I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 9 05:01:01 +14 2021 I: pbuilder-time-stamp: 1623164461 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [kalign_3.3-1.dsc] I: copying [./kalign_3.3.orig.tar.gz] I: copying [./kalign_3.3-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.D_LJ0xpq/trustedkeys.kbx': General error gpgv: Signature made Fri Nov 6 23:40:45 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./kalign_3.3-1.dsc dpkg-source: info: extracting kalign in kalign-3.3 dpkg-source: info: unpacking kalign_3.3.orig.tar.gz dpkg-source: info: unpacking kalign_3.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying simde dpkg-source: info: applying no-native-build dpkg-source: info: applying keep-debugging I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1422/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/1422/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1422/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=5e9db9ed60344be6a5fbad425f1d388e LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1422 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/pbuilderrc_t1Hn --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/b2 --logfile b2/build.log --extrapackages usrmerge kalign_3.3-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin total 5780 -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp -rwxr-xr-x 1 root root 128724 Dec 11 03:23 dash -rwxr-xr-x 1 root root 124904 Sep 23 2020 date -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd -rwxr-xr-x 1 root root 100752 Sep 23 2020 df -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln -rwxr-xr-x 1 root root 55572 Feb 8 2020 login -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jun 9 05:04 sh -> bash lrwxrwxrwx 1 root root 4 Jun 8 23:26 sh.distrib -> dash -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch -rwxr-xr-x 1 root root 34664 Sep 23 2020 true -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/1422/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libsimde-dev; however: Package libsimde-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsimde-dev{a} libsub-override-perl{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 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 18.8 MB of archives. After unpacking 72.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-6 [8776 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 libsimde-dev all 0.7.2-4 [259 kB] Fetched 18.8 MB in 12s (1579 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../07-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../10-libsigsegv2_2.13-1_i386.deb ... Unpacking libsigsegv2:i386 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_i386.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.11.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.11.0-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../23-libelf1_0.183-1_i386.deb ... Unpacking libelf1:i386 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_i386.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:i386. Preparing to unpack .../25-libicu67_67.1-6_i386.deb ... Unpacking libicu67:i386 (67.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7_i386.deb ... Unpacking libxml2:i386 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_i386.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../31-libsimde-dev_0.7.2-4_all.deb ... Unpacking libsimde-dev (0.7.2-4) ... Setting up libpipeline1:i386 (1.5.3-1) ... Setting up libsimde-dev (0.7.2-4) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:i386 (67.1-6) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:i386 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:i386 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:i386 (0.183-1) ... Setting up libxml2:i386 (2.9.10+dfsg-6.7) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-12) ... 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... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (778 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 21797 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package I: Running cd /build/kalign-3.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package kalign dpkg-buildpackage: info: source version 1:3.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT' configure.ac:5: installing './compile' configure.ac:16: installing './config.guess' configure.ac:16: installing './config.sub' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' 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-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking 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 whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking for gawk... (cached) mawk 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 whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking whether make supports nested variables... (cached) yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- debian/rules override_dh_auto_build make[1]: Entering directory '/build/kalign-3.3' mkdir -p /build/kalign-3.3/debian/kalign/usr mkdir -p /build/kalign-3.3/debian/kalign/usr/lib/kalign make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2" && dh_auto_build && cp src/kalign src/kalign-avx2 && cp src/timescorealn src/timescorealn-avx2 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx" && dh_auto_build && cp src/kalign src/kalign-avx && cp src/timescorealn src/timescorealn-avx && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse4.1" && dh_auto_build && cp src/kalign src/kalign-sse4.1 && cp src/timescorealn