Diff of the two buildlogs: -- --- b1/build.log 2021-08-24 14:23:11.620905888 +0000 +++ b2/build.log 2021-08-24 14:27:31.147304913 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 26 08:36:51 -12 2022 -I: pbuilder-time-stamp: 1664224611 +I: Current time: Wed Aug 25 04:23:15 +14 2021 +I: pbuilder-time-stamp: 1629814995 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 [./fasta3_36.3.8h.2020-02-11-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.dVXe2LlC/trustedkeys.kbx': General error -gpgv: Signature made Fri Apr 17 21:54:39 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.cKKpXQ5x/trustedkeys.kbx': General error +gpgv: Signature made Sat Apr 18 23:54:39 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./fasta3_36.3.8h.2020-02-11-3.dsc @@ -31,135 +31,169 @@ dpkg-source: info: applying adjust-scripts I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/12614/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14429/tmp/hooks/D01_modify_environment starting +debug: Running on codethink10-arm64. +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/14429/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14429/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='12614' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=14429 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.Sclw7NKuLo/pbuilderrc_AsaG --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Sclw7NKuLo/b1 --logfile b1/build.log fasta3_36.3.8h.2020-02-11-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.Sclw7NKuLo/pbuilderrc_TkIV --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Sclw7NKuLo/b2 --logfile b2/build.log fasta3_36.3.8h.2020-02-11-3.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink15-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 2021 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 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 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 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 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 178400 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 93744 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 2021 more - -rwsr-xr-x 1 root root 51360 Jul 28 2021 mount - -rwxr-xr-x 1 root root 14496 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 2021 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 2021 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 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/12614/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 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 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 09:09 more + -rwsr-xr-x 1 root root 51360 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 14496 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Aug 25 04:23 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 09:09 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/14429/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -229,7 +263,7 @@ Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libsimde-dev all 0.7.2-4 [259 kB] -Fetched 18.2 MB in 4s (4564 kB/s) +Fetched 18.2 MB in 0s (44.4 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 ... 19646 files and directories currently installed.) @@ -373,7 +407,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/fasta3-36.3.8h.2020-02-11/ && 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 > ../fasta3_36.3.8h.2020-02-11-3_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/fasta3-36.3.8h.2020-02-11/ && 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 > ../fasta3_36.3.8h.2020-02-11-3_source.changes dpkg-buildpackage: info: source package fasta3 dpkg-buildpackage: info: source version 36.3.8h.2020-02-11-3 dpkg-buildpackage: info: source distribution unstable @@ -411,6 +446,7 @@ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_THR -c mshowalign2.c -o mshowalign2_t.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c htime.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c apam.c +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c compacc2e.c: In function 'save_best': compacc2e.c:2547:80: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] 2547 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", @@ -435,7 +471,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c doinit.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DFASTA initfa.c -o init_fa.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLOCAL_SCORE -c scaleswn.c -o scale_se.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c karlin.c @@ -492,38 +527,6 @@ | ~~~~~~ | | | fseek_t {aka long int} -mmgetaa.c: In function 'check_mmap': -mmgetaa.c:1077:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1077:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - | ~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} -mmgetaa.c:1077:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] - 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", - | ~~~^ - | | - | long long int - | %ld - 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], - 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | MM_OFF {aka long int} nmgetlib.c: In function 'agetlib': nmgetlib.c:621:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 621 | fgets(&lm_fd->lline[strlen(lm_fd->lline)],MAX_STR/2,lm_fd->libf); @@ -608,10 +611,42 @@ nmgetlib.c:1136:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1136 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mmgetaa.c: In function 'check_mmap': +mmgetaa.c:1077:31: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} +mmgetaa.c:1077:37: warning: format '%lld' expects argument of type 'long long int', but argument 5 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + | ~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} nmgetlib.c: In function 'egetlib': nmgetlib.c:1220:1: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1220 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mmgetaa.c:1077:43: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type 'MM_OFF' {aka 'long int'} [-Wformat=] + 1077 | fprintf(stderr,"%d:\t%lld\t%lld\t%lld\n", + | ~~~^ + | | + | long long int + | %ld + 1078 | i,m_fd->d_pos_arr[i],m_fd->s_pos_arr[i], + 1079 | m_fd->d_pos_arr[i+1]-m_fd->s_pos_arr[i]); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | MM_OFF {aka long int} nmgetlib.c: In function 'eranlib': nmgetlib.c:1250:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1250 | fgets(lm_fd->lline,MAX_STR,lm_fd->libf); @@ -698,7 +733,6 @@ cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DSW_SSE2 -DSSEARCH initfa.c -o init_sw_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o dropgsw2_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c smith_waterman_sse2.c -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o ncbl2_mlib.c: In function 'ncbl2_getliba': ncbl2_mlib.c:1104:59: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'fseek_t' {aka 'long int'} [-Wformat=] 1104 | fprintf(stderr," could not read sequence record: %lld %ld != %ld\n", @@ -745,7 +779,6 @@ | | fseek_t {aka long int} | long long int | %ld -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o ncbl2_mlib.c: In function 'load_ncbl2': ncbl2_mlib.c:810:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 810 | fread(title_str,(size_t)1,(size_t)title_len,ifile); @@ -791,11 +824,14 @@ ncbl2_mlib.c:1915:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 1915 | fread(val,(size_t)slen,(size_t)1,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c wm_align.c -o lwm_align.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSSEARCH -c cal_cons2.c -o calcons_sw.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c pssm_asn_subs.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c comp_lib9.c -o comp_mlib9.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DCOMP_MLIB -c compacc2e.c -o compacc2_s.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DLALIGN -c mshowalign2.c -o lshowalign.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c -DLALIGN initfa.c -o init_lal.o +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c compacc2e.c: In function 'save_best': compacc2e.c:2547:80: warning: format '%lld' expects argument of type 'long long int', but argument 19 has type 'off_t' {aka 'long int'} [-Wformat=] 2547 | "%-12s %6d %d %.5f %.5f %4d %4d %4d %2d %2d %4d %4d %4d %2d %2d %5d %8lld\n", @@ -820,7 +856,6 @@ | ~~~~~~~~~~~~~~~~~~~~ | | | off_t {aka long int} -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c last_thresh.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -DSW_SSE2 -c dropgsw2.c -o droplal2_sse.o cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c lsim4.c cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -DLALIGN -DLCAL_CONS -g -O2 -fdebug-prefix-map=/build/fasta3-36.3.8h.2020-02-11=. -fstack-protector-strong -Wformat -Werror=format-security -flto -O3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DM10_CONS -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64 -c cal_cons2.c -o calcons_la.o @@ -878,7 +913,6 @@ | ~~~~~~~ | | | fseek_t {aka long int} -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread map_db.c:149:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 149 | fgets(lname,sizeof(lname),stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -890,7 +924,10 @@ map_db.c:524:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 524 | fread((char *)&b[0],(size_t)1,(size_t)4,fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasta36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fa.o drop_nfa.o wm_align.o calcons_fa.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ssearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_sw_sse.o dropgsw2_sse.o smith_waterman_sse2.o lwm_align.o calcons_sw.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2_sse.o smith_waterman_sse2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -931,8 +968,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/lalign36 comp_mlib9.o compacc2_s.o showbest.o build_ares.o re_getlib.o lshowalign.o htime.o apam.o doinit.o init_lal.o droplal2_sse.o smith_waterman_sse2.o lsim4.o calcons_la.o scale_se.o karlin.o last_thresh.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fs.o drop_fs2.o calcons_fs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -976,20 +1011,37 @@ compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ +compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] + 954 | re_openlib(struct lmf_str *, int outtty); + | ^ nmgetlib.c:503:3: note: type mismatch in parameter 2 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) | ^ +nmgetlib.c:503:3: note: type mismatch in parameter 2 + 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) + | ^ +nmgetlib.c:503:3: note: 're_openlib' was previously declared here +nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used nmgetlib.c:503:3: note: 're_openlib' was previously declared here nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); | ^ +mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] + 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); + | ^ +compacc2e.c:2290:1: note: type mismatch in parameter 1 + 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { + | ^ compacc2e.c:2290:1: note: type mismatch in parameter 1 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { | ^ compacc2e.c:2290:1: note: type 'long int' should match type 'int' compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used +compacc2e.c:2290:1: note: type 'long int' should match type 'int' +compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here +compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, | ^ @@ -999,37 +1051,20 @@ compacc2e.c:2178:1: note: type 'long int' should match type 'int' compacc2e.c:2178:1: note: 'get_annot' was previously declared here compacc2e.c:2178:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used -comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] - 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, - | ^ -mshowalign2.c:134:6: note: 'showalign' was previously declared here - 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, - | ^ -mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] - 954 | re_openlib(struct lmf_str *, int outtty); - | ^ -nmgetlib.c:503:3: note: type mismatch in parameter 2 - 503 | re_openlib(struct lmf_str *om_fptr, struct lib_struct *lib_p, int outtty) - | ^ -nmgetlib.c:503:3: note: 're_openlib' was previously declared here -nmgetlib.c:503:3: note: code may be misoptimized unless '-fno-strict-aliasing' is used -mshowbest.c:63:1: warning: type of 's_annot_to_aa1a' does not match original declaration [-Wlto-type-mismatch] - 63 | s_annot_to_aa1a(int n1, struct annot_str *annot_p, unsigned char *ann_arr); - | ^ -compacc2e.c:2290:1: note: type mismatch in parameter 1 - 2290 | s_annot_to_aa1a(long offset, int n1, struct annot_str *annot_p, unsigned char *ann_arr, char *tmp_line) { - | ^ -compacc2e.c:2290:1: note: type 'long int' should match type 'int' -compacc2e.c:2290:1: note: 's_annot_to_aa1a' was previously declared here -compacc2e.c:2290:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used comp_lib9.c:236:1: warning: type of 'process_hist' does not match original declaration [-Wlto-type-mismatch] 236 | process_hist(struct stat_str *sptr, int nstats, | ^ +comp_lib9.c:287:1: warning: type of 'showalign' does not match original declaration [-Wlto-type-mismatch] + 287 | showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1, int maxn, + | ^ scaleswt.c:164:1: note: type mismatch in parameter 7 164 | process_hist(struct stat_str *sptr, int nstats, | ^ +mshowalign2.c:134:6: note: 'showalign' was previously declared here + 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, + | ^ scaleswt.c:164:1: note: 'process_hist' was previously declared here +mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used scaleswt.c:164:1: note: code may be misoptimized unless '-fno-strict-aliasing' is used mshowbest.c:82:1: warning: type of 'get_annot' does not match original declaration [-Wlto-type-mismatch] 82 | get_annot(char *sname, struct mngmsg *m_msp, char *bline, int n1, struct annot_str **annot_p, @@ -1089,6 +1124,7 @@ | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastx36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfx.o drop_tfx.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o url_subs.o mrandom.o -lm -lpthread +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1129,7 +1165,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fasty36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fy.o drop_fz.o faatran.o scale_se.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -1239,6 +1274,15 @@ 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ In function 'strncpy', + inlined from 'build_ares_code' at build_ares.c:217:4: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +build_ares.c: In function 'build_ares_code': +build_ares.c:217:59: note: length computed here + 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); + | ^ +In function 'strncpy', inlined from 'add_annot_def' at doinit.c:627:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -1248,14 +1292,14 @@ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function 'strncpy', - inlined from 'build_ares_code' at build_ares.c:217:4: + inlined from 'add_annot_def' at doinit.c:627:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -build_ares.c: In function 'build_ares_code': -build_ares.c:217:59: note: length computed here - 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); - | ^ +doinit.c: In function 'add_annot_def': +doinit.c:627:7: note: length computed here + 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); + | ^ In function 'strncpy', inlined from 'add_annot_def' at doinit.c:627:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1335,15 +1379,6 @@ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function 'strncpy', - inlined from 'add_annot_def' at doinit.c:627:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -doinit.c: In function 'add_annot_def': -doinit.c:627:7: note: length computed here - 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); - | ^ -In function 'strncpy', inlined from 'set_opt_disp_defs' at doinit.c:991:4, inlined from 'f_init_opts' at initfa.c:476:3, inlined from 'f_initenv' at initfa.c:985:3, @@ -1552,6 +1587,15 @@ 2267 | fn_len = strlen(f_name); | ^ In function 'strncpy', + inlined from 'add_file' at lib_sel.c:317:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +lib_sel.c: In function 'add_file': +lib_sel.c:311:7: note: length computed here + 311 | len=strlen(tname)+1; + | ^ +In function 'strncpy', inlined from 'alloc_file_name' at nmgetlib.c:2274:5, inlined from 'open_lib' at nmgetlib.c:390:26: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1562,15 +1606,6 @@ 2267 | fn_len = strlen(f_name); | ^ In function 'strncpy', - inlined from 'add_file' at lib_sel.c:317:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -lib_sel.c: In function 'add_file': -lib_sel.c:311:7: note: length computed here - 311 | len=strlen(tname)+1; - | ^ -In function 'strncpy', inlined from 'alloc_file_name' at nmgetlib.c:2274:5, inlined from 'open_lib' at nmgetlib.c:390:26: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1676,15 +1711,6 @@ 311 | len=strlen(tname)+1; | ^ In function 'strncpy', - inlined from 'add_file' at lib_sel.c:317:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -lib_sel.c: In function 'add_file': -lib_sel.c:311:7: note: length computed here - 311 | len=strlen(tname)+1; - | ^ -In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -1694,28 +1720,14 @@ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function 'strncpy', - inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: + inlined from 'add_file' at lib_sel.c:317:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -compacc2e.c: In function 'next_annot_entry.constprop': -compacc2e.c:2035:2: note: length computed here - 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); - | ^ -initfa.c: In function 'get_lambda.constprop': -initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { - | ^ -/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here - 542 | extern void *calloc (size_t __nmemb, size_t __size) - | ^ -initfa.c: In function 'get_lambda.constprop': -initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { - | ^ -/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here - 542 | extern void *calloc (size_t __nmemb, size_t __size) - | ^ +lib_sel.c: In function 'add_file': +lib_sel.c:311:7: note: length computed here + 311 | len=strlen(tname)+1; + | ^ In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1743,6 +1755,13 @@ compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ +initfa.c: In function 'get_lambda.constprop': +initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { + | ^ +/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here + 542 | extern void *calloc (size_t __nmemb, size_t __size) + | ^ In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1752,6 +1771,13 @@ compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ +initfa.c: In function 'get_lambda.constprop': +initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { + | ^ +/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here + 542 | extern void *calloc (size_t __nmemb, size_t __size) + | ^ In function 'strncpy', inlined from 'showalign.constprop' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1783,15 +1809,6 @@ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function 'strncpy', - inlined from 'build_ares_code.isra' at build_ares.c:217:4: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -build_ares.c: In function 'build_ares_code.isra': -build_ares.c:217:59: note: length computed here - 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); - | ^ -In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -1801,26 +1818,16 @@ 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ In function 'strncpy', - inlined from 'showalign.constprop' at mshowalign2.c:577:8: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -mshowalign2.c: In function 'showalign.constprop': -mshowalign2.c:577:8: note: length computed here - 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); - | ^ -In function 'strncpy', - inlined from 'encode_json_lines' at url_subs.c:68:3, - inlined from 'do_url1' at url_subs.c:307:42, - inlined from 'do_show' at mshowalign2.c:864:7, - inlined from 'showalign.constprop' at mshowalign2.c:761:7: + inlined from 'build_ares_code.isra' at build_ares.c:217:4: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -mshowalign2.c: In function 'showalign.constprop': -url_subs.c:61:19: note: length computed here - 61 | n_tmp_annot_s = strlen(annot_s)+1; - | ^ +build_ares.c: In function 'build_ares_code.isra': +build_ares.c:217:59: note: length computed here + 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); + | ^ +/usr/bin/ld: /tmp/fasts36.hKXFqS.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function 'strncpy', inlined from 'showalign.constprop' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -1830,7 +1837,7 @@ mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ -/usr/bin/ld: /tmp/fasts36.2piXLk.ltrans0.ltrans.oIn function 'strncpy', +In function 'strncpy', inlined from 'encode_json_lines' at url_subs.c:68:3, inlined from 'do_url1' at url_subs.c:307:42, inlined from 'do_show' at mshowalign2.c:864:7, @@ -1842,8 +1849,6 @@ url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ -: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfasts36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tfs.o drop_tfs.o calcons_tfs.o scaleswts.o last_tat.o tatstats_fs.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); @@ -1929,6 +1934,15 @@ 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function 'strncpy', + inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +compacc2e.c: In function 'next_annot_entry.constprop': +compacc2e.c:2035:2: note: length computed here + 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); + | ^ +In function 'strncpy', inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -1971,6 +1985,27 @@ 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function 'strncpy', + inlined from 'showalign.constprop' at mshowalign2.c:577:8: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +mshowalign2.c: In function 'showalign.constprop': +mshowalign2.c:577:8: note: length computed here + 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); + | ^ +In function 'strncpy', + inlined from 'encode_json_lines' at url_subs.c:68:3, + inlined from 'do_url1' at url_subs.c:307:42, + inlined from 'do_show' at mshowalign2.c:864:7, + inlined from 'showalign.constprop' at mshowalign2.c:761:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +mshowalign2.c: In function 'showalign.constprop': +url_subs.c:61:19: note: length computed here + 61 | n_tmp_annot_s = strlen(annot_s)+1; + | ^ +In function 'strncpy', inlined from 'build_ares_code.isra' at build_ares.c:217:4: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -1997,21 +2032,9 @@ build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ -In function 'strncpy', - inlined from 'add_annot_def' at doinit.c:627:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -doinit.c: In function 'add_annot_def': -doinit.c:627:7: note: length computed here - 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); - | ^ -/usr/bin/ld: /tmp/ssearch36.qI7MY4.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -/usr/bin/ld: /tmp/fastx36.P195n1.ltrans0.ltrans.o: in function `main': +/usr/bin/ld: /tmp/fastx36.Ut9kvz.ltrans0.ltrans.o: in function `main': /build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_fm.o drop_fm.o calcons_fm.o scaleswts.o last_tat.o tatstats_fm.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -2053,6 +2076,21 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +/usr/bin/ld: /tmp/fasta36.ZCghkb.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +In function 'strncpy', + inlined from 'add_annot_def' at doinit.c:627:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +doinit.c: In function 'add_annot_def': +doinit.c:627:7: note: length computed here + 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); + | ^ +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastm36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_s.o htime.o apam.o doinit.o init_tfm.o drop_tfm.o calcons_tfm.o scaleswts.o tatstats_fm.o last_tat.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread +/usr/bin/ld: /tmp/fasty36.RrVfhi.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -2101,10 +2139,7 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -/usr/bin/ld: /tmp/tfastx36.OmkfPj.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/fastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_ff.o drop_ff2.o calcons_ff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o mrandom.o url_subs.o -lm -lpthread -/usr/bin/ld: /tmp/fasta36.qEcu3k.ltrans0.ltrans.o: in function `main': +/usr/bin/ld: /tmp/ssearch36.CGSMNs.ltrans0.ltrans.o: in function `main': /build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); @@ -2147,7 +2182,10 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +/usr/bin/ld: /tmp/tfastx36.IogIcT.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/tfastf36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_tf.o drop_tff.o calcons_tff.o scaleswtf.o last_tat.o tatstats_ff.