Tue Jun 8 14:59:33 UTC 2021 I: starting to build kalign/bullseye/i386 on jenkins on '2021-06-08 14:59' Tue Jun 8 14:59:33 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/14987/console.log Tue Jun 8 14:59:33 UTC 2021 I: Downloading source for bullseye/kalign=1:3.3-1 --2021-06-08 14:59:33-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kalign/kalign_3.3-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1941 (1.9K) Saving to: ‘kalign_3.3-1.dsc’ 0K . 100% 113M=0s 2021-06-08 14:59:33 (113 MB/s) - ‘kalign_3.3-1.dsc’ saved [1941/1941] Tue Jun 8 14:59:33 UTC 2021 I: kalign_3.3-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: kalign Binary: kalign Architecture: any Version: 1:3.3-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://msa.sbc.su.se/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/kalign Vcs-Git: https://salsa.debian.org/med-team/kalign.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsimde-dev Package-List: kalign deb science optional arch=any Checksums-Sha1: f1f270aabed1ec034e9b34beb4eb683bd3d25c51 940232 kalign_3.3.orig.tar.gz fb872a4011d95bea9d8d9c7e38d1321fc8848775 14048 kalign_3.3-1.debian.tar.xz Checksums-Sha256: bb49b531ad320881154976194acb8cc0c519715b0d422eac7a171cc246f88d59 940232 kalign_3.3.orig.tar.gz 10c07e8fd2ea72d3e5426b228164834eed87d327b2c1fbb2ff910120372c8476 14048 kalign_3.3-1.debian.tar.xz Files: f160bffa437f8a5f13eb66ea100883bd 940232 kalign_3.3.orig.tar.gz 10caf1590fe5fdf47ab8170bf0462bac 14048 kalign_3.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl+lGh0ACgkQPCZ2P2xn 5uL7pBAApxfNaf7prTNWGh2vvfGs8Wdg4Gf00TRVdvikVGYtCx3rgY6zqD1dTmzx ezk9XCY3RZzZmp1Vc9dTW6wTbfL0hUs+QWywz7sXKU2IGyoyYeijhhTXwkSJcTaD VxwDFjdKYE98LZbUu9SoddsFrt+T9+eQSQ05AthC8hYdGtQQzD0OD0APx5R0vrld EjZ48mNUNYtvvlKm0kqegNK3CYchQxzn0CR8vzldc9RDnxAu2Q9dWZY7wnSQxjbz O+7Wg1joZTo4Ejgj/7e1S52gO9VNvHt6zCnARy8R3j9AxeQsSYx5Zg1qpjT4m2of Rj5EPlYSowYu/S5sRXN70JoXrWS4hync9h45aEM0XTiPbpOZKkn4BTPL6Cp+EuqW 06iFDZGrl1tP85h9zhKMJCDnkclLL3AmTI053u87q1FvPpqV82FlX6ttNVvaQOdm vAgbyBQXaFQiLY+32NiFrN940o6ZDz3/DoGlz5nImuKJdKlY1ot6UoJFHACyRJNh ebRxob9+rPZTBXBj3r64NKu4ofRf9D21vv+2W6MiSbHimiRetvFmqNQLocPCSvew NzpNQIs+85KruQ9NblcKyMSHWDgIdPwehA0Ii5JWuOMWwCb9dngjxAvpYxLIIeKa vpELFHr1BncN5VKzxbmxPc+3Zvfd+DfCSO6rM5pJBsUd9P4NUzI= =Eh2o -----END PGP SIGNATURE----- Tue Jun 8 14:59:33 UTC 2021 I: Checking whether the package is not for us Tue Jun 8 14:59:33 UTC 2021 I: Starting 1st build on remote node ionos6-i386.debian.net. Tue Jun 8 14:59:33 UTC 2021 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Tue Jun 8 15:00:58 UTC 2021 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 11 09:22:35 -12 2022 I: pbuilder-time-stamp: 1657574555 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.wBYiqsos/trustedkeys.kbx': General error gpgv: Signature made Thu Nov 5 21:40:45 2020 -12 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/56904/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='efcd49ae89014ba494952090b74bb31c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='56904' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/pbuilderrc_KDaZ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/b1 --logfile b1/build.log kalign_3.3-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 7 2021 more -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 10 03:46 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Feb 7 2021 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/56904/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 0s (68.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 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) ... 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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 I: Building the package I: Running cd /build/kalign-3.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-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... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking 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... /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... /bin/sed checking for fgrep... /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... /bin/dd checking how to truncate binary pipes... /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: pbuilder1 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... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking 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... /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... /bin/sed checking for fgrep... /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... /bin/dd checking how to truncate binary pipes... /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: pbuilder1 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 -j18 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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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 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 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 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 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 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 -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 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... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for 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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: pbuilder1 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 -j18 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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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 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 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 -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 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 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 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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: pbuilder1 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 -j18 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 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 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 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 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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ^~~~~~ 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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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 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 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 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 -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 genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_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 -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: pbuilder1 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 -j18 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 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 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 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 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 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_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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) | ^~~~~~ 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/bash ../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/bash ../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/bash ../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 /bin/bash ../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 /bin/bash ../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/bash ../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 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 -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 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 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 -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 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 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 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(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: pbuilder1 