Diff of the two buildlogs: -- --- b1/build.log 2021-11-13 22:13:06.219398190 +0000 +++ b2/build.log 2021-11-13 22:21:24.326313950 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Dec 16 16:31:01 -12 2022 -I: pbuilder-time-stamp: 1671251461 +I: Current time: Sun Nov 14 12:13:08 +14 2021 +I: pbuilder-time-stamp: 1636841588 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./last-align_1179-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.BsScvKkS/trustedkeys.kbx': General error -gpgv: Signature made Sun Jan 31 22:40:51 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.N4uebQ6Y/trustedkeys.kbx': General error +gpgv: Signature made Tue Feb 2 00:40:51 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying fix-959866.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3435206/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/210176/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/210176/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/210176/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='495fb2e1a40e4cf1a9135176470b8d05' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3435206' - PS1='# ' - PS2='> ' + INVOCATION_ID=bad865e046ce4e5396ef5c726777daac + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=210176 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.YeXO4vwVMc/pbuilderrc_lpaa --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YeXO4vwVMc/b1 --logfile b1/build.log last-align_1179-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.YeXO4vwVMc/pbuilderrc_Bo0w --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YeXO4vwVMc/b2 --logfile b2/build.log last-align_1179-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 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 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 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 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 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 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 23 06:04 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 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/3435206/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Nov 14 12:13 sh -> bash + lrwxrwxrwx 1 root root 4 Oct 22 01:41 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/210176/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -271,7 +305,7 @@ Get: 65 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3 [445 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] -Fetched 27.4 MB in 0s (77.8 MB/s) +Fetched 27.4 MB in 1s (39.3 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 ... 19655 files and directories currently installed.) @@ -557,7 +591,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/last-align-1179/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../last-align_1179-1_source.changes +hostname: Name or service not known +I: Running cd /build/last-align-1179/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../last-align_1179-1_source.changes dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 1179-1 dpkg-buildpackage: info: source distribution unstable @@ -570,37 +605,37 @@ make[1]: Entering directory '/build/last-align-1179' for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \ dh_auto_clean -- SFX=-${SIMD} ; done - make -j16 clean SFX=-avx2 + make -j15 clean SFX=-avx2 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' rm -f lastdb-avx2 lastal-avx2 last-split-avx2 last-merge-batches-avx2 last-pair-probs-avx2 lastdb8-avx2 lastal8-avx2 last-split8-avx2 *.o* */*.o* make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 clean SFX=-avx + make -j15 clean SFX=-avx make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' rm -f lastdb-avx lastal-avx last-split-avx last-merge-batches-avx last-pair-probs-avx lastdb8-avx lastal8-avx last-split8-avx *.o* */*.o* make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 clean SFX=-sse4.1 + make -j15 clean SFX=-sse4.1 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' rm -f lastdb-sse4.1 lastal-sse4.1 last-split-sse4.1 last-merge-batches-sse4.1 last-pair-probs-sse4.1 lastdb8-sse4.1 lastal8-sse4.1 last-split8-sse4.1 *.o* */*.o* make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 clean SFX=-ssse3 + make -j15 clean SFX=-ssse3 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' rm -f lastdb-ssse3 lastal-ssse3 last-split-ssse3 last-merge-batches-ssse3 last-pair-probs-ssse3 lastdb8-ssse3 lastal8-ssse3 last-split8-ssse3 *.o* */*.o* make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 clean SFX=-sse3 + make -j15 clean SFX=-sse3 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' rm -f lastdb-sse3 lastal-sse3 last-split-sse3 last-merge-batches-sse3 last-pair-probs-sse3 lastdb8-sse3 lastal8-sse3 last-split8-sse3 *.o* */*.o* make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 clean SFX=-sse2 + make -j15 clean SFX=-sse2 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' rm -f lastdb-sse2 lastal-sse2 last-split-sse2 last-merge-batches-sse2 last-pair-probs-sse2 lastdb8-sse2 lastal8-sse2 last-split8-sse2 *.o* */*.o* @@ -630,7 +665,7 @@ find . -name '*.o' -delete ; \ find . -name '*.o8' -delete ; \ done - make -j16 "INSTALL=install --strip-program=true" all SFX=-avx2 + make -j15 "INSTALL=install --strip-program=true" all SFX=-avx2 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc @@ -654,7 +689,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc dna_words_finder.cc: In member function 