib/ -o hmmsearch-pvm hmmsearch-pvm.o alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o -lpvm3 `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg/src' /usr/bin/ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o display.o emit.o emulation.o fast_algorithms.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o postprob.o prior.o pvm.o threads.o tophits.o trace.o a - alphabet.o a - core_algorithms.o a - debug.o a - display.o a - emit.o a - emulation.o a - fast_algorithms.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - postprob.o a - prior.o a - pvm.o a - threads.o a - tophits.o a - trace.o ranlib libhmmer.a chmod 644 libhmmer.a make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/src' make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg/testsuite' gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c alignalign_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c evd_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c masks_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c parsingviterbi_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c tophits_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c trace_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c viterbi_exercise.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_CONFIG_H `pkg-config --cflags libsquid` -I../src -c weeviterbi_test.c gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o alignalign_test -L../src alignalign_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o evd_test -L../src evd_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o masks_test -L../src masks_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o parsingviterbi_test -L../src parsingviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o tophits_test -L../src tophits_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o trace_test -L../src trace_test.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o viterbi_exercise -L../src viterbi_exercise.o -lhmmer `pkg-config --libs libsquid` -lm gcc -g -O2 -ffile-prefix-map=/build/hmmer2-2.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -pthread -Wl,-z,relro -Wl,-z,now -DHAVE_CONFIG_H -o weeviterbi_test -L../src weeviterbi_test.o -lhmmer `pkg-config --libs libsquid` -lm make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' dh_auto_test make -j3 check VERBOSE=1 make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg' (cd testsuite; make check) make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg/testsuite' make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Running test suite exercises. Warning: some tests may take several minutes to complete. ./sqc 2 exercises.sqc . ../src exercise 1 [ hmmalign] ... ok. exercise 2 [ hmmalign/h] ... ok. exercise 3 [ hmmalign/m] ... ok. exercise 4 [ hmmalign/o] ... ok. exercise 5 [ hmmalign/q] ... ok. exercise 6 [ hmmalign/informat] ... ok. exercise 7 [ hmmalign/selex] ... ok. exercise 8 [ hmmalign/a2m] ... ok. exercise 9 [ hmmalign/clustal] ... ok. exercise 10 [ hmmalign/msf] ... ok. exercise 11 [ hmmalign/phylip] ... ok. exercise 12 [ hmmalign/oneline] ... ok. exercise 13 [ hmmalign/withali] ... ok. exercise 14 [ hmmalign/mapali] ... ok. exercise 15 [ hmmbuild] ... ok. exercise 16 [ hmmbuild/h] ... ok. exercise 17 [ hmmbuild/F] ... ok. exercise 18 [ hmmbuild/n] ... ok. exercise 19 [ hmmbuild/o] ... ok. exercise 20 [ hmmbuild/A] ... ok. exercise 21 [ hmmbuild/f] ... ok. exercise 22 [ hmmbuild/g] ... ok. exercise 23 [ hmmbuild/s] ... ok. exercise 24 [ hmmbuild/fast] ... ok. exercise 25 [ hmmbuild/hand] ... ok. exercise 26 [ hmmbuild/null] ... ok. exercise 27 [ hmmbuild/pam] ... ok. exercise 28 [ hmmbuild/prior] ... ok. exercise 29 [ hmmbuild/wblosum] ... ok. exercise 