src/timescorealn-sse4.1 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3" && dh_auto_build && cp src/kalign src/kalign-ssse3 && cp src/timescorealn src/timescorealn-ssse3 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3" && dh_auto_build && cp src/kalign src/kalign-sse3 && cp src/timescorealn src/timescorealn-sse3 && true make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2" 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 whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking for gawk... (cached) mawk 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 whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for ranlib... ranlib checking whether make supports nested variables... (cached) yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... (cached) ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx" 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 whether gcc understands -c and -o together... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 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(cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mavx -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_seqseq.o aln_seqseq.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o aln_profileprofile.o aln_profileprofile.c bpm.c: In function 'add256': bpm.c:590:9: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 590 | __m256i add256(uint32_t carry, __m256i A, __m256i B) | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse4.1 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mssse3" 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 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(cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_mem.o aln_mem.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o aln_profileprofile.o aln_profileprofile.c bpm.c: In function 'add256': bpm.c:590:9: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 590 | __m256i add256(uint32_t carry, __m256i A, __m256i B) | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o create_run_cmds.o create_run_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -mssse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3" 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 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(cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether C compiler accepts -D_FORTIFY_SOURCE=2... yes checking whether C compiler accepts -ffunction-sections... yes checking whether C compiler accepts -fdata-sections... yes checking whether C compiler accepts --gc-sections... no checking for OpenMP flag of C compiler... -fopenmp checking for _Generic... yes checking for sqrt in -lm... yes checking for main in -lpthread... yes checking for library containing clock_gettime... none required checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking mach/mach.h usability... no checking mach/mach.h presence... no checking for mach/mach.h... no checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int8_t... yes checking for int32_t... yes checking for int16_t... yes checking for int64_t... yes checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_task.o aln_task.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o aln_profileprofile.o aln_profileprofile.c bpm.c: In function 'add256': bpm.c:590:9: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 590 | __m256i add256(uint32_t carry, __m256i A, __m256i B) | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse3 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make clean ; dh_auto_configure && dh_auto_build && \ cp src/kalign src/kalign-plain && \ cp src/timescorealn src/timescorealn-plain make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm 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(cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_run.o aln_run.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqseq.o aln_seqseq.c bpm.c: In function 'add256': bpm.c:590:9: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 590 | __m256i add256(uint32_t carry, __m256i A, __m256i B) | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o create_run_cmds.o create_run_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2" && dh_auto_build && cp src/kalign src/kalign-sse2 && cp src/timescorealn src/timescorealn-sse2 && make clean ; dh_auto_configure -- CFLAGS="-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse" && dh_auto_build && cp src/kalign src/kalign-sse && cp src/timescorealn src/timescorealn-sse && true make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse2" checking for gcc... gcc checking whether the C compiler works... yes checking for C 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(cached) yes checking for GNU libc compatible realloc... yes checking for working strnlen... yes checking for error_at_line... yes checking for gettimeofday... yes checking for pow... yes checking for realpath... yes checking for sqrt... yes checking for strstr... yes checking for memset... yes checking for clock_gettime... yes checking for gethrtime... no checking for gettimeofday... (cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o misc.o misc.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o bpm.o bpm.