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o faatran.o mrandom.o url_subs.o -lm -lpthread +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw_sse.o droplnw_sse.o glocal_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -2189,38 +2227,6 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used -/usr/bin/ld: /tmp/lalign36.WIktld.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -/usr/bin/ld: /tmp/fasty36.qiCCTt.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -In function 'strncpy', - inlined from 'set_opt_disp_defs' at doinit.c:991:4, - inlined from 'f_init_opts' at initfa.c:476:3, - inlined from 'f_initenv' at initfa.c:985:3, - inlined from 'initenv' at doinit.c:359:4, - inlined from 'main' at comp_lib9.c:576:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -comp_lib9.c: In function 'main': -doinit.c:991:4: note: length computed here - 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); - | ^ -In function 'strncpy', - inlined from 'pre_parse_markx' at doinit.c:785:5, - inlined from 'initenv' at doinit.c:402:4, - inlined from 'main' at comp_lib9.c:576:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -comp_lib9.c: In function 'main': -doinit.c:785:5: note: length computed here - 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); - | ^ -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/glsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_lnw_sse.o droplnw_sse.o glocal_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread -cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread -/usr/bin/ld: /tmp/tfasty36.0dJgpY.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -2261,6 +2267,33 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +/usr/bin/ld: /tmp/lalign36.EWpt3J.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +cc -Wl,-z,relro -Wl,-z,now -flto -Wdate-time -D_FORTIFY_SOURCE=2 -o ../bin/ggsearch36 comp_mthr9.o work_thr2.o pthr_subs2.o compacc2_t.o showbest.o build_ares.o re_getlib.o mshowalign2_t.o htime.o apam.o doinit.o init_gnw_sse.o dropgnw_sse.o global_sse2.o gwm_align.o calcons_sw.o scale_sn.o karlin.o lgetlib.o lgetaa_m.o c_dispn.o ncbl2_mlib.o lib_sel.o url_subs.o mrandom.o pssm_asn_subs.o -lm -lpthread +In function 'strncpy', + inlined from 'set_opt_disp_defs' at doinit.c:991:4, + inlined from 'f_init_opts' at initfa.c:476:3, + inlined from 'f_initenv' at initfa.c:985:3, + inlined from 'initenv' at doinit.c:359:4, + inlined from 'main' at comp_lib9.c:576:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +comp_lib9.c: In function 'main': +doinit.c:991:4: note: length computed here + 991 | strncpy(this_opt->s_param,s_param,strlen(s_param)); + | ^ +In function 'strncpy', + inlined from 'pre_parse_markx' at doinit.c:785:5, + inlined from 'initenv' at doinit.c:402:4, + inlined from 'main' at comp_lib9.c:576:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +comp_lib9.c: In function 'main': +doinit.c:785:5: note: length computed here + 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); + | ^ compacc2e.c:954:1: warning: type of 're_openlib' does not match original declaration [-Wlto-type-mismatch] 954 | re_openlib(struct lmf_str *, int outtty); | ^ @@ -2301,6 +2334,8 @@ 134 | void showalign (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn, | ^ mshowalign2.c:134:6: note: code may be misoptimized unless '-fno-strict-aliasing' is used +/usr/bin/ld: /tmp/tfasty36.jrc92M.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function 'strncpy', inlined from 'build_ares_code' at build_ares.c:217:4: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2320,15 +2355,6 @@ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function 'strncpy', - inlined from 'build_ares_code' at build_ares.c:217:4: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -build_ares.c: In function 'build_ares_code': -build_ares.c:217:59: note: length computed here - 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); - | ^ -In function 'strncpy', inlined from 'add_annot_def' at doinit.c:627:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -2338,14 +2364,14 @@ 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); | ^ In function 'strncpy', - inlined from 'add_annot_def' at doinit.c:627:7: + inlined from 'build_ares_code' at build_ares.c:217:4: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -doinit.c: In function 'add_annot_def': -doinit.c:627:7: note: length computed here - 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); - | ^ +build_ares.c: In function 'build_ares_code': +build_ares.c:217:59: note: length computed here + 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); + | ^ In function 'strncpy', inlined from 'add_annot_def' at doinit.c:627:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2470,6 +2496,15 @@ 785 | strncpy(tmp_markx->out_file, bp+1, strlen(bp+1)); | ^ In function 'strncpy', + inlined from 'add_annot_def' at doinit.c:627:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +doinit.c: In function 'add_annot_def': +doinit.c:627:7: note: length computed here + 627 | strncpy(m_msp->ann_arr_def[i_ann], bp+1,strlen(bp+1)); + | ^ +In function 'strncpy', inlined from 'set_opt_disp_defs' at doinit.c:991:4, inlined from 'f_init_opts' at initfa.c:476:3, inlined from 'f_initenv' at initfa.c:985:3, @@ -2528,6 +2563,15 @@ 2267 | fn_len = strlen(f_name); | ^ In function 'strncpy', + inlined from 'add_file' at lib_sel.c:317:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +lib_sel.c: In function 'add_file': +lib_sel.c:311:7: note: length computed here + 311 | len=strlen(tname)+1; + | ^ +In function 'strncpy', inlined from 'alloc_file_name' at nmgetlib.c:2274:5, inlined from 'open_lib' at nmgetlib.c:390:26: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2558,15 +2602,6 @@ 2267 | fn_len = strlen(f_name); | ^ In function 'strncpy', - inlined from 'add_file' at lib_sel.c:317:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -lib_sel.c: In function 'add_file': -lib_sel.c:311:7: note: length computed here - 311 | len=strlen(tname)+1; - | ^ -In function 'strncpy', inlined from 'alloc_file_name' at nmgetlib.c:2274:5, inlined from 'open_lib' at nmgetlib.c:390:26: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2577,15 +2612,6 @@ 2267 | fn_len = strlen(f_name); | ^ In