I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 22 07:52:51 -12 2020 I: pbuilder-time-stamp: 1600804371 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: using eatmydata during job I: Copying source file I: copying [infernal_1.1.2-2.dsc] I: copying [./infernal_1.1.2.orig.tar.gz] I: copying [./infernal_1.1.2-2.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 Jul 15 22:31:51 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 ./infernal_1.1.2-2.dsc dpkg-source: info: extracting infernal in infernal-1.1.2 dpkg-source: info: unpacking infernal_1.1.2.orig.tar.gz dpkg-source: info: unpacking infernal_1.1.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch dpkg-source: info: applying autoreconf.patch dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/6482/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='041d6c31e75e41848745a4808ad8df3b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='6482' 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/tmp.Xo0adYPxVm/pbuilderrc_kN6m --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Xo0adYPxVm/b1 --logfile b1/build.log infernal_1.1.2-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux profitbricks-build12-i386 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 20 20:25 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/6482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), libperl4-corelibs-perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libperl4-corelibs-perl; however: Package libperl4-corelibs-perl 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-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} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libperl4-corelibs-perl{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 70.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libperl4-corelibs-perl all 0.004-1+deb10u1 [38.4 kB] Fetched 19.4 MB in 1s (16.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_i386.deb ... Unpacking libicu63:i386 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_i386.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libperl4-corelibs-perl. Preparing to unpack .../33-libperl4-corelibs-perl_0.004-1+deb10u1_all.deb ... Unpacking libperl4-corelibs-perl (0.004-1+deb10u1) ... Setting up libpipeline1:i386 (1.5.1-2) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:i386 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libperl4-corelibs-perl (0.004-1+deb10u1) ... Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/infernal-1.1.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package infernal dpkg-buildpackage: info: source version 1.1.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/infernal-1.1.2' if [ -r Makefile ]; then /usr/bin/make distclean; fi cd documentation/userguide && if [ -r Makefile ]; then make distclean; fi cd easel/documentation && if [ -r Makefile ]; then make distclean; fi dh_clean *.1 */*.log *.log */Makefile Makefile documentation/manpages/*.1 make[1]: Leaving directory '/build/infernal-1.1.2' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking configure: Configuring Infernal for your system. checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu configure: Full Infernal source distribution - using full configuration 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 C compiler vendor... gnu 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 gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking for a BSD-compatible install... /usr/bin/install -c checking how to run the C preprocessor... gcc -E checking for C compiler vendor... (cached) gnu checking for gcc option to accept ISO C99... none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking whether you have a GNU make... yes, you do; and we assume you will use it! ./configure: line 5445: AX_CC_MAXOPT: command not found checking for gcc option to produce PIC... -fPIC checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -msse2 -msse3... yes checking compiler support for sse2 cast functions... yes checking whether SSE2 is supported... yes checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes configure: Activating Intel/AMD SSE optimized DP implementation checking compiler support --start-group... yes checking for gzip... /bin/gzip checking for library containing clock_gettime... none required checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E 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 emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking pmmintrin.h usability... yes checking pmmintrin.h presence... yes checking for pmmintrin.h... yes checking xmmintrin.h usability... yes checking xmmintrin.h presence... yes checking for xmmintrin.h... yes checking whether byte ordering is bigendian... no 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 for mkstemp... yes checking for popen... yes checking for strcasecmp... yes checking for times... yes checking for getpid... yes checking for sysctl... yes checking for sysconf... yes checking for getcwd... yes checking for stat... yes checking for fstat... yes checking for ntohs... yes checking for ntohl... yes checking for htons... yes checking for htonl... yes 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... 