Diff of the two buildlogs: -- --- b1/build.log 2023-08-03 16:23:36.834921552 +0000 +++ b2/build.log 2023-08-03 16:24:34.372988192 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 3 04:22:32 -12 2023 -I: pbuilder-time-stamp: 1691079752 +I: Current time: Thu Sep 5 12:46:42 +14 2024 +I: pbuilder-time-stamp: 1725490002 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./libpsortb_1.0+dfsg-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.vowFShZC/trustedkeys.kbx': General error -gpgv: Signature made Thu Dec 3 09:17:09 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.kiZAReay/trustedkeys.kbx': General error +gpgv: Signature made Fri Dec 4 11:17:09 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,135 +31,166 @@ dpkg-source: info: applying use_debian_packaged_libsvm.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1776016/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1860778/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Sep 5 12:46 /bin/sh -> /bin/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/1860778/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1860778/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='927b426ab8fb4dc582ef69dd3d28a404' - 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='1776016' - PS1='# ' - PS2='> ' + INVOCATION_ID=3f5c9dfe6ad24c8ab50f6c5206bae9ed + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1860778 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/r-b-build.2hxLrf3m/pbuilderrc_AaDx --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2hxLrf3m/b1 --logfile b1/build.log libpsortb_1.0+dfsg-4.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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/r-b-build.2hxLrf3m/pbuilderrc_C3BB --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.2hxLrf3m/b2 --logfile b2/build.log libpsortb_1.0+dfsg-4.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jan 20 2022 more - -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount - -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 6 21:24 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jan 20 2022 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1776016/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jan 21 2022 more + -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount + -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Sep 5 12:46 sh -> /bin/bash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jan 21 2022 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1860778/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -244,7 +275,7 @@ Get: 37 http://deb.debian.org/debian bullseye/main amd64 libsvm3 amd64 3.24+ds-6 [43.6 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libsvm-dev amd64 3.24+ds-6 [64.2 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] -Fetched 20.2 MB in 0s (51.5 MB/s) +Fetched 20.2 MB in 0s (75.7 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 ... 19707 files and directories currently installed.) @@ -417,7 +448,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/libpsortb-1.0+dfsg/ && 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 > ../libpsortb_1.0+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/1860778/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1860778/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libpsortb-1.0+dfsg/ && 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 > ../libpsortb_1.0+dfsg-4_source.changes dpkg-buildpackage: info: source package libpsortb dpkg-buildpackage: info: source version 1.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable @@ -593,19 +628,19 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j15 + make -j16 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' make all-recursive make[2]: Entering directory '/build/libpsortb-1.0+dfsg' Making all in svmloc make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -fPIC -DPIC -o .libs/binding.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o binding.lo binding.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o svmloc.lo svmloc.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -fPIC -DPIC -o .libs/svmloc.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -fPIC -DPIC -o .libs/binding.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c binding.cpp -o binding.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c svmloc.cpp -o svmloc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm +/bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -lsvm -Wl,-z,relro -Wl,-z,now -o libsvmloc.la -rpath /usr/lib/x86_64-linux-gnu binding.lo svmloc.lo -lm libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o .libs/binding.o .libs/svmloc.o -lsvm -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsvmloc.so.0 -o .libs/libsvmloc.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libsvmloc.so.0" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so.0") libtool: link: (cd ".libs" && rm -f "libsvmloc.so" && ln -s "libsvmloc.so.0.0.0" "libsvmloc.so") @@ -615,66 +650,34 @@ make[3]: Leaving directory '/build/libpsortb-1.0+dfsg/svmloc' Making all in modhmm0.92b make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o core_algorithms_multialpha.lo core_algorithms_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o debug_funcs.lo debug_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hmmsearch.lo hmmsearch.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm.lo readhmm.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readhmm_multialpha.lo readhmm_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readseqs_multialpha.lo readseqs_multialpha.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_calculation_funcs.lo std_calculation_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o std_funcs.lo std_funcs.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o training_algorithms_multialpha.lo training_algorithms_multialpha.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -fPIC -DPIC -o .libs/hmmsearch.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -fPIC -DPIC -o .libs/debug_funcs.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -fPIC -DPIC -o .libs/readhmm.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -fPIC -DPIC -o .libs/core_algorithms_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -fPIC -DPIC -o .libs/training_algorithms_multialpha.