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o aln_profileprofile.o aln_profileprofile.c bpm.c: In function 'add256': bpm.c:590:9: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 590 | __m256i add256(uint32_t carry, __m256i A, __m256i B) | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse2 -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[2]: Entering directory '/build/kalign-3.3' Making clean in src make[3]: Entering directory '/build/kalign-3.3/src' rm -f kalign kchaos rm -f edist alphabet misc_test bpm_test rwaln rstdin_test test -z "ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5" || rm -f ihmm_seq_itest_read_test.fa test_model_file.txt test.lfa test_dna.lfa libhdf5gluetest_exp.h5 libhdf5gluetest.h5 model_at_*h5 test1.h5 test2.h5 rm -rf .libs _libs rm -f timescorealn benchrunner genruncmds genkaligndiffcmds rm -f *.o test -z "edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log" || rm -f edist.log alphabet.log misc_test.log bpm_test.log rstdin_test.log test -z "edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs" || rm -f edist.trs alphabet.trs misc_test.trs bpm_test.trs rstdin_test.trs test -z "test-suite.log" || rm -f test-suite.log rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/src' Making clean in dev make[3]: Entering directory '/build/kalign-3.3/dev' test -z "rwtest.clu rwtest.fasta rwtest.msf test.afa" || rm -f rwtest.clu rwtest.fasta rwtest.msf test.afa rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' rm -rf .libs _libs rm -f *.lo make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "CFLAGS=-g -O2 -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse" 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 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(cached) yes checking for localtime_r... yes checking for strcspn... yes checking for valgrind... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating dev/Makefile config.status: creating src/config.h config.status: src/config.h is unchanged config.status: executing depfiles commands config.status: executing libtool commands configure: --------------------------------------------------------- configure: Configuration complete - kalign-3.3 configure: configure: General Information: configure: Version: 3.3 configure: Configured on: configure: Configured by: pbuilder2 configure: Host system: i686-pc-linux-gnu configure: Uname information: configure: Installation point: /usr configure: CFLAGS: -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse configure: CPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2 configure: LDFLAGS: -Wl,-z,relro -Wl,-z,now configure: SIMD flags: configure: --------------------------------------------------------- make -j10 make[2]: Entering directory '/build/kalign-3.3' Making all in src make[3]: Entering directory '/build/kalign-3.3/src' make all-am make[4]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o run_kalign.o run_kalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o idata.o idata.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o tldevel.o tldevel.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o tlmisc.o tlmisc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o esl_stopwatch.o esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o tlrng.o tlrng.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o parameters.o parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o alphabet.o alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o alignment_parameters.o alignment_parameters.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o pick_anchor.o pick_anchor.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bisectingKmeans.o bisectingKmeans.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o sequence_distance.o sequence_distance.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o euclidean_dist.o euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o weave_alignment.o weave_alignment.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o rwalign.o rwalign.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o misc.o misc.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bpm.o bpm.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_task.o aln_task.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_mem.o aln_mem.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_setup.o aln_setup.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_run.o aln_run.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_controller.o aln_controller.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_seqseq.o aln_seqseq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_seqprofile.o aln_seqprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o aln_profileprofile.o aln_profileprofile.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o queue.o queue.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o kchaos.o kchaos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o time_and_score_aln.o time_and_score_aln.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o benchrunner.o benchrunner.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o create_run_cmds.o create_run_cmds.