'void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)': dna_words_finder.cc:50:41: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -662,14 +696,13 @@ dna_words_finder.cc:51:63: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc LastalArguments.cc: In member function 'void cbrc::LastalArguments::writeCommented(std::ostream&) const': LastalArguments.cc:615:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) @@ -677,6 +710,8 @@ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc @@ -750,7 +785,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-avx2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 "INSTALL=install --strip-program=true" all SFX=-avx + make -j15 "INSTALL=install --strip-program=true" all SFX=-avx make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc @@ -774,7 +809,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc dna_words_finder.cc: In member function 'void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)': dna_words_finder.cc:50:41: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -782,14 +816,13 @@ dna_words_finder.cc:51:63: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc LastalArguments.cc: In member function 'void cbrc::LastalArguments::writeCommented(std::ostream&) const': LastalArguments.cc:615:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) @@ -797,6 +830,8 @@ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc @@ -870,7 +905,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mavx -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-avx Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 "INSTALL=install --strip-program=true" all SFX=-sse4.1 + make -j15 "INSTALL=install --strip-program=true" all SFX=-sse4.1 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc @@ -894,7 +929,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc dna_words_finder.cc: In member function 'void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)': dna_words_finder.cc:50:41: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -902,6 +936,7 @@ dna_words_finder.cc:51:63: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc @@ -909,7 +944,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc LastalArguments.cc: In member function 'void cbrc::LastalArguments::writeCommented(std::ostream&) const': LastalArguments.cc:615:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) @@ -920,7 +954,7 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAligner2qual.cc:3: + from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -936,7 +970,7 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerDna.cc:4: + from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -949,10 +983,11 @@ /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAligner.cc:49: + from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1030,7 +1065,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse4.1 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse4.1 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 "INSTALL=install --strip-program=true" all SFX=-ssse3 + make -j15 "INSTALL=install --strip-program=true" all SFX=-ssse3 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc @@ -1054,7 +1089,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc dna_words_finder.cc: In member function 'void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)': dna_words_finder.cc:50:41: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1062,14 +1096,13 @@ dna_words_finder.cc:51:63: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc LastalArguments.cc: In member function 'void cbrc::LastalArguments::writeCommented(std::ostream&) const': LastalArguments.cc:615:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 615 | if( isTranslated() ) @@ -1077,10 +1110,12 @@ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerDna.cc:4: + from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1088,16 +1123,15 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerPssm.cc:3: + from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerFrame.cc:4: + from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1105,7 +1139,7 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAligner2qual.cc:3: + from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1113,11 +1147,12 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAligner.cc:49: + from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc @@ -1182,15 +1217,15 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -mssse3 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-ssse3 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-ssse3 last-pair-probs.o last-pair-probs-main.o -lz +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-ssse3 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -mssse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-ssse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 "INSTALL=install --strip-program=true" all SFX=-sse3 + make -j15 "INSTALL=install --strip-program=true" all SFX=-sse3 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc @@ -1214,7 +1249,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc dna_words_finder.cc: In member function 'void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)': dna_words_finder.cc:50:41: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1222,6 +1256,7 @@ dna_words_finder.cc:51:63: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc @@ -1229,14 +1264,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerFrame.o GappedXdropAlignerFrame.