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -fPIC -DPIC -o .libs/std_funcs.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm_multialpha.c -fPIC -DPIC -o .libs/readhmm_multialpha.o -hmmsearch.c: In function 'get_scores': -hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] - 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); - | ^ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readseqs_multialpha.c -fPIC -DPIC -o .libs/readseqs_multialpha.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_calculation_funcs.c -fPIC -DPIC -o .libs/std_calculation_funcs.o debug_funcs.c: In function 'dump_viterbi_path': debug_funcs.c:320:38: warning: implicit declaration of function 'get_mtx_index' [-Wimplicit-function-declaration] 320 | dump_viterbi_path(viterbi_mtxp + get_mtx_index(row-1, cur->prev, row_size), hmmp, | ^~~~~~~~~~~~~ -hmmsearch.c: In function 'get_nullmodel_score_multi': -hmmsearch.c:656:35: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:674:37: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:693:37: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); - | ~^ ~~~~~~~~~ - | | | - | char * struct letter_s * -hmmsearch.c:712:37: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] - 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); - | ~^ ~~~~~~~ - | | | - | char * struct letter_s * debug_funcs.c: In function 'dump_replacement_letters': -std_calculation_funcs.c: In function 'update_labelings': -std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1295 | cur_address = (int)((cur_rowp+v)->labeling); - | ^ debug_funcs.c:861:14: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 861 | printf("%c ", (*(replacement_letters->letters + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s -std_calculation_funcs.c:1309:5: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { - | ^ debug_funcs.c: In function 'dump_replacement_letters_multi': debug_funcs.c:915:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 915 | printf("%c ", (*(replacement_letters->letters_1 + i))); @@ -686,43 +689,73 @@ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s -std_calculation_funcs.c: In function 'deallocate_row_labelings': -std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1425 | cur_address = (int)((prev_rowp+v)->labeling); - | ^ debug_funcs.c:921:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 921 | printf("%c ", (*(replacement_letters->letters_3 + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s -std_calculation_funcs.c:1430:5: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { - | ^ debug_funcs.c:924:16: warning: format '%c' expects argument of type 'int', but argument 2 has type 'struct letter_s' [-Wformat=] 924 | printf("%c ", (*(replacement_letters->letters_4 + i))); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int struct letter_s +hmmsearch.c: In function 'get_scores': +hmmsearch.c:535:19: warning: assignment to 'struct helix_site *' from incompatible pointer type 'helix_sites *' [-Wincompatible-pointer-types] + 535 | hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); + | ^ +hmmsearch.c: In function 'get_nullmodel_score_multi': +hmmsearch.c:656:35: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 656 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:674:37: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 674 | printf("Could not find letter %s when scoring null model\n", &seq_2[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +hmmsearch.c:693:37: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 693 | printf("Could not find letter %s when scoring null model\n", &seq_3[l]); + | ~^ ~~~~~~~~~ + | | | + | char * struct letter_s * +readhmm.c: In function 'readhmm': +readhmm.c:121:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +hmmsearch.c:712:37: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'struct letter_s *' [-Wformat=] + 712 | printf("Could not find letter %s when scoring null model\n", &seq[l]); + | ~^ ~~~~~~~ + | | | + | char * struct letter_s * +readhmm.c: In function 'readanhmm': +readhmm.c:397:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ +readhmm_multialpha.c: In function 'copy_hmm_struct': +readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ readseqs_multialpha.c: In function 'get_sequence_fasta_multi': readseqs_multialpha.c:83:39: warning: assignment to 'char' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 83 | (seq_infop->seqs + seq_nr)->name[0] = "s"; | ^ +readhmm_multialpha.c: In function 'readhmm_multialpha': +std_funcs.c: In function 'get_replacement_letter_index_single': +readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] + 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + | ^ readseqs_multialpha.c: In function 'get_sequence_std_multi': readseqs_multialpha.c:121:55: warning: unknown escape sequence: '\s' 121 | if(line[0] == '<' || line[0] == '#' || line[0] == '\s' || line[0] == '\n' || line[0] == '/') { | ^~~~ +std_funcs.c:683:62: warning: comparison between pointer and integer + 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { + | ^~ readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': readseqs_multialpha.c:372:18: warning: unknown escape sequence: '\s' 372 | else if(i == '\s' && i == '\n') { | ^~~~ -readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] - 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ - | read_prior_file_multi -readhmm.c: In function 'readhmm': -readhmm.c:121:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 121 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ core_algorithms_multialpha.c: In function 'msa_forward_multi': core_algorithms_multialpha.c:1192:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1192 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); @@ -733,6 +766,10 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readseqs_multialpha.c:389:22: warning: implicit declaration of function 'read_multi_prior_file_multi'; did you mean 'read_prior_file_multi'? [-Wimplicit-function-declaration] + 389 | read_priorfile = read_multi_prior_file_multi(&em_di_1, hmmp, priorfile_a1, 1); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ + | read_prior_file_multi core_algorithms_multialpha.c:1199:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1199 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -760,14 +797,10 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readhmm.c: In function 'readanhmm': -readhmm.c:397:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 397 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -readseqs_multialpha.c: In function 'get_sequence_std_multi': -readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c: In function 'readhmm': +readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c: In function 'msa_backward_multi': core_algorithms_multialpha.c:1419:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1419 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); @@ -787,7 +820,6 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': core_algorithms_multialpha.c:1435:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1435 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -806,19 +838,14 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c: In function 'msa_baum_welch_dirichlet_multi': +core_algorithms_multialpha.c: In function 'msa_viterbi_multi': training_algorithms_multialpha.c:701:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 701 | alphabet = hmmp->alphabet; | ^ training_algorithms_multialpha.c:710:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 710 | alphabet = hmmp->alphabet_2; | ^ -training_algorithms_multialpha.c:719:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 719 | alphabet = hmmp->alphabet_3; - | ^ -training_algorithms_multialpha.c:728:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] - 728 | alphabet = hmmp->alphabet_4; - | ^ -core_algorithms_multialpha.c: In function 'msa_viterbi_multi': core_algorithms_multialpha.c:1608:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1608 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -828,6 +855,12 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +training_algorithms_multialpha.c:719:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 719 | alphabet = hmmp->alphabet_3; + | ^ +training_algorithms_multialpha.c:728:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] + 728 | alphabet = hmmp->alphabet_4; + | ^ core_algorithms_multialpha.c:1615:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1615 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -842,10 +875,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * +readhmm.c: In function 'readanhmm': In file included from core_algorithms_multialpha.c:7: funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 345 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1633:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1633 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -855,38 +892,39 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': -readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 625 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c: In function 'get_reverse_msa_seq': core_algorithms_multialpha.c: In function 'msa_one_best_multi': -readseqs_multialpha.c:754:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 754 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c: In function 'read_module': core_algorithms_multialpha.c:1892:87: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1892 | a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * -readseqs_multialpha.c:874:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 874 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from core_algorithms_multialpha.c:7: funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ -readseqs_multialpha.c:995:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 995 | fgets(line, MAX_LINE, seqfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 751 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ core_algorithms_multialpha.c:1899:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1899 | a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ | | | char * +readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 786 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from core_algorithms_multialpha.c:7: funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 821 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1908:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1908 | a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -896,6 +934,12 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +readhmm.c:850:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 850 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm.c:854:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 854 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ core_algorithms_multialpha.c:1917:86: warning: passing argument 1 of 'get_alphabet_index' from incompatible pointer type [-Wincompatible-pointer-types] 1917 | a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ @@ -905,22 +949,40 @@ funcs.h:136:24: note: expected 'struct letter_s *' but argument is of type 'char *' 136 | int get_alphabet_index(struct letter_s*, char*, int); | ^~~~~~~~~~~~~~~~ +std_funcs.c: In function 'get_reverse_msa_seq_multi': +std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] + 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + | ^ training_algorithms_multialpha.c: In function 'extended_msa_baum_welch_dirichlet_multi': +std_funcs.c: In function 'update_shares_prior_multi': training_algorithms_multialpha.c:1639:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1639 | alphabet = hmmp->alphabet; | ^ +readhmm.c: In function 'read_prior_files': +std_funcs.c:2471:5: warning: 'return' with no value, in function returning non-void + 2471 | return; + | ^~~~~~ training_algorithms_multialpha.c:1646:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1646 | alphabet = hmmp->alphabet_2; | ^ +readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1231 | fgets(ps, 2048, priorfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1653:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1653 | alphabet = hmmp->alphabet_3; | ^ +std_funcs.c:2457:5: note: declared here + 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +std_calculation_funcs.c: In function 'update_labelings': training_algorithms_multialpha.c:1660:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1660 | alphabet = hmmp->alphabet_4; | ^ -readhmm.c: In function 'readhmm': -readhmm.