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o create_run_kalign_diff_cmds.o create_run_kalign_diff_cmds.c create_run_cmds.c: In function 'main': create_run_cmds.c:54:164: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 6845 and 8101 [-Wformat-truncation=] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~ ~~~ create_run_cmds.c:54:76: note: directive argument in the range [0, 65535] 54 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch ~/tmp --gpo %f -gpe %f -tgpe %f -matadd %f -program kalign -test %s -ref %s -o big_run_out.csv -u %d \n", gpo,gpe,tgpe,matadd, ret,ret, i << 12| j << 8 | c << 4 | f); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 124 and 17766 bytes into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c: In function 'main': create_run_kalign_diff_cmds.c:158:42: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size 512 [-Wformat-truncation=] 158 | snprintf(filename, 512, "%s", ret); | ^~ ~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin_snprintf' output between 1 and 8192 bytes into a destination of size 512 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:181:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:181:52: note: directive argument in the range [1, 2147483647] 181 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program muscle -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret,filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:185:113: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7625 and 8136 [-Wformat-truncation=] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:185:52: note: directive argument in the range [2, 2147483647] 185 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 74 or more bytes (assuming 8785) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:189:120: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7618 and 8129 [-Wformat-truncation=] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:189:52: note: directive argument in the range [3, 2147483647] 189 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:1@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 81 or more bytes (assuming 8792) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ create_run_kalign_diff_cmds.c:193:122: warning: '%s' directive output may be truncated writing up to 8191 bytes into a region of size between 7616 and 8127 [-Wformat-truncation=] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~ ~~~ create_run_kalign_diff_cmds.c:193:52: note: directive argument in the range [4, 2147483647] 193 | rc = snprintf(out, BUFSIZ, "benchrunner --scratch %s @-n:4@ --runname %s -program kalign -test %s -ref %s -o %s -u %d \n", param->scratchdir, runname,ret, filename,param->outfile, c); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from tldevel.h:5, from create_run_kalign_diff_cmds.c:1: /usr/include/i386-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output 83 or more bytes (assuming 8794) into a destination of size 8192 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bpm.c: In function 'add256': bpm.c:590:9: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 590 | __m256i add256(uint32_t carry, __m256i A, __m256i B) | ^~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kchaos tldevel.o queue.o kchaos.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genruncmds tldevel.o create_run_cmds.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o benchrunner benchrunner.o tldevel.o tlmisc.o rwalign.o esl_stopwatch.o alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o kalign run_kalign.o idata.o tldevel.o tlmisc.o esl_stopwatch.o tlrng.o parameters.o alphabet.o alignment_parameters.o pick_anchor.o bisectingKmeans.o sequence_distance.o euclidean_dist.o weave_alignment.o rwalign.o misc.o bpm.o aln_task.o aln_mem.o aln_setup.o aln_run.o aln_controller.o aln_seqseq.o aln_seqprofile.o aln_profileprofile.o -lpthread -lm -fopenmp make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' Making all in dev make[3]: Entering directory '/build/kalign-3.3/dev' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/kalign-3.3/dev' make[3]: Entering directory '/build/kalign-3.3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/kalign-3.3' make[2]: Leaving directory '/build/kalign-3.3' make[1]: Leaving directory '/build/kalign-3.3' dh_auto_test make -j10 check VERBOSE=1 make[1]: Entering directory '/build/kalign-3.3' Making check in src make[2]: Entering directory '/build/kalign-3.3/src' make edist alphabet misc_test bpm_test rwaln rstdin_test make[3]: Entering directory '/build/kalign-3.3/src' gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o edist-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o edist-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o edist-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DITEST_EDIST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o edist-euclidean_dist.o `test -f 'euclidean_dist.c' || echo './'`euclidean_dist.c gcc -DHAVE_CONFIG_H -I. -DITEST_ALPHABET -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o alphabet-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_ALPHABET -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o alphabet-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o misc_test-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o misc_test-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o misc_test-misc.o `test -f 'misc.c' || echo './'`misc.c gcc -DHAVE_CONFIG_H -I. -DITEST_MISC -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o misc_test-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bpm_test-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bpm_test-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bpm_test-tlrng.o `test -f 'tlrng.c' || echo './'`tlrng.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bpm_test-bpm.o `test -f 'bpm.c' || echo './'`bpm.c gcc -DHAVE_CONFIG_H -I. -DBPM_UTEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o bpm_test-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o rwaln-tldevel.o `test -f 'tldevel.c' || echo './'`tldevel.