30 [ hmmbuild/wgsc] ... ok. exercise 31 [ hmmbuild/wme] ... ok. exercise 32 [ hmmbuild/wpb] ... ok. exercise 33 [ hmmbuild/wvoronoi] ... ok. exercise 34 [ hmmbuild/wnone] ... ok. exercise 35 [ hmmbuild/noeff] ... ok. exercise 36 [ hmmbuild/pbswitch] ... ok. exercise 37 [ hmmbuild/amino] ... ok. exercise 38 [ hmmbuild/nucleic] ... ok. exercise 39 [ hmmbuild/archpri] ... ok. exercise 40 [ hmmbuild/binary] ... ok. exercise 41 [ hmmbuild/cfile] ... ok. exercise 42 [ hmmbuild/gapmax] ... ok. exercise 43 [ hmmbuild/idlevel] ... ok. exercise 44 [ hmmbuild/informat] ... ok. exercise 45 [ hmmbuild/pamwgt] ... ok. exercise 46 [ hmmbuild/swentry] ... ok. exercise 47 [ hmmbuild/swexit] ... ok. exercise 48 [ hmmbuild/verbose] ... ok. exercise 49 [ hmmcalibrate] ... ok. exercise 50 [ hmmcalibrate/h] ... ok. exercise 51 [ hmmcalibrate/fixed] ... ok. exercise 52 [ hmmcalibrate/mean] ... ok. exercise 53 [ hmmcalibrate/hist] ... ok. exercise 54 [ hmmcalibrate/num] ... ok. exercise 55 [ hmmcalibrate/sd] ... ok. exercise 56 [ hmmcalibrate/seed] ... ok. exercise 57 [ hmmconvert] ... ok. exercise 58 [ hmmconvert/h] ... ok. exercise 59 [ hmmconvert/F] ... ok. exercise 60 [ hmmconvert/a] ... ok. exercise 61 [ hmmconvert/A] ... ok. exercise 62 [ hmmconvert/b] ... ok. exercise 63 [ hmmconvert/p] ... ok. exercise 64 [ hmmconvert/P] ... ok. exercise 65 [ hmmemit] ... ok. exercise 66 [ hmmemit/a] ... ok. exercise 67 [ hmmemit/c] ... ok. exercise 68 [ hmmemit/h] ... ok. exercise 69 [ hmmemit/n] ... ok. exercise 70 [ hmmemit/o] ... ok. exercise 71 [ hmmemit/q] ... ok. exercise 72 [ hmmemit/seed] ... ok. exercise 73 [ hmmindex] ... ok. exercise 74 [ hmmindex/h] ... ok. exercise 75 [ hmmfetch] ... ok. exercise 76 [ hmmfetch/h] ... ok. exercise 77 [ hmmfetch/n] ... ok. exercise 78 [ hmmpfam] ... ok. exercise 79 [ hmmpfam/h] ... ok. exercise 80 [ hmmpfam/n] ... ok. exercise 81 [ hmmpfam/A] ... ok. exercise 82 [ hmmpfam/E] ... ok. exercise 83 [ hmmpfam/T] ... ok. exercise 84 [ hmmpfam/Z] ... ok. exercise 85 [ hmmpfam/acc] ... ok. exercise 86 [ hmmpfam/compat] ... ok. exercise 87 [ hmmpfam/cut_ga] ... ok. exercise 88 [ hmmpfam/cut_nc] ... ok. exercise 89 [ hmmpfam/cut_tc] ... ok. exercise 90 [ hmmpfam/domE] ... ok. exercise 91 [ hmmpfam/domT] ... ok. exercise 92 [ hmmpfam/forward] ... ok. exercise 93 [ hmmpfam/informat] ... ok. exercise 94 [ hmmpfam/null2] ... ok. exercise 95 [ hmmpfam/xnu] ... ok. exercise 96 [ hmmsearch] ... ok. exercise 97 [ hmmsearch/h] ... ok. exercise 98 [ hmmsearch/A] ... ok. exercise 99 [ hmmsearch/E] ... ok. exercise 100 [ hmmsearch/T] ... ok. exercise 101 [ hmmsearch/Z] ... ok. exercise 102 [ hmmsearch/compat] ... ok. exercise 103 [ hmmsearch/cut_ga] ... ok. exercise 104 [ hmmsearch/cut_nc] ... ok. exercise 105 [ hmmsearch/cut_tc] ... ok. exercise 106 [ hmmsearch/domE] ... ok. exercise 107 [ hmmsearch/domT] ... ok. exercise 108 [ hmmsearch/forward] ... ok. exercise 109 [ hmmsearch/informat] ... ok. exercise 110 [ hmmsearch/null2] ... ok. exercise 111 [ hmmsearch/xnu] ... ok. exercise 112 [ align_align] ... ok. exercise 113 [ evd] ... ok. exercise 114 [ masks] ... ok. exercise 115 [ parsingv] ... ok. exercise 116 [ tophits] ... ok. exercise 117 [ trace] ... ok. exercise 118 [ viterbi] ... ok. exercise 119 [ weeviterbi] ... ok. exercise 120 [ test1/conversion] ... ok. All 120 exercises at level <= 2 passed. System information: Thu May 28 16:01:01 -12 2020 Linux odu3a 4.19.0-9-armmp #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg/testsuite' make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg' dh_auto_install -- prefix=/build/hmmer2-2.3.2+dfsg/debian/tmp make -j3 install DESTDIR=/build/hmmer2-2.3.