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | fgets(s, MAX_LINE, file); +std_calculation_funcs.c:1295:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1295 | cur_address = (int)((cur_rowp+v)->labeling); + | ^ +readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c:1784:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1784 | alphabet = hmmp->alphabet; @@ -928,60 +990,77 @@ training_algorithms_multialpha.c:1791:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1791 | alphabet = hmmp->alphabet_2; | ^ +std_calculation_funcs.c:1309:5: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1309 | if((int)((cur_rowp+w)->labeling) == cur_address && (cur_rowp + w)->is_updated == NO) { + | ^ training_algorithms_multialpha.c:1798:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1798 | alphabet = hmmp->alphabet_3; | ^ training_algorithms_multialpha.c:1805:12: warning: assignment to 'int' from 'char *' makes integer from pointer without a cast [-Wint-conversion] 1805 | alphabet = hmmp->alphabet_4; | ^ -readhmm.c: In function 'readanhmm': -readhmm.c:345:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 345 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c: In function 'get_replacement_letter_index_single': -readhmm.c: In function 'read_module': -readhmm.c:751:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 751 | fgets(s, MAX_LINE, file); +std_calculation_funcs.c: In function 'deallocate_row_labelings': +std_calculation_funcs.c:1425:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1425 | cur_address = (int)((prev_rowp+v)->labeling); + | ^ +std_calculation_funcs.c:1430:5: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 1430 | if((int)((prev_rowp+w)->labeling) == cur_address) { + | ^ +readseqs_multialpha.c: In function 'get_sequence_std_multi': +readseqs_multialpha.c:286:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c: In function 'read_module_multi': +readhmm_multialpha.c:1042:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1042 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -std_funcs.c:683:62: warning: comparison between pointer and integer - 683 | if(((replacement_letters->letters + a_index)->letter)[0] == c) { - | ^~ -readhmm.c:786:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 786 | fgets(s, MAX_LINE, file); +readhmm_multialpha.c:1077:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1077 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:821:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 821 | fgets(s, MAX_LINE, file); +readhmm_multialpha.c:1111:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1111 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:850:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 850 | fgets(s, MAX_LINE, file); +readhmm_multialpha.c:1140:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1140 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c:854:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 854 | fgets(s, MAX_LINE, file); +readhmm_multialpha.c:1143:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1143 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1169 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1172:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1172 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1198:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1198 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1202:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1202 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1229:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1229 | fgets(s, MAX_LINE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +readhmm_multialpha.c:1236:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1236 | fgets(s, MAX_LINE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm.c: In function 'read_prior_files': -readhmm.c:1231:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1231 | fgets(ps, 2048, priorfile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c: In function 'copy_hmm_struct': -readhmm_multialpha.c:273:34: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 273 | retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ -std_funcs.c: In function 'get_reverse_msa_seq': -readhmm_multialpha.c: In function 'readhmm_multialpha': -std_funcs.c:2076:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2076 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ -readhmm_multialpha.c:469:28: warning: assignment to 'struct transition_s *' from incompatible pointer type 'int *' [-Wincompatible-pointer-types] - 469 | hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); - | ^ +readseqs_multialpha.c: In function 'get_sequences_msa_std_multi': +readseqs_multialpha.c:625:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 625 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:754:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 754 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:874:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 874 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +readseqs_multialpha.c:995:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 995 | fgets(line, MAX_LINE, seqfile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ training_algorithms_multialpha.c: In function 'add_to_E_multi': -std_funcs.c: In function 'get_reverse_msa_seq_multi': training_algorithms_multialpha.c:3564:5: warning: implicit declaration of function 'add_to_E_continuous' [-Wimplicit-function-declaration] 3564 | add_to_E_continuous(E, Eka_base, msa_seq, p, k, a_size, emissions); | ^~~~~~~~~~~~~~~~~~~ -std_funcs.c:2184:74: warning: assignment to 'int *' from 'int' makes pointer from integer without a cast [-Wint-conversion] - 2184 | *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; - | ^ training_algorithms_multialpha.c:3589:8: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_nr_occ' makes pointer from integer without a cast [-Wint-conversion] 3589 | alphabet); | ^~~~~~~~ @@ -1009,10 +1088,6 @@ funcs.h:238:68: note: expected 'char *' but argument is of type 'int' 238 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ -std_funcs.c: In function 'update_shares_prior_multi': -std_funcs.c:2471:5: warning: 'return' with no value, in function returning non-void - 2471 | return; - | ^~~~~~ training_algorithms_multialpha.c:3622:7: warning: passing argument 9 of 'add_to_E_subst_mtx_dot_product_prior' makes pointer from integer without a cast [-Wint-conversion] 3622 | alphabet); | ^~~~~~~~ @@ -1022,46 +1097,6 @@ funcs.h:240:67: note: expected 'char *' but argument is of type 'int' 240 | int k, int a_size, int normalize, double *subst_mtx, char *alphabet); | ~~~~~~^~~~~~~~ -std_funcs.c:2457:5: note: declared here - 2457 | int update_shares_prior_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:326:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c: In function 'read_module_multi': -readhmm_multialpha.c:1042:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1042 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1077:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1077 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1111:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1111 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1140:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1140 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1143:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1143 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1169:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1169 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1172:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1172 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1198:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1198 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1202:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1202 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1229:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1229 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -readhmm_multialpha.c:1236:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1236 | fgets(s, MAX_LINE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c hmmsearch.c -o hmmsearch.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c debug_funcs.c -o debug_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c readhmm.c -o readhmm.o >/dev/null 2>&1 @@ -1083,7 +1118,7 @@ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c std_funcs.c -o std_funcs.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c core_algorithms_multialpha.c -o core_algorithms_multialpha.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c training_algorithms_multialpha.c -o training_algorithms_multialpha.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm +/bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/build/libpsortb-1.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:0:0 -Wl,-z,relro -Wl,-z,now -o libmodhmm.la -rpath /usr/lib/x86_64-linux-gnu core_algorithms_multialpha.lo debug_funcs.lo hmmsearch.lo readhmm.lo readhmm_multialpha.lo readseqs_multialpha.lo std_calculation_funcs.lo std_funcs.lo training_algorithms_multialpha.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/core_algorithms_multialpha.o .libs/debug_funcs.o .libs/hmmsearch.o .libs/readhmm.o .libs/readhmm_multialpha.o .libs/readseqs_multialpha.o .libs/std_calculation_funcs.o .libs/std_funcs.o .libs/training_algorithms_multialpha.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libmodhmm.so.0 -o .libs/libmodhmm.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libmodhmm.so.0" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so.0") libtool: link: (cd ".libs" && rm -f "libmodhmm.so" && ln -s "libmodhmm.so.0.0.0" "libmodhmm.so") @@ -1096,7 +1131,7 @@ make[2]: Leaving directory '/build/libpsortb-1.0+dfsg' make[1]: Leaving directory '/build/libpsortb-1.0+dfsg' dh_auto_test - make -j15 check VERBOSE=1 + make -j16 check VERBOSE=1 make[1]: Entering directory '/build/libpsortb-1.0+dfsg' Making check in svmloc make[2]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' @@ -1120,7 +1155,7 @@ make[3]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/svmloc' /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libsvmloc.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsvmloc.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libsvmloc.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so.0 || { rm -f libsvmloc.so.0 && ln -s libsvmloc.so.0.0.0 libsvmloc.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libsvmloc.so.0.0.0 libsvmloc.so || { rm -f libsvmloc.so && ln -s libsvmloc.so.0.0.0 libsvmloc.so; }; }) @@ -1136,7 +1171,7 @@ make[3]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' make[4]: Entering directory '/build/libpsortb-1.0+dfsg/modhmm0.92b' /bin/mkdir -p '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libmodhmm.la '/build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libmodhmm.so.0.0.0 /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libmodhmm.so.0.0.0 libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so.0 || { rm -f libmodhmm.so.0 && ln -s libmodhmm.so.0.0.0 libmodhmm.so.0; }; }) libtool: install: (cd /build/libpsortb-1.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libmodhmm.so.0.0.0 libmodhmm.so || { rm -f libmodhmm.so && ln -s libmodhmm.so.0.0.0 libmodhmm.so; }; }) @@ -1207,10 +1242,10 @@ dh_builddeb dpkg-deb: building package 'libmodhmm0' in '../libmodhmm0_1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libmodhmm0-dbgsym' in '../libmodhmm0-dbgsym_1.0+dfsg-4_amd64.deb'. -dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libsvmloc0' in '../libsvmloc0_1.0+dfsg-4_amd64.deb'. -dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-4_amd64.deb'. +dpkg-deb: building package 'libmodhmm-dev' in '../libmodhmm-dev_1.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'libsvmloc-dev' in '../libsvmloc-dev_1.0+dfsg-4_amd64.deb'. +dpkg-deb: building package 'libsvmloc0-dbgsym' in '../libsvmloc0-dbgsym_1.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libpsortb_1.0+dfsg-4_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1218,12 +1253,14 @@ 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/1860778/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1860778/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/1776016 and its subdirectories -I: Current time: Thu Aug 3 04:23:36 -12 2023 -I: pbuilder-time-stamp: 1691079816 +I: removing directory /srv/workspace/pbuilder/1860778 and its subdirectories +I: Current time: Thu Sep 5 12:47:37 +14 2024 +I: pbuilder-time-stamp: 1725490057