64 configure: creating ./config.status config.status: creating src/Makefile config.status: creating src/impl_sse/Makefile config.status: creating testsuite/Makefile config.status: creating rmark/Makefile config.status: creating documentation/Makefile config.status: creating documentation/manpages/Makefile config.status: creating documentation/userguide/Makefile config.status: creating hmmer/documentation/Makefile config.status: creating hmmer/documentation/man/Makefile config.status: creating hmmer/documentation/userguide/Makefile config.status: creating hmmer/src/Makefile config.status: creating hmmer/testsuite/Makefile config.status: creating hmmer/profmark/Makefile config.status: creating hmmer/src/impl_sse/Makefile config.status: creating hmmer/libdivsufsort/Makefile config.status: creating hmmer/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/Makefile config.status: creating easel/documentation/Makefile config.status: creating Makefile config.status: creating src/config.h config.status: creating hmmer/src/p7_config.h config.status: creating hmmer/libdivsufsort/divsufsort.h config.status: creating easel/esl_config.h config.status: executing hmmer/src/impl commands configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking INFERNAL configuration: compiler: gcc -g -O2 -ffile-prefix-map=/build/infernal-1.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -msse3 -pthread -fPIC linker: -Wl,-z,relro -Wl,-z,now libraries: DP implementation: sse dh_auto_build make -j10 make[1]: Entering directory '/build/infernal-1.1.2' SUBDIR easel make[2]: Entering directory '/build/infernal-1.1.2/easel' CC easel.o CC esl_alphabet.o CC esl_avx.o CC esl_buffer.o CC esl_cluster.o CC esl_composition.o CC esl_dirichlet.o CC esl_distance.o CC esl_dmatrix.o CC esl_dsqdata.o CC esl_exponential.o CC esl_fileparser.o CC esl_gamma.o esl_fileparser.c: In function 'esl_fileparser_NextLine': esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^~ esl_fileparser.c:278:14: note: did you mean to dereference the pointer? while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^ esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^~ esl_fileparser.c:359:10: note: did you mean to dereference the pointer? while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^ CC esl_gencode.o CC esl_getopts.o CC esl_gev.o CC esl_gumbel.o CC esl_heap.o CC esl_histogram.o CC esl_hmm.o CC esl_hyperexp.o CC esl_keyhash.o CC esl_mem.o CC esl_minimizer.o CC esl_mixgev.o CC esl_mpi.o CC esl_msa.o CC esl_msacluster.o CC esl_msafile.o CC esl_msafile2.o CC esl_msafile_a2m.o CC esl_msafile_afa.o CC esl_msafile_clustal.o CC esl_msafile_phylip.o CC esl_msafile_psiblast.o CC esl_msafile_selex.o CC esl_msafile_stockholm.o CC esl_msashuffle.o CC esl_msaweight.o CC esl_normal.o CC esl_paml.o CC esl_random.o CC esl_randomseq.o CC esl_ratematrix.o CC esl_recorder.o CC esl_regexp.o CC esl_rootfinder.o CC esl_scorematrix.o CC esl_sq.o CC esl_sqio.o CC esl_sqio_ascii.o CC esl_sqio_ncbi.o CC esl_sse.o CC esl_ssi.o CC esl_stack.o CC esl_stats.o CC esl_stopwatch.o CC esl_stretchexp.o CC esl_threads.o CC esl_tree.o CC esl_vectorops.o CC esl_vmx.o CC esl_weibull.o CC esl_workqueue.o CC esl_wuss.o AR libeasel.a SUBDIR miniapps make[3]: Entering directory '/build/infernal-1.1.2/easel/miniapps' CC esl-afetch.o CC esl-alimanip.o CC esl-alimap.o CC esl-alimask.o CC esl-alimerge.o CC esl-alipid.o CC esl-alirev.o CC esl-alistat.o CC esl-cluster.o CC esl-compalign.o CC esl-compstruct.o CC esl-construct.o CC esl-histplot.o CC esl-mask.o CC esl-reformat.o CC esl-selectn.o CC esl-seqrange.o CC esl-seqstat.o CC esl-sfetch.o CC esl-shuffle.o CC esl-ssdraw.o CC esl-translate.o CC esl-weight.o GEN esl-afetch GEN esl-alimap GEN esl-alimask GEN esl-alipid GEN esl-alirev GEN esl-cluster GEN esl-compalign GEN esl-compstruct GEN esl-construct GEN esl-histplot GEN esl-mask GEN esl-reformat GEN esl-selectn GEN esl-seqrange GEN esl-seqstat GEN esl-sfetch GEN esl-shuffle GEN esl-translate GEN esl-weight GEN esl-alimerge GEN esl-alistat GEN esl-alimanip GEN esl-ssdraw make[3]: Leaving directory '/build/infernal-1.1.2/easel/miniapps' make[2]: Leaving directory '/build/infernal-1.1.2/easel' SUBDIR hmmer/libdivsufsort make[2]: Entering directory '/build/infernal-1.1.2/hmmer/libdivsufsort' CC divsufsort.o AR libdivsufsort.a make[2]: Leaving directory '/build/infernal-1.1.2/hmmer/libdivsufsort' SUBDIR hmmer make[2]: Entering directory '/build/infernal-1.1.2/hmmer' SUBDIR ../easel make[3]: Entering directory '/build/infernal-1.1.2/easel' SUBDIR miniapps make[4]: Entering directory '/build/infernal-1.1.2/easel/miniapps' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/infernal-1.1.2/easel/miniapps' make[3]: Leaving directory '/build/infernal-1.1.2/easel' SUBDIR libdivsufsort make[3]: Entering directory '/build/infernal-1.1.2/hmmer/libdivsufsort' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/infernal-1.1.2/hmmer/libdivsufsort' SUBDIR src make[3]: Entering directory '/build/infernal-1.1.2/hmmer/src' CC alimask.o CC build.o CC cachedb.o CC emit.o CC errors.o CC evalues.o CC eweight.o CC generic_decoding.o CC generic_fwdback.o CC generic_fwdback_chk.o CC generic_fwdback_banded.o CC generic_null2.o CC generic_msv.o CC generic_optacc.o CC generic_stotrace.o CC generic_viterbi.o CC generic_vtrace.o CC h2_io.o CC heatmap.o CC hmmlogo.o CC hmmdmstr.o CC hmmdwrkr.o CC hmmdutils.o CC hmmer.o CC logsum.o CC modelconfig.o CC modelstats.o CC mpisupport.o CC seqmodel.o CC tracealign.o CC p7_alidisplay.o CC p7_bg.o CC p7_builder.o CC p7_domaindef.o CC p7_gbands.o CC p7_gmx.o CC p7_gmxb.o CC p7_gmxchk.o CC p7_hmm.o CC p7_hmmcache.o CC p7_hmmfile.o CC p7_hmmwindow.o CC p7_null3.o CC p7_pipeline.o CC p7_prior.o CC p7_profile.o CC p7_spensemble.o CC p7_tophits.o CC p7_trace.o CC p7_scoredata.o CC hmmpgmd2msa.o CC fm_alphabet.o CC fm_general.o CC fm_sse.o CC fm_ssv.o CC hmmalign.o CC hmmbuild.o CC hmmconvert.o CC hmmemit.o CC hmmfetch.o CC hmmpress.o CC hmmscan.o CC hmmsearch.o CC hmmsim.o CC hmmstat.o CC jackhmmer.o CC phmmer.o CC nhmmer.o CC nhmmscan.o CC hmmpgmd.o CC hmmc2.o CC makehmmerdb.o CC hmmerfm-exactmatch.o AR libhmmer-src.stamp SUBDIR impl_sse make[4]: Entering directory '/build/infernal-1.1.2/hmmer/src/impl_sse' CC decoding.o CC fwdback.o CC io.o CC ssvfilter.o CC msvfilter.o CC null2.o CC optacc.o CC stotrace.o CC vitfilter.o CC p7_omx.o CC p7_oprofile.o CC mpi.o AR libhmmer-impl.stamp