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/hmmer2-2.3.2\+dfsg/debian/tmp make[2]: Entering directory '/build/hmmer2-2.3.2+dfsg' mkdir -p /build/hmmer2-2.3.2+dfsg/debian/tmp/bin mkdir -p /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch hmmcalibrate-pvm hmmpfam-pvm hmmsearch-pvm; do\ cp src/$file /build/hmmer2-2.3.2+dfsg/debian/tmp/bin/;\ done for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\ cp documentation/man/$file.man /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/$file.1;\ done make[2]: Leaving directory '/build/hmmer2-2.3.2+dfsg' # lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1: rename 's/^hmm/hmm2/;' /build/hmmer2-2.3.2+dfsg/debian/tmp/bin/* cd /build/hmmer2-2.3.2+dfsg/debian/tmp/bin; rename 's/^hmm/hmm2/;' * cd /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' * mv /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmm2er.1 /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/hmmer2.1 # lkajan: resolve man page hypen issue: sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/hmmer2-2.3.2+dfsg/debian/tmp/share/man/man1/* make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg' dh_installchangelogs -k 00README make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' debian/rules override_dh_installexamples make[1]: Entering directory '/build/hmmer2-2.3.2+dfsg' dh_installexamples mkdir -p /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples; sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc rm -f testsuite/*.ssi; cp -a testsuite/* /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/; mkdir /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; cp -a tutorial/* /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial; sed -i "s#../tut#./tut#g" /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc find /build/hmmer2-2.3.2+dfsg/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/hmmer2-2.3.2+dfsg^.^g" make[1]: Leaving directory '/build/hmmer2-2.3.2+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package hmmer2-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package libhmmer2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2+dfsg-6_armhf.deb'. dpkg-deb: building package 'hmmer2-pvm' in '../hmmer2-pvm_2.3.2+dfsg-6_armhf.deb'. dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2+dfsg-6_all.deb'. dpkg-deb: building package 'libhmmer2-dev' in '../libhmmer2-dev_2.3.2+dfsg-6_armhf.deb'. dpkg-deb: building package 'hmmer2-pvm-dbgsym' in '../hmmer2-pvm-dbgsym_2.3.2+dfsg-6_armhf.deb'. dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2+dfsg-6_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hmmer2_2.3.2+dfsg-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/8038 and its subdirectories I: Current time: Thu May 28 16:01:26 -12 2020 I: pbuilder-time-stamp: 1590724886 Fri May 29 04:01:42 UTC 2020 I: 1st build successful. Starting 2nd build on remote node jtx1b-armhf-rb.debian.net. Fri May 29 04:01:42 UTC 2020 I: Preparing to do remote build '2' on jtx1b-armhf-rb.debian.net. Fri May 29 04:04:18 UTC 2020 I: Deleting $TMPDIR on jtx1b-armhf-rb.debian.net. Fri May 29 04:04:21 UTC 2020 I: hmmer2_2.3.2+dfsg-6_armhf.changes: Format: 1.8 Date: Mon, 24 Sep 2018 11:34:02 +0200 Source: hmmer2 Binary: hmmer2 hmmer2-dbgsym hmmer2-doc hmmer2-pvm hmmer2-pvm-dbgsym libhmmer2-dev Architecture: armhf all Version: 2.3.2+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: hmmer2 - profile hidden Markov models for protein sequence analysis hmmer2-doc - profile hidden Markov models for protein sequence analysis (docs) hmmer2-pvm - HMMER programs with PVM (Parallel Virtual Machine) support libhmmer2-dev - profile hidden Markov models for protein sequence analysis (devel Changes: hmmer2 (2.3.2+dfsg-6) unstable; urgency=medium . * Update watch file * Update d/copyright * Stick to debhelper 10 (in compat level 11 dh_auto_configure passes --runstatedir=/run to ./configure. This causes FTBFS.) * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 Checksums-Sha1: 8f35291fe56bd3ce8cd4863dbd10a8753c23ed09 1513460 hmmer2-dbgsym_2.3.2+dfsg-6_armhf.deb 3ce272d7b871b6937a32ac24d3fa5f51418424ba 79500 hmmer2-doc_2.3.2+dfsg-6_all.deb 2668d26b844b8c023dfa8da91a94cc5ae27f6328 506300 hmmer2-pvm-dbgsym_2.3.2+dfsg-6_armhf.deb e0b03a0543ed9491a6c7d83738abd113b95bc6be 79508 hmmer2-pvm_2.3.2+dfsg-6_armhf.deb 9d8b5f286cfd31ef5b969e15708996630cd2f9e7 6385 hmmer2_2.3.2+dfsg-6_armhf.buildinfo f0b752e4f2db82272738b580114d88d65b696e50 1530160 hmmer2_2.3.2+dfsg-6_armhf.deb d5c5abfaffe0362d05d8a28c5d3a7cfa9633f488 88980 libhmmer2-dev_2.3.2+dfsg-6_armhf.deb Checksums-Sha256: 940a2ff7a060e8004b09826239a04b9df5e340921de7daea77758cf9e720fd00 1513460 hmmer2-dbgsym_2.3.2+dfsg-6_armhf.deb 5aa29cd94b61422a7bd61f439b1b9a3fd1e4b894acae85debba40fdaa3f0f9e3 79500 hmmer2-doc_2.3.2+dfsg-6_all.deb ee0513eb219713ca91a779b1e70b0cab639d13893d810d05760521b9e0715443 506300 hmmer2-pvm-dbgsym_2.3.2+dfsg-6_armhf.deb 40ce578ccb0366a7bcbe5451cc08133bae0a31b931c73a79babf62f3fffa2982 79508 hmmer2-pvm_2.3.2+dfsg-6_armhf.deb db1d0e77a210be727a796fc82ae9d07fce5cad00a0c05b9132dba5881962dd86 6385 hmmer2_2.3.2+dfsg-6_armhf.buildinfo deb703555c809432def0e4e6485148fa5908130e0563d9e520a8c82f550ae739 1530160 hmmer2_2.3.2+dfsg-6_armhf.deb 7cec932038a336634ab3bf4f07988a7579bdc896c809c8879b278e0066ff8776 88980 libhmmer2-dev_2.3.2+dfsg-6_armhf.deb Files: d52f3cb3cf3bb4fd5008a2a0e23e5726 1513460 debug optional hmmer2-dbgsym_2.3.2+dfsg-6_armhf.deb c6b56133572c25f80b333569c20627f1 79500 doc optional hmmer2-doc_2.3.2+dfsg-6_all.deb 5424a0aa91c0b5e34301ce4b7840cbcd 506300 debug optional hmmer2-pvm-dbgsym_2.3.2+dfsg-6_armhf.deb 362b7c27665056dbea7d77997b4e925e 79508 science optional hmmer2-pvm_2.3.2+dfsg-6_armhf.deb 55a624b73619e388355f8383940e2c59 6385 science optional hmmer2_2.3.2+dfsg-6_armhf.buildinfo 756f5490e662c4d009fd80ad2d740d44 1530160 science optional hmmer2_2.3.2+dfsg-6_armhf.deb 4a38be465e641d8f87623c9585d98997 88980 libdevel optional libhmmer2-dev_2.3.2+dfsg-6_armhf.deb Fri May 29 04:04:24 UTC 2020 I: diffoscope 145 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.Og9iwk3w0A/hmmer2_2.3.2+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.Og9iwk3w0A/hmmer2_2.3.2+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.Og9iwk3w0A/hmmer2_2.3.2+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.Og9iwk3w0A/b1/hmmer2_2.3.2+dfsg-6_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.Og9iwk3w0A/b2/hmmer2_2.3.2+dfsg-6_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.690s) 0.690s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.119s) 0.119s 10 calls diffoscope.comparators.binary.FilesystemFile Fri May 29 04:05:56 UTC 2020 I: diffoscope 145 found no differences in the changes files, and a .buildinfo file also exists. Fri May 29 04:05:56 UTC 2020 I: hmmer2 from buster built successfully and reproducibly on armhf. Fri May 29 04:05:57 UTC 2020 I: Submitting .buildinfo files to external archives: Fri May 29 04:05:57 UTC 2020 I: Submitting 8.0K b1/hmmer2_2.3.2+dfsg-6_armhf.buildinfo.asc Fri May 29 04:05:59 UTC 2020 I: Submitting 8.0K b2/hmmer2_2.3.2+dfsg-6_armhf.buildinfo.asc Fri May 29 04:06:00 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 29 04:06:00 UTC 2020 I: Done submitting .buildinfo files. Fri May 29 04:06:00 UTC 2020 I: Removing signed hmmer2_2.3.2+dfsg-6_armhf.buildinfo.asc files: removed './b1/hmmer2_2.3.2+dfsg-6_armhf.buildinfo.asc' removed './b2/hmmer2_2.3.2+dfsg-6_armhf.buildinfo.asc'