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc -LastalArguments.cc: In member function 'void cbrc::LastalArguments::writeCommented(std::ostream&) const': -LastalArguments.cc:615:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 615 | if( isTranslated() ) - | ^~ -LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 616 | stream << " F="; writeIntList(stream, frameshiftCosts); - | ^~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, @@ -1245,6 +1272,13 @@ /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +LastalArguments.cc: In member function 'void cbrc::LastalArguments::writeCommented(std::ostream&) const': +LastalArguments.cc:615:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 615 | if( isTranslated() ) + | ^~ +LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 616 | stream << " F="; writeIntList(stream, frameshiftCosts); + | ^~~~~~~~~~~~ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, @@ -1256,28 +1290,29 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerPssm.cc:3: + from GappedXdropAlignerFrame.cc:4: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAligner.cc:49: + from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerFrame.cc:4: + from GappedXdropAligner.cc:49: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastEvaluer.o LastEvaluer.cc @@ -1350,7 +1385,7 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse3 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse3 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz make[3]: Leaving directory '/build/last-align-1179/src' make[2]: Leaving directory '/build/last-align-1179' - make -j16 "INSTALL=install --strip-program=true" all SFX=-sse2 + make -j15 "INSTALL=install --strip-program=true" all SFX=-sse2 make[2]: Entering directory '/build/last-align-1179' make[3]: Entering directory '/build/last-align-1179/src' g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o Alphabet.o Alphabet.cc @@ -1374,7 +1409,6 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc dna_words_finder.cc: In member function 'void DnaWordsFinder::set(unsigned int, unsigned int, const uchar*, const uchar*, bool)': dna_words_finder.cc:50:41: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | baseToCode[lettersToNumbers["ACGT"[i]]] = c; @@ -1382,6 +1416,7 @@ dna_words_finder.cc:51:63: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | if (!isMaskLowercase) baseToCode[lettersToNumbers["acgt"[i]]] = c; | ~~~~~~~~^ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o lastdb.o lastdb.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GappedXdropAlignerDna.o GappedXdropAlignerDna.cc @@ -1396,11 +1431,10 @@ LastalArguments.cc:616:22: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 616 | stream << " F="; writeIntList(stream, frameshiftCosts); | ^~~~~~~~~~~~ -g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerDna.cc:4: + from GappedXdropAlignerPssm.cc:3: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1408,7 +1442,7 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAlignerPssm.cc:3: + from GappedXdropAligner2qual.cc:3: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1416,7 +1450,7 @@ In file included from /usr/include/simde/x86/avx2.h:33, from mcf_simd.hh:8, from GappedXdropAligner.hh:51, - from GappedXdropAligner2qual.cc:3: + from GappedXdropAlignerDna.cc:4: /usr/include/simde/x86/avx.h: In function '__vector(4) long int simde__m256i_from_private(simde__m256i_private)': /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { @@ -1437,6 +1471,7 @@ /usr/include/simde/x86/avx.h:271:1: note: the ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 271 | simde__m256i_from_private(simde__m256i_private v) { | ^~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_frameshift_xdrop_aligner.o mcf_frameshift_xdrop_aligner.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o mcf_gap_costs.o mcf_gap_costs.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc @@ -1502,9 +1537,9 @@ g++ -DLAST_INT_TYPE=unsigned -DALPHABET_CAPACITY=66 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -I. -c -o LastdbArguments.o LastdbArguments.cc cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -msse2 -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches-sse2 last-merge-batches.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs-sse2 last-pair-probs.o last-pair-probs-main.o -lz +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o last-split8-sse2 Alphabet.o LambdaCalculator.o fileMap.o cbrc_linalg.o mcf_substitution_matrix_stats.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -DSIMDE_ENABLE_OPENMP -g -O2 -fdebug-prefix-map=/build/last-align-1179=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -fopenmp-simd -O3 -msse2 -O3 -std=c++11 -pthread -DHAS_CXX_THREADS -Wl,-z,relro -Wl,-z,now -pthread -o lastal8-sse2 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o dna_words_finder.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerDna.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GappedXdropAlignerFrame.o mcf_frameshift_xdrop_aligner.o mcf_gap_costs.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o cbrc_linalg.o mcf_substitution_matrix_stats.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz @@ -1625,12 +1660,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/210176/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/210176/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3435206 and its subdirectories -I: Current time: Fri Dec 16 16:36:07 -12 2022 -I: pbuilder-time-stamp: 1671251767 +I: removing directory /srv/workspace/pbuilder/210176 and its subdirectories +I: Current time: Sun Nov 14 12:21:24 +14 2021 +I: pbuilder-time-stamp: 1636842084