make[4]: Leaving directory '/build/infernal-1.1.2/hmmer/src/impl_sse' GEN alimask GEN hmmalign GEN hmmbuild GEN hmmconvert GEN hmmemit GEN hmmfetch GEN hmmlogo GEN hmmpress GEN hmmscan GEN hmmsearch GEN hmmsim GEN hmmstat GEN jackhmmer GEN phmmer GEN nhmmer GEN nhmmscan GEN hmmpgmd GEN hmmc2 GEN makehmmerdb GEN hmmerfm-exactmatch make[3]: Leaving directory '/build/infernal-1.1.2/hmmer/src' SUBDIR profmark make[3]: Entering directory '/build/infernal-1.1.2/hmmer/profmark' CC create-profmark.o CC rocplot.o GEN rocplot GEN create-profmark make[3]: Leaving directory '/build/infernal-1.1.2/hmmer/profmark' make[2]: Leaving directory '/build/infernal-1.1.2/hmmer' SUBDIR src make[2]: Entering directory '/build/infernal-1.1.2/src' CC cmalign.o CC cm.o CC cm_alidisplay.o CC cm_alndata.o CC cm_dpalign.o CC cm_dpalign_trunc.o CC cm_dpsearch.o CC cm_dpsearch_trunc.o CC cm_dpsmall.o CC cm_file.o cm_alidisplay.c: In function 'cm_alidisplay_Create': cm_alidisplay.c:376:28: warning: '%*d' directive output between 1 and 2147483647 bytes may cause result to exceed 'INT_MAX' [-Wformat-overflow=] sprintf(ad->model+pos, "*[%*d]*", numwidth, qinset); ^~~ cm_alidisplay.c:376:25: note: directive argument in the range [-2147483647, 2147483647] sprintf(ad->model+pos, "*[%*d]*", numwidth, qinset); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from cm_alidisplay.c:19: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2147483652 bytes into a destination of size 4294967295 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cm_alidisplay.c:377:27: warning: '%*d' directive output between 1 and 2147483647 bytes may cause result to exceed 'INT_MAX' [-Wformat-overflow=] sprintf(ad->aseq+pos, "*[%*d]*", numwidth, tinset); ^~~ cm_alidisplay.c:377:24: note: directive argument in the range [-2147483647, 2147483647] sprintf(ad->aseq+pos, "*[%*d]*", numwidth, tinset); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from cm_alidisplay.c:19: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2147483652 bytes into a destination of size 4294967295 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC cm_modelconfig.o CC cm_modelmaker.o CC cm_mx.o CC cm_parsetree.o CC cm_pipeline.o CC cm_qdband.o CC cm_submodel.o CC cm_tophits.o CC cm_trunc.o CC cm_p7_band.o CC cm_p7_domaindef.o CC cm_p7_modelconfig_trunc.o CC cm_p7_modelmaker.o CC cp9.o CC cp9_dp.o CC cp9_modelmaker.o CC cp9_mx.o CC cp9_trace.o CC alphabet.o CC display.o CC errors.o CC eweight.o CC hmmband.o display.c: In function 'CreateFancyAli': display.c:416:28: warning: '%*d' directive output between 1 and 2147483647 bytes may cause result to exceed 'INT_MAX' [-Wformat-overflow=] sprintf(ali->cseq+pos, "*[%*d]*", numwidth, qinset); ^~~ display.c:416:25: note: directive argument in the range [-2147483647, 2147483647] sprintf(ali->cseq+pos, "*[%*d]*", numwidth, qinset); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from display.c:23: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2147483652 bytes into a destination of size 4294967295 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ display.c:228:28: warning: '%*d' directive output between 1 and 2147483647 bytes may cause result to exceed 'INT_MAX' [-Wformat-overflow=] sprintf(ali->cseq+pos, "*[%*d]*", numwidth, qinset); ^~~ display.c:228:25: note: directive argument in the range [-2147483647, 2147483647] sprintf(ali->cseq+pos, "*[%*d]*", numwidth, qinset); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from display.c:23: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2147483652 bytes into a destination of size 4294967295 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ display.c:229:28: warning: '%*d' directive output between 1 and 2147483647 bytes may cause result to exceed 'INT_MAX' [-Wformat-overflow=] sprintf(ali->aseq+pos, "*[%*d]*", numwidth, tinset); ^~~ display.c:229:25: note: directive argument in the range [-2147483647, 2147483647] sprintf(ali->aseq+pos, "*[%*d]*", numwidth, tinset); ^~~~~~~~~ In file included from /usr/include/stdio.h:873, from display.c:23: /usr/include/i386-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 2147483652 bytes into a destination of size 4294967295 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC logsum.o CC mpisupport.o CC prior.o CC rnamat.o CC stats.o CC truncyk.o CC cmbuild.o CC cmcalibrate.o CC cmconvert.o CC cmemit.o CC cmfetch.o CC cmpress.o CC cmscan.o CC cmsearch.o CC cmstat.o CC trcyk.o CC bandcyk-montecarlo-test.o CC bandcyk-truncation-test.o CC cp9-test.o CC sub_cm-test.o CC truncyk_check.o AR libinfernal-src.stamp SUBDIR impl_sse make[3]: Entering directory '/build/infernal-1.1.2/src/impl_sse' CC cm_optimized.o CC sse_cm_dpsearch.o CC sse_cm_dpsmall.o CC sse_cmcons_hitmx.o CC sse_cmcons_mscyk.o CC sse_util.o AR libinfernal-impl.stamp make[3]: Leaving directory '/build/infernal-1.1.2/src/impl_sse' GEN cmalign GEN cmbuild GEN cmcalibrate GEN cmconvert GEN cmemit GEN cmfetch GEN cmpress GEN cmscan GEN cmsearch GEN cmstat GEN trcyk GEN bandcyk-montecarlo-test GEN bandcyk-truncation-test GEN cp9-test GEN sub_cm-test GEN truncyk_check make[2]: Leaving directory '/build/infernal-1.1.2/src' SUBDIR rmark make[2]: Entering directory '/build/infernal-1.1.2/rmark' CC rmark-create.o CC rmark-rocplot.o GEN rmark-rocplot GEN rmark-create make[2]: Leaving directory '/build/infernal-1.1.2/rmark' SUBDIR src/impl_sse make[2]: Entering directory '/build/infernal-1.1.2/src/impl_sse' CC sse_cmsearch.o GEN sse_cmsearch make[2]: Leaving directory '/build/infernal-1.1.2/src/impl_sse' make[1]: Leaving directory '/build/infernal-1.1.2' dh_auto_test make -j10 check VERBOSE=1 make[1]: Entering directory '/build/infernal-1.1.2' SUBDIR easel make[2]: Entering directory '/build/infernal-1.1.2/easel' GEN easel_utest GEN esl_buffer_utest GEN esl_alphabet_utest GEN esl_dirichlet_utest GEN