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o rwaln-tlmisc.o `test -f 'tlmisc.c' || echo './'`tlmisc.c euclidean_dist.c: In function 'hsum256_ps_avx': euclidean_dist.c:193:7: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 193 | float hsum256_ps_avx(__m256 v) | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o rwaln-esl_stopwatch.o `test -f 'esl_stopwatch.c' || echo './'`esl_stopwatch.c bpm.c: In function 'print_256': bpm.c:365:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 365 | fprintf(stdout,"%lu ", debug[0]); | ~~^ ~~~~~~~~ | | | | | uint64_t {aka long long unsigned int} | long unsigned int | %llu bpm.c: In function 'print_256_all': bpm.c:375:35: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 375 | fprintf(stdout,"%lu ", debug[i]); | ~~^ ~~~~~~~~ | | | | | uint64_t {aka long long unsigned int} | long unsigned int | %llu gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o rwaln-rwalign.o `test -f 'rwalign.c' || echo './'`rwalign.c gcc -DHAVE_CONFIG_H -I. -DRWALIGN_TEST -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o rwaln-alphabet.o `test -f 'alphabet.c' || echo './'`alphabet.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -c -o read_from_stdin_test.o read_from_stdin_test.c bpm.c: In function 'print_256': bpm.c:361:6: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 361 | void print_256(__m256i X) | ^~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o alphabet alphabet-tldevel.o alphabet-alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o alphabet alphabet-tldevel.o alphabet-alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o edist edist-tldevel.o edist-esl_stopwatch.o edist-tlrng.o edist-euclidean_dist.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o edist edist-tldevel.o edist-esl_stopwatch.o edist-tlrng.o edist-euclidean_dist.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o misc_test misc_test-tldevel.o misc_test-tlrng.o misc_test-misc.o misc_test-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o misc_test misc_test-tldevel.o misc_test-tlrng.o misc_test-misc.o misc_test-alphabet.o -lpthread -lm -fopenmp /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o bpm_test bpm_test-tldevel.o bpm_test-esl_stopwatch.o bpm_test-tlrng.o bpm_test-bpm.o bpm_test-alphabet.o -lpthread -lm /bin/sh ../libtool --tag=CC --mode=link gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bpm_test bpm_test-tldevel.o bpm_test-esl_stopwatch.o bpm_test-tlrng.o bpm_test-bpm.o bpm_test-alphabet.o -lpthread -lm -fopenmp libtool: link: gcc -fopenmp -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -g -fdebug-prefix-map=/build/kalign-3.3=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -msse -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm -fopenmp make[3]: Leaving directory '/build/kalign-3.3/src' make check-TESTS make[3]: Entering directory '/build/kalign-3.3/src' make[4]: Entering directory '/build/kalign-3.3/src' PASS: alphabet PASS: misc_test PASS: rstdin_test PASS: edist PASS: bpm_test ============================================================================ Testsuite summary for kalign 3.3 ============================================================================ # TOTAL: 5 # PASS: 5 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/kalign-3.3/src' make[3]: Leaving directory '/build/kalign-3.3/src' make[2]: Leaving directory '/build/kalign-3.3/src' Making check in dev make[2]: Entering directory '/build/kalign-3.3/dev' make check-TESTS make[3]: Entering directory '/build/kalign-3.3/dev' Running kalign basic io test: a2m.good.1 read/writea2m.good.1 SUCCESS a2m.good.2 read/writea2m.good.2 SUCCESS afa.good.1 read/writeafa.good.1 SUCCESS afa.good.2 read/writeafa.good.2 SUCCESS afa.good.3 read/writeafa.good.3 SUCCESS clustal.good.1 read/writeclustal.good.1 SUCCESS clustal.good.2 read/writeclustal.good.2 SUCCESS PASS: run_io_test.sh Running kalign basic alignment tests: BB11001.msf read/writeBB11001.msf SUCCESS BB11001_EOF.msf read/writeBB11001_EOF.msf SUCCESS BB11001.tfa read/writeBB11001.tfa SUCCESS BB12006.msf read/writeBB12006.msf SUCCESS BB12006.tfa read/writeBB12006.tfa SUCCESS BB30014.msf read/writeBB30014.msf SUCCESS BB30014.tfa read/writeBB30014.tfa SUCCESS PASS: run_aln_test.sh ================== All 2 tests passed ================== make[3]: Leaving directory '/build/kalign-3.3/dev' make[2]: Leaving directory '/build/kalign-3.3/dev' make[2]: Entering directory '/build/kalign-3.3' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/kalign-3.3' make[1]: Leaving directory '/build/kalign-3.3' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/kalign-3.3' dh_install debian/bin/simd-dispatch /usr/lib/kalign/ dh_install src/kalign-* usr/lib/kalign/ dh_install src/timescorealn-* usr/lib/kalign/ mkdir -p /build/kalign-3.3/debian/kalign/usr/bin cd /build/kalign-3.3/debian/kalign/usr/bin \ && ln -s ../lib/kalign/simd-dispatch kalign && ln -s ../lib/kalign/simd-dispatch timescorealn && true make[1]: Leaving directory '/build/kalign-3.3' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/build/kalign-3.3' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), " make[1]: Leaving directory '/build/kalign-3.3' dh_md5sums dh_builddeb dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_3.3-1_i386.deb'. dpkg-deb: building package 'kalign' in '../kalign_3.3-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../kalign_3.3-1_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: user script /srv/workspace/pbuilder/1422/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1422/tmp/hooks/B01_cleanup finished 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/1422 and its subdirectories I: Current time: Wed Jun 9 05:08:52 +14 2021 I: pbuilder-time-stamp: 1623164932