function 'strncpy', - inlined from 'add_file' at lib_sel.c:317:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -lib_sel.c: In function 'add_file': -lib_sel.c:311:7: note: length computed here - 311 | len=strlen(tname)+1; - | ^ -In function 'strncpy', inlined from 'showalign.constprop' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -2644,24 +2670,14 @@ 2267 | fn_len = strlen(f_name); | ^ In function 'strncpy', - inlined from 'alloc_file_name' at nmgetlib.c:2274:5, - inlined from 'open_lib' at nmgetlib.c:390:26: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^ -nmgetlib.c: In function 'open_lib': -nmgetlib.c:2267:12: note: length computed here - 2267 | fn_len = strlen(f_name); - | ^ -In function 'strncpy', - inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: + inlined from 'add_file' at lib_sel.c:317:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -compacc2e.c: In function 'next_annot_entry.constprop': -compacc2e.c:2035:2: note: length computed here - 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); - | ^ +lib_sel.c: In function 'add_file': +lib_sel.c:311:7: note: length computed here + 311 | len=strlen(tname)+1; + | ^ In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2702,32 +2718,30 @@ 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function 'strncpy', - inlined from 'showalign.constprop' at mshowalign2.c:577:8: + inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -mshowalign2.c: In function 'showalign.constprop': -mshowalign2.c:577:8: note: length computed here - 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); - | ^ +compacc2e.c: In function 'next_annot_entry.constprop': +compacc2e.c:2035:2: note: length computed here + 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); + | ^ In function 'strncpy', - inlined from 'encode_json_lines' at url_subs.c:68:3, - inlined from 'do_url1' at url_subs.c:307:42, - inlined from 'do_show' at mshowalign2.c:864:7, - inlined from 'showalign.constprop' at mshowalign2.c:761:7: + inlined from 'alloc_file_name' at nmgetlib.c:2274:5, + inlined from 'open_lib' at nmgetlib.c:390:26: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -mshowalign2.c: In function 'showalign.constprop': -url_subs.c:61:19: note: length computed here - 61 | n_tmp_annot_s = strlen(annot_s)+1; - | ^ +nmgetlib.c: In function 'open_lib': +nmgetlib.c:2267:12: note: length computed here + 2267 | fn_len = strlen(f_name); + | ^ In function 'strncpy', - inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8: + inlined from 'showalign.constprop' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -mshowalign2.c: In function 'showalign.constprop.isra': +mshowalign2.c: In function 'showalign.constprop': mshowalign2.c:577:8: note: length computed here 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); | ^ @@ -2735,11 +2749,11 @@ inlined from 'encode_json_lines' at url_subs.c:68:3, inlined from 'do_url1' at url_subs.c:307:42, inlined from 'do_show' at mshowalign2.c:864:7, - inlined from 'showalign.constprop.isra' at mshowalign2.c:761:7: + inlined from 'showalign.constprop' at mshowalign2.c:761:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -mshowalign2.c: In function 'showalign.constprop.isra': +mshowalign2.c: In function 'showalign.constprop': url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ @@ -2774,6 +2788,15 @@ 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ In function 'strncpy', + inlined from 'build_ares_code.isra' at build_ares.c:217:4: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +build_ares.c: In function 'build_ares_code.isra': +build_ares.c:217:59: note: length computed here + 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); + | ^ +In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); @@ -2782,24 +2805,29 @@ compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ +/usr/bin/ld: /tmp/tfasts36.LTTh81.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function 'strncpy', - inlined from 'add_file' at lib_sel.c:317:5: + inlined from 'showalign.constprop.isra' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -lib_sel.c: In function 'add_file': -lib_sel.c:311:7: note: length computed here - 311 | len=strlen(tname)+1; - | ^ +mshowalign2.c: In function 'showalign.constprop.isra': +mshowalign2.c:577:8: note: length computed here + 577 | SAFE_STRNCPY(annot_var_s10,annot_var_dyn->string,strlen(annot_var_dyn->string)); + | ^ In function 'strncpy', - inlined from 'build_ares_code.isra' at build_ares.c:217:4: + inlined from 'encode_json_lines' at url_subs.c:68:3, + inlined from 'do_url1' at url_subs.c:307:42, + inlined from 'do_show' at mshowalign2.c:864:7, + inlined from 'showalign.constprop.isra' at mshowalign2.c:761:7: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -build_ares.c: In function 'build_ares_code.isra': -build_ares.c:217:59: note: length computed here - 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); - | ^ +mshowalign2.c: In function 'showalign.constprop.isra': +url_subs.c:61:19: note: length computed here + 61 | n_tmp_annot_s = strlen(annot_s)+1; + | ^ In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2809,24 +2837,15 @@ compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ -/usr/bin/ld: /tmp/tfasts36.Lu9ogT.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -initfa.c: In function 'get_lambda.constprop': -initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { - | ^ -/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here - 542 | extern void *calloc (size_t __nmemb, size_t __size) - | ^ In function 'strncpy', - inlined from 'build_ares_code.isra' at build_ares.c:217:4: + inlined from 'add_file' at lib_sel.c:317:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^ -build_ares.c: In function 'build_ares_code.isra': -build_ares.c:217:59: note: length computed here - 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); - | ^ +lib_sel.c: In function 'add_file': +lib_sel.c:311:7: note: length computed here + 311 | len=strlen(tname)+1; + | ^ initfa.c: In function 'get_lambda.constprop': initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { @@ -2861,6 +2880,17 @@ compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ +/usr/bin/ld: /tmp/fastm36.PSGmYY.