esl_cluster_utest GEN esl_distance_utest GEN esl_exponential_utest GEN esl_fileparser_utest GEN esl_dmatrix_utest GEN esl_dsqdata_utest ./esl_fileparser.c: In function 'esl_fileparser_NextLine': ./esl_fileparser.c:278:21: warning: comparison between pointer and zero character constant [-Wpointer-compare] while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^~ ./esl_fileparser.c:278:14: note: did you mean to dereference the pointer? while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^ ./esl_fileparser.c: In function 'esl_fileparser_NextLinePeeked': ./esl_fileparser.c:359:17: warning: comparison between pointer and zero character constant [-Wpointer-compare] while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^~ ./esl_fileparser.c:359:10: note: did you mean to dereference the pointer? while (efp->s != '\0' && isspace(*(efp->s))) efp->s++; ^ GEN esl_gamma_utest GEN esl_gencode_utest GEN esl_getopts_utest ./esl_buffer.c: In function 'main': ./esl_buffer.c:2354:31: warning: '.gz' directive output may be truncated writing 3 bytes into a region of size between 1 and 32 [-Wformat-truncation=] snprintf(gzipfile, 32, "%s.gz", tmpfile); ^~~ ./esl_buffer.c:2354:3: note: 'snprintf' output between 4 and 35 bytes into a destination of size 32 snprintf(gzipfile, 32, "%s.gz", tmpfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GEN esl_gumbel_utest ./esl_dsqdata.c: In function 'utest_readwrite': ./esl_dsqdata.c:1501:29: warning: '-db.dsqi' directive output may be truncated writing 8 bytes into a region of size between 1 and 32 [-Wformat-truncation=] snprintf(basename, 32, "%s-db.dsqi", tmpfile); remove(basename); ^~~~~~~~ ./esl_dsqdata.c:1501:3: note: 'snprintf' output between 9 and 40 bytes into a destination of size 32 snprintf(basename, 32, "%s-db.dsqi", tmpfile); remove(basename); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./esl_dsqdata.c:1502:29: warning: '-db.dsqm' directive output may be truncated writing 8 bytes into a region of size between 1 and 32 [-Wformat-truncation=] snprintf(basename, 32, "%s-db.dsqm", tmpfile); remove(basename); ^~~~~~~~ ./esl_dsqdata.c:1502:3: note: 'snprintf' output between 9 and 40 bytes into a destination of size 32 snprintf(basename, 32, "%s-db.dsqm", tmpfile); remove(basename); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./esl_dsqdata.c:1503:29: warning: '-db.dsqs' directive output may be truncated writing 8 bytes into a region of size between 1 and 32 [-Wformat-truncation=] snprintf(basename, 32, "%s-db.dsqs", tmpfile); remove(basename); ^~~~~~~~ ./esl_dsqdata.c:1503:3: note: 'snprintf' output between 9 and 40 bytes into a destination of size 32 snprintf(basename, 32, "%s-db.dsqs", tmpfile); remove(basename); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GEN esl_heap_utest GEN esl_histogram_utest GEN esl_hmm_utest GEN esl_hyperexp_utest GEN esl_keyhash_utest GEN esl_mem_utest GEN esl_msa_utest GEN esl_msacluster_utest GEN esl_msafile_utest GEN esl_msafile2_utest GEN esl_msafile_a2m_utest GEN esl_msafile_afa_utest GEN esl_msafile_clustal_utest GEN esl_msafile_phylip_utest GEN esl_msafile_psiblast_utest GEN esl_msafile_selex_utest GEN esl_msafile_stockholm_utest GEN esl_msaweight_utest GEN esl_normal_utest GEN esl_random_utest GEN esl_randomseq_utest GEN esl_ratematrix_utest GEN esl_recorder_utest GEN esl_regexp_utest GEN esl_rootfinder_utest GEN esl_scorematrix_utest GEN esl_sq_utest GEN esl_sqio_utest GEN esl_sse_utest GEN esl_ssi_utest GEN esl_stack_utest GEN esl_stats_utest GEN esl_stretchexp_utest GEN esl_tree_utest ./esl_sqio.c: In function 'main': ./esl_sqio.c:1897:23: warning: '.ssi' directive writing 4 bytes into a region of size between 1 and 32 [-Wformat-overflow=] sprintf(ssifile, "%s.ssi", tmpfile); ^~~~ ./esl_sqio.c:1897:3: note: 'sprintf' output between 5 and 36 bytes into a destination of size 32 sprintf(ssifile, "%s.ssi", tmpfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GEN esl_vectorops_utest GEN esl_weibull_utest GEN esl_wuss_utest SUBDIR miniapps make[3]: Entering directory '/build/infernal-1.1.2/easel/miniapps' make[3]: Nothing to be done for 'tests'. make[3]: Leaving directory '/build/infernal-1.1.2/easel/miniapps' make[2]: Leaving directory '/build/infernal-1.1.2/easel' SUBDIR hmmer/libdivsufsort make[2]: Entering directory '/build/infernal-1.1.2/hmmer/libdivsufsort' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/infernal-1.1.2/hmmer/libdivsufsort' SUBDIR hmmer make[2]: Entering directory '/build/infernal-1.1.2/hmmer' SUBDIR ../easel make[3]: Entering directory '/build/infernal-1.1.2/easel' SUBDIR miniapps make[4]: Entering directory '/build/infernal-1.1.2/easel/miniapps' make[4]: Nothing to be done for 'tests'. make[4]: Leaving directory '/build/infernal-1.1.2/easel/miniapps' make[3]: Leaving directory '/build/infernal-1.1.2/easel' SUBDIR src make[3]: Entering directory '/build/infernal-1.1.2/hmmer/src' SUBDIR impl_sse CC itest_brute.o make[4]: Entering directory '/build/infernal-1.1.2/hmmer/src/impl_sse' make[4]: 'libhmmer-impl.stamp' is up to date. make[4]: Leaving directory '/build/infernal-1.1.2/hmmer/src/impl_sse' GEN build_utest GEN generic_fwdback_utest GEN generic_fwdback_chk_utest GEN generic_stotrace_utest GEN generic_msv_utest GEN generic_viterbi_utest GEN logsum_utest GEN hmmer_utest GEN modelconfig_utest GEN seqmodel_utest GEN p7_alidisplay_utest GEN p7_bg_utest GEN p7_gmx_utest GEN p7_gmxchk_utest GEN p7_hmm_utest GEN p7_hmmfile_utest GEN p7_profile_utest GEN p7_tophits_utest GEN p7_trace_utest GEN p7_scoredata_utest GEN hmmpgmd2msa_utest GEN itest_brute SUBDIR impl_sse make[4]: Entering directory '/build/infernal-1.1.2/hmmer/src/impl_sse' GEN decoding_utest GEN fwdback_utest GEN io_utest GEN null2_utest GEN msvfilter_utest GEN optacc_utest GEN stotrace_utest GEN vitfilter_utest make[4]: Leaving directory '/build/infernal-1.1.2/hmmer/src/impl_sse' make[3]: Leaving directory '/build/infernal-1.1.2/hmmer/src' make[2]: Leaving directory '/build/infernal-1.1.2/hmmer' SUBDIR src make[2]: Entering directory '/build/infernal-1.1.2/src' SUBDIR impl_sse make[3]: Entering directory '/build/infernal-1.1.2/src/impl_sse' make[3]: 'libinfernal-impl.stamp' is up to date. make[3]: Leaving directory '/build/infernal-1.1.2/src/impl_sse' CC itest_brute.o GEN cm_tophits_utest GEN itest_brute SUBDIR impl_sse make[3]: Entering directory '/build/infernal-1.1.2/src/impl_sse' make[3]: Nothing to be done for 'tests'. make[3]: Leaving directory '/build/infernal-1.1.2/src/impl_sse' make[2]: Leaving directory '/build/infernal-1.1.2/src' SUBDIR easel make[2]: Entering directory '/build/infernal-1.1.2/easel' SUBDIR miniapps make[3]: Entering directory '/build/infernal-1.1.2/easel/miniapps' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/infernal-1.1.2/easel/miniapps' SUBDIR testsuite make[3]: Entering directory '/build/infernal-1.1.2/easel/testsuite' Running Easel test suite... exercise 1 [ alphabet-utest] ... ok. exercise 2 [ buffer-utest] ... ok. exercise 3 [ cluster-utest] ... ok. exercise 4 [ dirichlet-utest] ... ok. exercise 5 [ distance-utest] ... ok. exercise 6 [ dmatrix-utest] ... ok. exercise 7 [ dsqdata-utest] ... ok. exercise 8 [ easel-utest] ... ok. exercise 9 [ exponential-utest] ... ok. exercise 10 [ fileparser-utest] ... ok. exercise 11 [ gamma-utest] ... ok. exercise 12 [ gencode-utest] ... ok. exercise 13 [ getopts-utest] ... ok. exercise 14 [ gumbel-utest] ... ok. exercise 15 [ heap-utest] ... ok. exercise 16 [ histogram-utest] ... ok. exercise 17 [ hyperexp-utest] ... ok. exercise 18 [ keyhash-utest] ... ok. exercise 19 [ mem-utest] ... ok. exercise 20 [ msa-utest] ... ok. exercise 21 [ msacluster-utest] ... ok. exercise 22 [ msafile] ... ok. exercise 23 [ msafile2] ... ok. exercise 24 [ msafile-a2m] ... ok. exercise 25 [ msafile-afa] ... ok. exercise 26 [ msafile-clustal] ... ok. exercise 27 [ msafile-phylip] ... ok. exercise 28 [ msafile-psiblast] ... ok. exercise 29 [ msafile-selex] ... ok. exercise 30 [ msafile-stockholm] ... ok. exercise 31 [ msaweight-utest] ... ok. exercise 32 [ normal-utest] ... ok. exercise 33 [ random-utest] ... ok. exercise 34 [ randomseq-utest] ... ok. exercise 35 [ ratematrix-utest] ... ok. exercise 36 [ recorder-utest] ... ok. exercise 37 [ regexp-utest] ... ok. exercise 38 [ rootfinder-utest] ... ok. exercise 39 [ scorematrix-utest] ... ok. exercise 40 [ sq-utest] ... ok. exercise 41 [ sqio-utest] ... ok. exercise 42 [ sse-utest] ... ok. exercise 43 [ ssi-utest] ... ok. exercise 44 [ stack-utest] ... ok. exercise 45 [ stats-utest] ... ok. exercise 46 [ stretchexp-utest] ... ok. exercise 47 [ tree-utest] ... ok. exercise 48 [ vectorops-utest] ... ok. exercise 49 [ weibull-utest] ... ok. exercise 50 [ wuss-utest] ... ok. exercise 51 [ e2] ... ok. exercise 52 [ degen-residues] ... ok. exercise 53 [ ncbi-indices] ... ok. exercise 54 [ blank-gf] ... ok. exercise 55 [ esl-translate] ... FAILED [crash!] exercise 56 [ esl-afetch] ... ok. exercise 57 [ esl-alimanip] ... ok. exercise 58 [ esl-alimap] ... ok. exercise 59 [ esl-alimask] ... ok. exercise 60 [ esl-alimerge] ... ok. exercise 61 [ esl-alistat] ... ok. exercise 62 [ esl-compalign] ... ok. exercise 63 [ esl-construct] ... ok. exercise 64 [ esl-mask] ... ok. exercise 65 [ esl-seqrange] ... ok. exercise 66 [ esl-shuffle] ... ok. exercise 67 [ esl-ssdraw] ... ok. 1 of 67 exercises at level <= 2 FAILED. System information: Tue Sep 22 07:58:02 -12 2020 Linux profitbricks-build12-i386 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux make[3]: Leaving directory '/build/infernal-1.1.2/easel/testsuite' make[2]: Leaving directory '/build/infernal-1.1.2/easel' if test -d hmmer/easel && ! test -e hmmer/easel/miniapps/esl-afetch; then cp easel/miniapps/esl-afetch hmmer/easel/miniapps; fi if test -d hmmer/easel && ! test -e hmmer/easel/miniapps/esl-reformat; then cp easel/miniapps/esl-reformat hmmer/easel/miniapps; fi if test -d hmmer/easel && ! test -e hmmer/easel/miniapps/esl-sfetch; then cp easel/miniapps/esl-sfetch hmmer/easel/miniapps; fi if test -d hmmer/easel && ! test -e hmmer/easel/miniapps/esl-sfetch; then cp easel/miniapps/esl-shuffle hmmer/easel/miniapps; fi if ! test -d hmmer/easel; then cd hmmer; ln -s ../easel .; cd ..; fi if ! test -d ./hmmer/easel; then ln -s ./easel ./hmmer/easel; fi SUBDIR hmmer/testsuite make[2]: Entering directory '/build/infernal-1.1.2/hmmer/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 [ logsum] ... ok. exercise 8 [ modelconfig] ... ok. exercise 9 [ seqmodel] ... ok. exercise 10 [ p7_alidisplay] ... ok. exercise 11 [ p7_bg] ... ok. exercise 12 [ p7_gmx] ... ok. exercise 13 [ p7_hmm] ... ok. exercise 14 [ p7_hmmfile] ... ok. exercise 15 [ p7_profile] ... ok. exercise 16 [ p7_tophits] ... ok. exercise 17 [ p7_trace] ... ok. exercise 18 [ p7_scoredata] ... ok. exercise 19 [ decoding] ... ok. exercise 20 [ fwdback] ... ok. exercise 21 [ io] ... ok. exercise 22 [ msvfilter] ... ok. exercise 23 [ null2] ... ok. exercise 24 [ optacc] ... ok. exercise 25 [ stotrace] ... ok. exercise 26 [ vitfilter] ... ok. exercise 27 [ hmmalign] ... ok. exercise 28 [ hmmalign/-h] ... ok. exercise 29 [ hmmalign/-o] ... ok. exercise 30 [ hmmalign/--mapali] ... ok. exercise 31 [ hmmalign/--trim] ... ok. exercise 32 [ hmmalign/--amino] ... ok. exercise 33 [ hmmalign/--informat] ... ok. exercise 34 [ hmmalign/--outformat] ... ok. exercise 35 [ build] ... ok. exercise 36 [ build/-h] ... ok. exercise 37 [ build/-n] ... ok. exercise 38 [ build/-o] ... ok. exercise 39 [ build/-O] ... ok. exercise 40 [ build/--amino] ... ok. exercise 41 [ build/--dna] ... ok. exercise 42 [ build/--rna] ... ok. exercise 43 [ build/--fast] ... ok. exercise 