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 -j18 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 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 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 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 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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/bash ../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/bash ../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/bash ../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/bash ../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 /bin/bash ../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/bash ../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 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 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 -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 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 -rf .libs _libs 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: pbuilder1 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 -j18 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 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 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 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 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 -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/bash ../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/bash ../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/bash ../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 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 -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 /bin/bash ../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/bash ../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/bash ../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 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... 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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: pbuilder1 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 -j18 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 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 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 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 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 ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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/bash ../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 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 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 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 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 -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 timescorealn tldevel.o tlmisc.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.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 needed checking 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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: pbuilder1 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 -j18 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 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 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 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/bash ../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/bash ../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/bash ../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 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 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 genkaligndiffcmds tldevel.o tlmisc.o create_run_kalign_diff_cmds.o -lpthread -lm -fopenmp /bin/bash ../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/bash ../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/bash ../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 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 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 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 -j18 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 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 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: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 /bin/bash ../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 rstdin_test read_from_stdin_test.o tldevel.o -lpthread -lm -fopenmp 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) | ^~~~~~~~~ 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) | ^~~~~~~~~~~~~~ /bin/bash ../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 /bin/bash ../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 /bin/bash ../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 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 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 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 /bin/bash ../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 rwaln rwaln-tldevel.o rwaln-tlmisc.o rwaln-esl_stopwatch.o rwaln-rwalign.o rwaln-alphabet.o -lpthread -lm -fopenmp /bin/bash ../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 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 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' in '../kalign_3.3-1_i386.deb'. dpkg-deb: building package 'kalign-dbgsym' in '../kalign-dbgsym_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: 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/56904 and its subdirectories I: Current time: Mon Jul 11 09:23:58 -12 2022 I: pbuilder-time-stamp: 1657574638 Tue Jun 8 15:00:59 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Tue Jun 8 15:00:59 UTC 2021 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Tue Jun 8 15:08:52 UTC 2021 I: Deleting $TMPDIR on ionos12-i386.debian.net. Tue Jun 8 15:08:53 UTC 2021 I: kalign_3.3-1_i386.changes: Format: 1.8 Date: Fri, 06 Nov 2020 10:40:38 +0100 Source: kalign Binary: kalign kalign-dbgsym Architecture: i386 Version: 1:3.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: kalign - Global and progressive multiple sequence alignment Changes: kalign (1:3.3-1) unstable; urgency=medium . * Team upload. * debian/watch: fix syntax * refresh patches; drop "hardening", it was applied upstream. * Added a patch to retain debugging symbols Checksums-Sha1: c573aceba2d4cbfd7990c11cb9c6821a8b3eb0bc 1342464 kalign-dbgsym_3.3-1_i386.deb 22c5c0d2a2e8ba1ebd3a516a9396416dac2c52ad 4831 kalign_3.3-1_i386.buildinfo 3b348139e3647c0295cfdb744f340815c042c155 177216 kalign_3.3-1_i386.deb Checksums-Sha256: 816ed5a36de17de805b0664b3aefabcdad2aa8737758b93988b1e188bf99322d 1342464 kalign-dbgsym_3.3-1_i386.deb 97c42986d53e0f1e6d3fbc5b0fb36939a17d1ff03a6af13bb6f0c296240b93bd 4831 kalign_3.3-1_i386.buildinfo f67cbbd43e7455b015f739a70050a92047c35444c9b0dc3a62bb6e23a0d3864e 177216 kalign_3.3-1_i386.deb Files: 6af684ffc7123ccde7a53d6d17c1267c 1342464 debug optional kalign-dbgsym_3.3-1_i386.deb 229e912952784b02b3866a4e460b7c84 4831 science optional kalign_3.3-1_i386.buildinfo db5dd49d89e1bd987a1340703e158a24 177216 science optional kalign_3.3-1_i386.deb Tue Jun 8 15:08:54 UTC 2021 I: diffoscope 172 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/kalign_3.3-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/kalign_3.3-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/kalign_3.3-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/b1/kalign_3.3-1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.sAzQFoF3B6/b2/kalign_3.3-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.280s) 0.280s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jun 8 15:08:56 UTC 2021 I: diffoscope 172 found no differences in the changes files, and a .buildinfo file also exists. Tue Jun 8 15:08:56 UTC 2021 I: kalign from bullseye built successfully and reproducibly on i386. Tue Jun 8 15:08:57 UTC 2021 I: Submitting .buildinfo files to external archives: Tue Jun 8 15:08:57 UTC 2021 I: Submitting 8.0K b1/kalign_3.3-1_i386.buildinfo.asc Tue Jun 8 15:08:58 UTC 2021 I: Submitting 8.0K b2/kalign_3.3-1_i386.buildinfo.asc Tue Jun 8 15:08:59 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jun 8 15:08:59 UTC 2021 I: Done submitting .buildinfo files. Tue Jun 8 15:08:59 UTC 2021 I: Removing signed kalign_3.3-1_i386.buildinfo.asc files: removed './b1/kalign_3.3-1_i386.buildinfo.asc' removed './b2/kalign_3.3-1_i386.buildinfo.asc'