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +In function 'strncpy', + inlined from 'build_ares_code.isra' at build_ares.c:217:4: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^ +build_ares.c: In function 'build_ares_code.isra': +build_ares.c:217:59: note: length computed here + 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); + | ^ In function 'strncpy', inlined from 'build_ares_code.isra' at build_ares.c:217:4: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2870,7 +2900,18 @@ build_ares.c:217:59: note: length computed here 217 | strncpy(cur_ares_p->annot_var_id,annot_str_dyn->string,strlen(annot_str_dyn->string)+2); | ^ -/usr/bin/ld: /tmp/fastm36.ytbxMk.ltrans0.ltrans.o: in function `main': +initfa.c: In function 'get_lambda.constprop': +initfa.c:2224:24: warning: argument 1 value '18446744071709551617' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 2224 | if ((pr = (double *) calloc(max - min + 1, sizeof(double))) == NULL) { + | ^ +/usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here + 542 | extern void *calloc (size_t __nmemb, size_t __size) + | ^ +/usr/bin/ld: /tmp/fastf36.LqUMI5.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +/usr/bin/ld: /tmp/tfastm36.STYe0f.ltrans0.ltrans.o: in function `main': +/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' +/usr/bin/ld: /tmp/tfastf36.WbIPDp.ltrans0.ltrans.o: in function `main': /build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function 'strncpy', inlined from 'next_annot_entry.constprop' at compacc2e.c:2035:2: @@ -2881,12 +2922,6 @@ compacc2e.c:2035:2: note: length computed here 2035 | strncpy(tmp_ann_entry_arr[n_annot].comment,tmp_comment,strlen(tmp_comment)); | ^ -/usr/bin/ld: /tmp/fastf36.fZ1VQZ.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -/usr/bin/ld: /tmp/tfastm36.ikJrtn.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -/usr/bin/ld: /tmp/tfastf36.1iTdBR.ltrans0.ltrans.o: in function `main': -/build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' In function 'strncpy', inlined from 'showalign.constprop' at mshowalign2.c:577:8: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] @@ -2929,9 +2964,9 @@ url_subs.c:61:19: note: length computed here 61 | n_tmp_annot_s = strlen(annot_s)+1; | ^ -/usr/bin/ld: /tmp/glsearch36.UFyRxr.ltrans0.ltrans.o: in function `main': +/usr/bin/ld: /tmp/glsearch36.PsuvlS.ltrans0.ltrans.o: in function `main': /build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' -/usr/bin/ld: /tmp/ggsearch36.RFMjiV.ltrans0.ltrans.o: in function `main': +/usr/bin/ld: /tmp/ggsearch36.ZYyFWa.ltrans0.ltrans.o: in function `main': /build/fasta3-36.3.8h.2020-02-11/src/compacc2e.c:1582: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[2]: Leaving directory '/build/fasta3-36.3.8h.2020-02-11/src' # convoluted, but necessary to allow cross builds @@ -2940,21 +2975,21 @@ make[1]: Entering directory '/build/fasta3-36.3.8h.2020-02-11' cd test ; ./test2G.sh && ./test.sh && ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg -STARTING FASTA36 Mon Sep 26 08:43:35 -12 2022 on codethink15-arm64 -Linux codethink15-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux +STARTING FASTA36 Wed Aug 25 04:25:11 +14 2021 on i-capture-the-hostname +Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux -starting prss36(ssearch/fastx) Mon Sep 26 08:43:35 -12 2022 +starting prss36(ssearch/fastx) Wed Aug 25 04:25:11 +14 2021 done -starting lalign36 Mon Sep 26 08:43:36 -12 2022 -FINISHED Mon Sep 26 08:44:38 -12 2022 +starting lalign36 Wed Aug 25 04:25:11 +14 2021 +FINISHED Wed Aug 25 04:26:11 +14 2021 -STARTING FASTA36 Mon Sep 26 08:44:38 -12 2022 on codethink15-arm64 -Linux codethink15-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux +STARTING FASTA36 Wed Aug 25 04:26:11 +14 2021 on i-capture-the-hostname +Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux -starting prss36(ssearch/fastx) Mon Sep 26 08:44:38 -12 2022 +starting prss36(ssearch/fastx) Wed Aug 25 04:26:11 +14 2021 done -starting lalign36 Mon Sep 26 08:44:39 -12 2022 -FINISHED Mon Sep 26 08:45:41 -12 2022 +starting lalign36 Wed Aug 25 04:26:11 +14 2021 +FINISHED Wed Aug 25 04:27:10 +14 2021 # ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg FASTA searches a protein or DNA sequence data bank version 36.3.8h Aug, 2019 @@ -2966,29 +3001,29 @@ Library: ../seq/prot_test.lseg 2267 residues in 12 sequences -Statistics: (shuffled [461]) MLE statistics: Lambda= 0.1602; K=0.004554 - statistics sampled from 4 (4) to 461 sequences +Statistics: (shuffled [453]) MLE statistics: Lambda= 0.1630; K=0.004734 + statistics sampled from 4 (4) to 453 sequences Algorithm: FASTA (3.8 Nov 2011) [optimized] Parameters: BL50 matrix (15:-5), open/ext: -10/-2 ktup: 2, E-join: 1 (0.667), E-opt: 0.2 (0.333), width: 16 Scan time: 0.010 The best scores are: opt bits E(12) -sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 296.7 2.8e-84 -sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 64.4 2.5e-14 -sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.4 0.14 -sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.5 1.2 -sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 17.9 1.4 -sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.7 2.3 -sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.5 2.6 -sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.5 3.7 -sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.6 4.1 -sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.1 4.2 -sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.7 4.4 -sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 14.9 6.4 +sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu ( 218) 1242 301.7 8.7e-86 +sp|P00502|GSTA1_RAT Glutathione S-transferase alph ( 222) 237 65.4 1.2e-14 +sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Ho ( 142) 51 21.6 0.12 +sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinas ( 351) 43 19.7 1 +sp|P14960|RBS_GUITH Ribulose bisphosphate carboxyl ( 139) 36 18.1 1.2 +sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG ( 108) 31 16.9 2.1 +sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodyte ( 105) 30 16.7 2.4 +sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle ( 160) 30 16.7 3.4 +sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A ( 567) 37 18.3 3.8 +sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A ( 95) 26 15.7 3.8 +sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococc ( 54) 22 14.8 4.1 +sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Ho ( 106) 23 15.0 6 >>sp|P09488|GSTM1_HUMAN Glutathione S-transferase Mu 1 O (218 aa) - initn: 1242 init1: 1242 opt: 1242 Z-score: 1564.8 bits: 296.7 E(12): 2.8e-84 + initn: 1242 init1: 1242 opt: 1242 Z-score: 1592.0 bits: 301.7 E(12): 8.7e-86 Smith-Waterman score: 1242; 78.0% identity (95.4% similar) in 218 aa overlap (1-218:1-218) 10 20 30 40 50 60 @@ -3016,7 +3051,7 @@ 190 200 210 >>sp|P00502|GSTA1_RAT Glutathione S-transferase alpha-1 (222 aa) - initn: 204 init1: 73 opt: 237 Z-score: 309.2 bits: 64.4 E(12): 2.5e-14 + initn: 204 init1: 73 opt: 237 Z-score: 314.6 bits: 65.4 E(12): 1.2e-14 Smith-Waterman score: 237; 27.4% identity (57.0% similar) in 223 aa overlap (4-218:6-218) 10 20 30 40 50 @@ -3044,7 +3079,7 @@ 180 190 200 210 220 >>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha OS=Homo s (142 aa) - initn: 40 init1: 40 opt: 51 Z-score: 80.3 bits: 21.4 E(12): 0.14 + initn: 40 init1: 40 opt: 51 Z-score: 81.7 bits: 21.6 E(12): 0.12 Smith-Waterman score: 51; 25.6% identity (69.2% similar) in 39 aa overlap (177-214:36-73) 150 160 170 180 190 200 @@ -3060,7 +3095,7 @@ 70 80 90 100 110 120 >>sp|P00517|KAPCA_BOVIN cAMP-dependent protein kinase ca (351 aa) - initn: 43 init1: 43 opt: 43 Z-score: 63.3 bits: 19.5 E(12): 1.2 + initn: 43 init1: 43 opt: 43 Z-score: 64.5 bits: 19.7 E(12): 1 Smith-Waterman score: 54; 23.6% identity (47.2% similar) in 72 aa overlap (137-206:229-300) 110 120 130 140 150 160 @@ -3079,7 +3114,7 @@ 320 330 340 350 >>sp|P14960|RBS_GUITH Ribulose bisphosphate carboxylase (139 aa) - initn: 56 init1: 36 opt: 36 Z-score: 61.8 bits: 17.9 E(12): 1.4 + initn: 56 init1: 36 opt: 36 Z-score: 62.8 bits: 18.1 E(12): 1.2 Smith-Waterman score: 36; 57.1% identity (85.7% similar) in 7 aa overlap (7-13:47-53) 10 20 30 @@ -3095,7 +3130,7 @@ 80 90 100 110 120 130 >>sp|P01593|KV101_HUMAN Ig kappa chain V-I region AG OS= (108 aa) - initn: 31 init1: 31 opt: 31 Z-score: 57.5 bits: 16.7 E(12): 2.3 + initn: 31 init1: 31 opt: 31 Z-score: 58.4 bits: 16.9 E(12): 2.1 Smith-Waterman score: 33; 36.0% identity (54.0% similar) in 50 aa overlap (150-190:16-64) 120 130 140 150 160 170 @@ -3111,7 +3146,7 @@ 50 60 70 80 90 100 >>sp|P99998|CYC_PANTR Cytochrome c OS=Pan troglodytes GN (105 aa) - initn: 30 init1: 30 opt: 30 Z-score: 56.5 bits: 16.5 E(12): 2.6 + initn: 30 init1: 30 opt: 30 Z-score: 57.4 bits: 16.7 E(12): 2.4 Smith-Waterman score: 36; 26.5% identity (54.4% similar) in 68 aa overlap (129-193:28-88) 100 110 120 130 140 150 @@ -3130,7 +3165,7 @@ sp|P10 SNK >>sp|P02585|TNNC2_HUMAN Troponin C, skeletal muscle OS=H (160 aa) - initn: 30 init1: 30 opt: 30 Z-score: 53.2 bits: 16.5 E(12): 3.7 + initn: 30 init1: 30 opt: 30 Z-score: 54.1 bits: 16.7 E(12): 3.4 Smith-Waterman score: 41; 25.9% identity (63.0% similar) in 54 aa overlap (44-92:13-62) 20 30 40 50 60 70 @@ -3145,21 +3180,8 @@ sp|P02 ELGTVMRMLGQTPTKEELDAIIEEVDEDGSGTIDFEEFLVMMVRQMKEDAKGKSEEELAE 40 50 60 70 80 90 ->>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) - initn: 26 init1: 26 opt: 26 Z-score: 52.3 bits: 15.6 E(12): 4.1 -Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) - - 90 100 110 120 130 140 -sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK - : :: ::.: -sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG - 60 70 80 90 - - 150 160 170 180 190 200 -sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI - >>sp|P03435|HEMA_I75A3 Hemagglutinin OS=Influenza A viru (567 aa) - initn: 37 init1: 37 opt: 37 Z-score: 52.1 bits: 18.1 E(12): 4.2 + initn: 37 init1: 37 opt: 37 Z-score: 53.1 bits: 18.3 E(12): 3.8 Smith-Waterman score: 50; 28.2% identity (64.1% similar) in 39 aa overlap (74-111:399-437) 50 60 70 80 90 100 @@ -3174,8 +3196,21 @@ sp|P03 YVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYH 430 440 450 460 470 480 +>>sp|P60615|NXL1A_BUNMU Alpha-bungarotoxin isoform A31 O (95 aa) + initn: 26 init1: 26 opt: 26 Z-score: 53.1 bits: 15.7 E(12): 3.8 +Smith-Waterman score: 30; 54.5% identity (63.6% similar) in 11 aa overlap (115-125:86-94) + + 90 100 110 120 130 140 +sp|P10 HLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGK + : :: ::.: +sp|P60 SRGKVVELGCAATCPSKKPYEEVTCCSTDKC-NPH-PKQRPG + 60 70 80 90 + + 150 160 170 180 190 200 +sp|P10 RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYI + >>sp|P00193|FER_PEPAS Ferredoxin OS=Peptostreptococcus a (54 aa) - initn: 22 init1: 22 opt: 22 Z-score: 51.7 bits: 14.7 E(12): 4.4 + initn: 22 init1: 22 opt: 22 Z-score: 52.4 bits: 14.8 E(12): 4.1 Smith-Waterman score: 25; 50.0% identity (100.0% similar) in 4 aa overlap (171-174:15-18) 150 160 170 180 190 200 @@ -3191,7 +3226,7 @@ 50 >>sp|P01834|IGKC_HUMAN Ig kappa chain C region OS=Homo s (106 aa) - initn: 23 init1: 23 opt: 23 Z-score: 47.6 bits: 14.9 E(12): 6.4 + initn: 23 init1: 23 opt: 23 Z-score: 48.4 bits: 15.0 E(12): 6 Smith-Waterman score: 35; 18.3% identity (53.5% similar) in 71 aa overlap (58-124:12-82) 30 40 50 60 70 80 @@ -3217,8 +3252,8 @@ 218 residues in 1 query sequences 2267 residues in 12 library sequences Tcomplib [36.3.8h Aug, 2019] (8 proc in memory [0G]) - start: Mon Sep 26 08:45:41 2022 done: Mon Sep 26 08:45:41 2022 - Total Scan time: 0.010 Total Display time: 0.010 + start: Wed Aug 25 04:27:10 2021 done: Wed Aug 25 04:27:10 2021 + Total Scan time: 0.010 Total Display time: 0.000 Function used was FASTA [36.3.8h Aug, 2019] make[1]: Leaving directory '/build/fasta3-36.3.8h.2020-02-11' @@ -3251,8 +3286,8 @@ dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'fasta3-dbgsym' in '../fasta3-dbgsym_36.3.8h.2020-02-11-3_arm64.deb'. -dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8h.2020-02-11-3_all.deb'. dpkg-deb: building package 'fasta3' in '../fasta3_36.3.8h.2020-02-11-3_arm64.deb'. +dpkg-deb: building package 'fasta3-doc' in '../fasta3-doc_36.3.8h.2020-02-11-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../fasta3_36.3.8h.2020-02-11-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3260,12 +3295,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/14429/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14429/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/12614 and its subdirectories -I: Current time: Mon Sep 26 08:46:10 -12 2022 -I: pbuilder-time-stamp: 1664225170 +I: removing directory /srv/workspace/pbuilder/14429 and its subdirectories +I: Current time: Wed Aug 25 04:27:30 +14 2021 +I: pbuilder-time-stamp: 1629815250