44 [ build/--hand] ... ok. exercise 45 [ build/--symfrac] ... ok. exercise 46 [ build/--fragthresh] ... ok. exercise 47 [ build/--wpb] ... ok. exercise 48 [ build/--wgsc] ... ok. exercise 49 [ build/--wblosum] ... ok. exercise 50 [ build/--wnone] ... ok. exercise 51 [ build/--wid] ... ok. exercise 52 [ build/--eent] ... ok. exercise 53 [ build/--eclust] ... ok. exercise 54 [ build/--enone] ... ok. exercise 55 [ build/--eset] ... ok. exercise 56 [ build/--ere] ... ok. exercise 57 [ build/--esigma] ... ok. exercise 58 [ build/--eid] ... ok. exercise 59 [ build/--pnone] ... ok. exercise 60 [ build/--plaplace] ... ok. exercise 61 [ build/--EmL] ... ok. exercise 62 [ build/--EmN] ... ok. exercise 63 [ build/--EvL] ... ok. exercise 64 [ build/--EvN] ... ok. exercise 65 [ build/--EfL] ... ok. exercise 66 [ build/--EfN] ... ok. exercise 67 [ build/--Eft] ... ok. exercise 68 [ build/--informat] ... ok. exercise 69 [ build/--seed] ... ok. exercise 70 [ hmmemit] ... ok. exercise 71 [ hmmemit/-h] ... ok. exercise 72 [ hmmemit/-c] ... ok. exercise 73 [ hmmemit/-o] ... ok. exercise 74 [ hmmemit/-p] ... ok. exercise 75 [ hmmemit/-N] ... ok. exercise 76 [ hmmemit/-L] ... ok. exercise 77 [ hmmemit/--local] ... ok. exercise 78 [ hmmemit/--unilocal] ... ok. exercise 79 [ hmmemit/--glocal] ... ok. exercise 80 [ hmmemit/--uniglocal] ... ok. exercise 81 [ search] ... ok. exercise 82 [ search/-h] ... ok. exercise 83 [ search/-o] ... ok. exercise 84 [ search/-A] ... ok. exercise 85 [ search/--tblout] ... ok. exercise 86 [ search/--domtblout] ... ok. exercise 87 [ search/--pfamtblout] ... ok. exercise 88 [ search/--acc] ... ok. exercise 89 [ search/--noali] ... ok. exercise 90 [ search/--notextw] ... ok. exercise 91 [ search/--textw] ... ok. exercise 92 [ search/-E] ... ok. exercise 93 [ search/-T] ... ok. exercise 94 [ search/--domE] ... ok. exercise 95 [ search/--domT] ... ok. exercise 96 [ search/--incE] ... ok. exercise 97 [ search/--incT] ... ok. exercise 98 [ search/--incdomE] ... ok. exercise 99 [ search/--incdomT] ... ok. exercise 100 [ search/--cut_ga] ... ok. exercise 101 [ search/--cut_nc] ... ok. exercise 102 [ search/--cut_tc] ... ok. exercise 103 [ search/--max] ... ok. exercise 104 [ search/--F1] ... ok. exercise 105 [ search/--F2] ... ok. exercise 106 [ search/--F3] ... ok. exercise 107 [ search/--nobias] ... ok. exercise 108 [ search/--nonull2] ... ok. exercise 109 [ search/-Z] ... ok. exercise 110 [ search/--domZ] ... ok. exercise 111 [ search/--seed] ... ok. exercise 112 [ search/--tformat] ... ok. exercise 113 [ jackhmmer] ... ok. exercise 114 [ j/-h] ... ok. exercise 115 [ j/-N] ... ok. exercise 116 [ j/-o] ... ok. exercise 117 [ j/-A] ... ok. exercise 118 [ j/--tblout] ... ok. exercise 119 [ j/--domtblout] ... ok. exercise 120 [ j/--chkhmm] ... ok. exercise 121 [ j/--chkali] ... ok. exercise 122 [ j/--acc] ... ok. exercise 123 [ j/--noali] ... ok. exercise 124 [ j/--notextw] ... ok. exercise 125 [ j/--textw] ... ok. exercise 126 [ j/--popen] ... ok. exercise 127 [ j/--pextend] ... ok. exercise 128 [ j/--mxfile] ... ok. exercise 129 [ j/-E] ... ok. exercise 130 [ j/-T] ... ok. exercise 131 [ j/--domE] ... ok. exercise 132 [ j/--domT] ... ok. exercise 133 [ j/--incE] ... ok. exercise 134 [ j/--incT] ... ok. exercise 135 [ j/--incdomE] ... ok. exercise 136 [ j/--incdomT] ... ok. exercise 137 [ j/--max] ... ok. exercise 138 [ j/--F1] ... ok. exercise 139 [ j/--F2] ... ok. exercise 140 [ j/--F3] ... ok. exercise 141 [ j/--nobias] ... ok. exercise 142 [ j/--EmL] ... ok. exercise 143 [ j/--EmN] ... ok. exercise 144 [ j/--EvL] ... ok. exercise 145 [ j/--EvN] ... ok. exercise 146 [ j/--EfL] ... ok. exercise 147 [ j/--EfN] ... ok. exercise 148 [ j/--Eft] ... ok. exercise 149 [ j/--nonull2] ... ok. exercise 150 [ j/-Z] ... ok. exercise 151 [ j/--domZ] ... ok. exercise 152 [ j/--seed] ... ok. exercise 153 [ j/--qformat] ... ok. exercise 154 [ j/--tformat] ... ok. exercise 155 [ phmmer] ... ok. exercise 156 [ phmmer/-h] ... ok. exercise 157 [ phmmer/-o] ... ok. exercise 158 [ phmmer/-A] ... ok. exercise 159 [ phmmer/--tblout] ... ok. exercise 160 [ phmmer/--domtblout] ... ok. exercise 161 [ phmmer/--pfamtblout] ... ok. exercise 162 [ phmmer/--acc] ... ok. exercise 163 [ phmmer/--noali] ... ok. exercise 164 [ phmmer/--notextw] ... ok. exercise 165 [ phmmer/--textw] ... ok. exercise 166 [ phmmer/--popen] ... ok. exercise 167 [ phmmer/--pextend] ... ok. exercise 168 [ phmmer/--mxfile] ... ok. exercise 169 [ phmmer/-E] ... ok. exercise 170 [ phmmer/-T] ... ok. exercise 171 [ phmmer/--domE] ... ok. exercise 172 [ phmmer/--domT] ... ok. exercise 173 [ phmmer/--incE] ... ok. exercise 174 [ phmmer/--incT] ... ok. exercise 175 [ phmmer/--incdomE] ... ok. exercise 176 [ phmmer/--incdomT] ... ok. exercise 177 [ phmmer/--max] ... ok. exercise 178 [ phmmer/--F1] ... ok. exercise 179 [ phmmer/--F2] ... ok. exercise 180 [ phmmer/--F3] ... ok. exercise 181 [ phmmer/--nobias] ... ok. exercise 182 [ phmmer/--EmL] ... ok. exercise 183 [ phmmer/--EmN] ... ok. exercise 184 [ phmmer/--EvL] ... ok. exercise 185 [ phmmer/--EvN] ... ok. exercise 186 [ phmmer/--EfL] ... ok. exercise 187 [ phmmer/--EfN] ... ok. exercise 188 [ phmmer/--Eft] ... ok. exercise 189 [ phmmer/--nonull2] ... ok. exercise 190 [ phmmer/-Z] ... ok. exercise 191 [ phmmer/--domZ] ... ok. exercise 192 [ phmmer/--seed] ... ok. exercise 193 [ phmmer/--qformat] ... ok. exercise 194 [ phmmer/--tformat] ... ok. exercise 195 [ nhmmer] ... ok. exercise 196 [ nhmmer/-h] ... ok. exercise 197 [ nhmmer/-o] ... ok. exercise 198 [ nhmmer/-A] ... ok. exercise 199 [ nhmmer/--tblout] ... ok. exercise 200 [ nhmmer/--dfamtblout] ... ok. exercise 201 [ nhmmer/--acc] ... ok. exercise 202 [ nhmmer/--noali] ... ok. exercise 203 [ nhmmer/--notextw] ... ok. exercise 204 [ nhmmer/--textw] ... ok. exercise 205 [ nhmmer/-E] ... ok. exercise 206 [ nhmmer/-T] ... ok. exercise 207 [ nhmmer/--incE] ... ok. exercise 208 [ nhmmer/--incT] ... ok. exercise 209 [ nhmmer/--max] ... ok. exercise 210 [ nhmmer/--F1] ... ok. exercise 211 [ nhmmer/--F2] ... ok. exercise 212 [ nhmmer/--F3] ... ok. exercise 213 [ nhmmer/--nobias] ... ok. exercise 214 [ nhmmer/--nonull2] ... ok. exercise 215 [ nhmmer/-Z] ... ok. exercise 216 [ nhmmer/--seed] ... ok. exercise 217 [ nhmmscan] ... ok. exercise 218 [ nhmmscan/-h] ... ok. exercise 219 [ nhmmscan/-o] ... ok. exercise 220 [ nhmmscan/--tblout] ... ok. exercise 221 [nhmmscan/--dfamtblout] ... ok. exercise 222 [ nhmmscan/--acc] ... ok. exercise 223 [ nhmmscan/--noali] ... ok. exercise 224 [ nhmmscan/--notextw] ... ok. exercise 225 [ nhmmscan/--textw] ... ok. exercise 226 [ nhmmscan/-E] ... ok. exercise 227 [ nhmmscan/-T] ... ok. exercise 228 [ nhmmscan/--incE] ... ok. exercise 229 [ nhmmscan/--incT] ... ok. exercise 230 [ nhmmscan/--max] ... ok. exercise 231 [ nhmmscan/--F1] ... ok. exercise 232 [ nhmmscan/--F2] ... ok. exercise 233 [ nhmmscan/--F3] ... ok. exercise 234 [ nhmmscan/--nobias] ... ok. exercise 235 [ nhmmscan/--nonull2] ... ok. exercise 236 [ nhmmscan/-Z] ... ok. exercise 237 [ nhmmscan/--seed] ... ok. exercise 238 [ hmmbuild_variation] ... ok. exercise 239 [ hmmscan_variation] ... ok. exercise 240 [ hmmsearch_variation] ... ok. exercise 241 [ phmmer_variation] ... ok. exercise 242 [ mapali] ... ok. exercise 243 [ fragments] ... ok. exercise 244 [ nonresidues] ... ok. exercise 245 [ opt-annotation] ... ok. exercise 246 [ dup-names] ... ok. exercise 247 [ mapali-again] ... ok. exercise 248 [ delete-corruption] ... ok. exercise 249 [ msa-integrity] ... ok. exercise 250 [ hmmemit-consensus] ... ok. exercise 251 [ hmmconvert] ... ok. exercise 252 [ stdin_pipes] ... ok. exercise 253 [ nhmmer_generic] ... ok. exercise 254 [ hmmpgmd_ga] ... ok. exercise 255 [ brute-itest] ... ok. exercise 256 [ hmmpress-itest] ... ok. exercise 257 [ h39] ... ok. exercise 258 [ h45] ... ok. exercise 259 [ h50] ... ok. exercise 260 [ h82] ... ok. All 260 exercises at level <= 2 passed. System information: Tue Sep 22 07:59:02 -12 2020 Linux profitbricks-build12-i386 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux make[2]: Leaving directory '/build/infernal-1.1.2/hmmer/testsuite' if test -L hmmer/easel; then rm hmmer/easel; fi if test -L ./hmmer/easel; then rm ./hmmer/easel; fi if test -e hmmer/easel/miniapps/esl-afetch; then rm hmmer/easel/miniapps/esl-afetch; fi if test -e hmmer/easel/miniapps/esl-reformat; then rm hmmer/easel/miniapps/esl-reformat; fi if test -e hmmer/easel/miniapps/esl-sfetch; then rm hmmer/easel/miniapps/esl-sfetch; fi if test -e hmmer/easel/miniapps/esl-shuffle; then rm hmmer/easel/miniapps/esl-shuffle; fi SUBDIR testsuite make[2]: Entering directory '/build/infernal-1.1.2/testsuite' Running Infernal test suite... exercise 1 [ utest/cm_tophits] ... ok. exercise 2 [ itest/mapali] ... ok. exercise 3 [ itest/dup-names] ... ok. exercise 4 [ itest/msa-integrity] ... ok. exercise 5 [ itest/stdin-pipes] ... ok. exercise 6 [ itest/pipeline] ... ok. exercise 7 [ itest/sensitivity] ... ok. exercise 8 [ itest/trunc] ... ok. exercise 9 [ itest/scan-glist] ... ok. exercise 10 [ itest/scan-overlaps] ... ok. exercise 11 [ itest/brute] ... ok. exercise 12 [ bug/i1-vault-sscons] ... ok. exercise 13 [ bug/i2-cmalign-leak] ... ok. exercise 14 [ bug/i11-bld-detach] ... ok. exercise 15 [ bug/i12-aln-outside] ... ok. exercise 16 [ bug/i13-aln-sub] ... ok. exercise 17 [ bug/i14-aln-oa-zero] ... ok. exercise 18 [ bug/i15-aln-bif-imp] ... ok. exercise 19 [ bug/i28-srch-bndcln] ... ok. exercise 20 [ bug/i29-cnv-1p0-nft] ... ok. exercise 21 [ bug/i30-srch-zeroln] ... ok. exercise 22 [ bug/i31-neg-dbsize] ... ok. exercise 23 [ bug/i32-refine-ss] ... ok. exercise 24 [ bug/i33-cmsearch-A] ... ok. exercise 25 [ bug/i34-cmalign-EL] ... ok. exercise 26 [ bug/i36-hbanded-tb] ... ok. exercise 27 [ bug/i37-bandshift] ... ok. exercise 28 [ bug/i38-mapali-noss] ... ok. exercise 29 [ bug/i39-build-O-0bp] ... ok. exercise 30 [ bug/i43-oa-loc-beg] ... ok. exercise 31 [ bug/i44-mapstr] ... ok. exercise 32 [ build/help/1] ... ok. exercise 33 [ build/help/2] ... ok. exercise 34 [ build/t] ... ok. exercise 35 [ build/v/o] ... ok. exercise 36 [ build/s/O] ... ok. exercise 37 [ build/zbp/O] ... ok. exercise 38 [ build/4/O] ... ok. exercise 39 [ search/help/1] ... ok. exercise 40 [ search/help/2] ... ok. exercise 41 [ search/t] ... ok. exercise 42 [ search/v] ... ok. exercise 43 [ search/s] ... ok. exercise 44 [ search/4] ... ok. exercise 45 [ search/zbp] ... ok. exercise 46 [ search/t/A] ... ok. exercise 47 [ search/4/A] ... ok. exercise 48 [ search/zbp/A] ... ok. exercise 49 [ stat/help/1] ... ok. exercise 50 [ stat/t] ... ok. exercise 51 [ stat/v] ... ok. exercise 52 [ stat/s] ... ok. exercise 53 [ stat/z] ... ok. exercise 54 [ stat/tC] ... ok. exercise 55 [ stat/vC] ... ok. exercise 56 [ stat/sC] ... ok. exercise 57 [ stat/zC] ... ok. exercise 58 [ press/tC] ... ok. exercise 59 [ press/vC] ... ok. exercise 60 [ press/sC] ... ok. exercise 61 [ press/zC] ... ok. exercise 62 [ press/4C] ... ok. exercise 63 [ press/5C] ... ok. exercise 64 [ scan/help/1] ... ok. exercise 65 [ scan/help/2] ... ok. exercise 66 [ scan/tC] ... ok. exercise 67 [ scan/vC] ... ok. exercise 68 [ scan/sC] ... ok. exercise 69 [ scan/zC] ... ok. exercise 70 [ scan/4C] ... ok. exercise 71 [ scan/5C] ... ok. exercise 72 [ emit/help/1] ... ok. exercise 73 [ emit/t] ... ok. exercise 74 [ emit/v] ... ok. exercise 75 [ emit/s] ... ok. exercise 76 [ emit/4] ... ok. exercise 77 [ emit/z] ... ok. exercise 78 [ emit/tC] ... ok. exercise 79 [ emit/vC] ... ok. exercise 80 [ emit/sC] ... ok. exercise 81 [ emit/4C] ... ok. exercise 82 [ emit/zC] ... ok. exercise 83 [ convert/help/1] ... ok. exercise 84 [ convert/t] ... ok. exercise 85 [ convert/v] ... ok. exercise 86 [ convert/s] ... ok. exercise 87 [ convert/4] ... ok. exercise 88 [ convert-emit/t] ... ok. exercise 89 [ convert-emit/v] ... ok. exercise 90 [ convert-emit/s] ... ok. exercise 91 [ convert-emit/4] ... ok. exercise 92 [ convert/t/b] ... ok. exercise 93 [ convert/v/b] ... ok. exercise 94 [ convert/s/b] ... ok. exercise 95 [ convert/4/b] ... ok. exercise 96 [ convert-emit/t/b] ... ok. exercise 97 [ convert-emit/v/b] ... ok. exercise 98 [ convert-emit/s/b] ... ok. exercise 99 [ convert-emit/4/b] ... ok. exercise 100 [ convert/t/1] ... ok. exercise 101 [ convert/v/1] ... ok. exercise 102 [ convert/s/1] ... ok. exercise 103 [ convert/4/1] ... ok. exercise 104 [ convert/t/1back] ... ok. exercise 105 [ convert/v/1back] ... ok. exercise 106 [ convert/s/1back] ... ok. exercise 107 [ convert/4/1back] ... ok. exercise 108 [ convert-emit/t/b] ... ok. exercise 109 [ convert-emit/v/b] ... ok. exercise 110 [ convert-emit/s/b] ... ok. exercise 111 [ convert-emit/4/b] ... ok. exercise 112 [ convertC/t] ... ok. exercise 113 [ convertC/v] ... ok. exercise 114 [ convertC/s] ... ok. exercise 115 [ convertC/4] ... ok. exercise 116 [ convertC-emit/t] ... ok. exercise 117 [ convertC-emit/v] ... ok. exercise 118 [ convertC-emit/s] ... ok. exercise 119 [ convertC-emit/4] ... ok. exercise 120 [ align/help/1] ... ok. exercise 121 [ align/t/1] ... ok. exercise 122 [ align/t/2] ... ok. exercise 123 [ calibrate/help/1] ... ok. exercise 124 [ calibrate/tFC] ... ok. exercise 125 [ calibrate/se] ... ok. exercise 126 [ fetch/4/index] ... ok. exercise 127 [ fetch/4/f] ... ok. exercise 128 [ fetch/4/o] ... ok. exercise 129 [ fetch/4/O] ... ok. exercise 130 [ emit/4/O] ... ok. exercise 131 [ fetch/4C/index] ... ok. exercise 132 [ fetch/4C/f] ... ok. exercise 133 [ fetch/4C/o] ... ok. exercise 134 [ fetch/4C/O] ... ok. exercise 135 [ emit/4C/O] ... ok. exercise 136 [ bandcykmc/trna] ... ok. exercise 137 [ bandcyktrunc/trna] ... ok. exercise 138 [ cp9/trna/1] ... ok. exercise 139 [ cp9/trna/2] ... ok. exercise 140 [ cp9/rp] ... ok. exercise 141 [ sub/trna1] ... ok. exercise 142 [ sub/rp] ... ok. exercise 143 [ sub/trna2] ... ok. All 143 exercises at level <= 1 passed. System information: Tue Sep 22 08:08:33 -12 2020 Linux profitbricks-build12-i386 4.19.0-10-686-pae #1 SMP Debian 4.19.132-1 (2020-07-24) i686 GNU/Linux make[2]: Leaving directory '/build/infernal-1.1.2/testsuite' make[1]: Leaving directory '/build/infernal-1.1.2' 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/infernal-1.1.2' /usr/bin/make install prefix=/build/infernal-1.1.2/debian/tmp make[2]: Entering directory '/build/infernal-1.1.2' /usr/bin/install -c -d /build/infernal-1.1.2/debian/tmp/bin /usr/bin/install -c -d /build/infernal-1.1.2/debian/tmp/share/man/man1 /usr/bin/install -c -d /build/infernal-1.1.2/debian/tmp/share/doc/infernal SUBDIR src make[3]: Entering directory '/build/infernal-1.1.2/src' for file in cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmscan cmsearch cmstat; do \ /usr/bin/install -c -m 0755 $file /build/infernal-1.1.2/debian/tmp/bin/ ;\ done make[3]: Leaving directory '/build/infernal-1.1.2/src' SUBDIR documentation make[3]: Entering directory '/build/infernal-1.1.2/documentation' SUBDIR manpages make[4]: Entering directory '/build/infernal-1.1.2/documentation/manpages' for file in infernal cmalign cmbuild cmcalibrate cmconvert cmemit cmfetch cmpress cmsearch cmscan cmstat; do \ /usr/bin/install -c -m 0755 ./$file.man /build/infernal-1.1.2/debian/tmp/share/man/man1/${file}.1 ;\ done make[4]: Leaving directory '/build/infernal-1.1.2/documentation/manpages' make[3]: Leaving directory '/build/infernal-1.1.2/documentation' make[2]: Leaving directory '/build/infernal-1.1.2' make[1]: Leaving directory '/build/infernal-1.1.2' debian/rules override_dh_install make[1]: Entering directory '/build/infernal-1.1.2' dh_install for bin in `ls /build/infernal-1.1.2/debian/infernal/usr/lib/infernal` ; do \ if [ $bin != cmalign ] ; then \ ln -s cmalign /build/infernal-1.1.2/debian/infernal/usr/bin/$bin ; \ fi ; \ done make[1]: Leaving directory '/build/infernal-1.1.2' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/infernal-1.1.2' dh_installexamples mkdir -p /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/src/; mkdir -p /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/easel/miniapps/; find ./src -name "*test" -exec cp \{\} /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/src/ \; cp ./src/itest_brute /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/src/; cp ./easel/miniapps/esl-reformat /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/easel/miniapps/; cp ./easel/miniapps/esl-shuffle /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/easel/miniapps/; cp ./easel/miniapps/esl-sfetch /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/easel/miniapps/; cp -aR testsuite /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/; cp ./easel/devkit/sqc /build/infernal-1.1.2/debian/infernal/usr/share/doc/infernal/examples/; make[1]: Leaving directory '/build/infernal-1.1.2' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/infernal-1.1.2' dh_compress -X.pdf make[1]: Leaving directory '/build/infernal-1.1.2' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package infernal-doc: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'infernal-doc' in '../infernal-doc_1.1.2-2_all.deb'. dpkg-deb: building package 'infernal-dbgsym' in '../infernal-dbgsym_1.1.2-2_i386.deb'. dpkg-deb: building package 'infernal' in '../infernal_1.1.2-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../infernal_1.1.2-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/6482 and its subdirectories I: Current time: Tue Sep 22 08:11:18 -12 2020 I: pbuilder-time-stamp: 1600805478