Diff of the two buildlogs: -- --- b1/build.log 2023-05-30 02:34:25.939287686 +0000 +++ b2/build.log 2023-05-30 02:42:45.157422059 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 29 14:30:14 -12 2023 -I: pbuilder-time-stamp: 1685413814 +I: Current time: Tue May 30 16:35:06 +14 2023 +I: pbuilder-time-stamp: 1685414106 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg.orig.tar.xz] I: copying [./t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Nov 24 22:17:33 2022 -12 +gpgv: Signature made Sat Nov 26 00:17:33 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -37,135 +37,167 @@ dpkg-source: info: applying increase_max_pid.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23078/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25824/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +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 May 30 16:36 /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/25824/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25824/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='da0cc5b1301347f89ac9fff8b93bed80' - 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='23078' - PS1='# ' - PS2='> ' + INVOCATION_ID=146e13022c0243c6ac17484403114c28 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=25824 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.5G1G7mHw/pbuilderrc_i0mQ --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5G1G7mHw/b1 --logfile b1/build.log t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.5G1G7mHw/pbuilderrc_4vso --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5G1G7mHw/b2 --logfile b2/build.log --extrapackages usrmerge t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux jtx1a 5.10.0-23-arm64 #1 SMP Debian 5.10.179-1 (2023-05-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 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 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 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 6460 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 8103 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/23078/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 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 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 30 16:36 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 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 6460 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 8103 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/25824/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -231,7 +263,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] -Fetched 18.0 MB in 1s (33.3 MB/s) +Fetched 18.0 MB in 0s (37.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19324 files and directories currently installed.) @@ -365,8 +397,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+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 > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/25824/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/25824/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+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 > ../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_source.changes dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -393,14 +436,16 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong" 'CC=$(CXX)' all - cd t_coffee_source && make -j3 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong" CC=\$\(CXX\) all + cd t_coffee_source && make -j4 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg/t_coffee_source' CC dev_lib/dev1.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/CUSTOM_evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c CC dp_lib/evaluate.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c + CC dp_lib/evaluate_dirichlet.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c In file included from ./io_lib_header.h:33, from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -412,7 +457,7 @@ 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate.c:34: + from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -420,6 +465,24 @@ dev_lib/dev1.c:89:26: warning: too many arguments for format [-Wformat-extra-args] 89 | fprintf (stdout, "Process positions\n", i); | ^~~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/evaluate.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': +dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 317 | fscanf(fp, "%f\n", &f); + | ~~~~~~^~~~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 319 | fscanf(fp, "%f", &f); + | ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 323 | fscanf(fp, "%f", &f); + | ~~~~~~^~~~~~~~~~~~~~ +dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fscanf(fp, "\n"); + | ~~~~~~^~~~~~~~~~ dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': dp_lib/evaluate.c:3070:67: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] 3070 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); @@ -445,10 +508,10 @@ | | | | int double | %3f - CC dp_lib/evaluate_dirichlet.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c CC dp_lib/evaluate_for_domain.c + CC dp_lib/evaluate_for_struc.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': dp_lib/evaluate.c:809:26: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 809 | fscanf (fp, "%d ", &res); @@ -464,30 +527,10 @@ 7626 | fscanf (fp, "%f %c %*s",&v1, &c1 ); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_dirichlet.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': -dp_lib/evaluate_dirichlet.c:317:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 317 | fscanf(fp, "%f\n", &f); - | ~~~~~~^~~~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:319:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 319 | fscanf(fp, "%f", &f); - | ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:323:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 323 | fscanf(fp, "%f", &f); - | ~~~~~~^~~~~~~~~~~~~~ -dp_lib/evaluate_dirichlet.c:326:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fscanf(fp, "\n"); - | ~~~~~~^~~~~~~~~~ - CC dp_lib/evaluate_for_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c In file included from ./io_lib_header.h:33, from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -495,15 +538,13 @@ | ^~~~~~~ CC dp_lib/fsa_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c + CC dp_lib/pavie_dp.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c In file included from ./io_lib_header.h:33, from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC dp_lib/pavie_dp.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c - CC dp_lib/showpair.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c In file included from ./io_lib_header.h:33, from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -524,11 +565,6 @@ dp_lib/pavie_dp.c:1365:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 1365 | fscanf (fp, "%s", mat); | ~~~~~~~^~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/showpair.c:32: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:33: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] 1078 | sprintf ( command, "cp %s %s", mat_name[a], latest); @@ -557,40 +593,43 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ + CC dp_lib/showpair.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c CC dp_lib/util_domain_dp.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp.c:33: + from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_domain_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c - CC dp_lib/util_dp_cdna_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_cdna_fasta_nw.c:33: + from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC dp_lib/util_dp_cdna_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/util_dp_clean_maln.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_cdna_fasta_nw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, from dp_lib/util_dp_clean_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ CC dp_lib/util_dp_drivers.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c - CC dp_lib/util_dp_est.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c - CC dp_lib/util_dp_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -600,16 +639,8 @@ dp_lib/util_dp_drivers.c:2051:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2051 | register int a; | ^ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_est.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_nw.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ + CC dp_lib/util_dp_est.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c dp_lib/util_dp_drivers.c: In function 'char* seq_file2msa_file(char*, char*, char*)': dp_lib/util_dp_drivers.c:1014:9: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1014 | chdir (dir); @@ -689,19 +720,24 @@ dp_lib/util_dp_drivers.c:2256:13: warning: ignoring return value of 'int atoi(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2256 | atoi(strtok (seq,SEPARATORS)); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + CC dp_lib/util_dp_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_est.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_fasta_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ dp_lib/util_dp_fasta_nw.c: In function 'int* makepointtable(int*, int*, int)': dp_lib/util_dp_fasta_nw.c:157:17: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 157 | register int *p; | ^ CC dp_lib/util_dp_fasta_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_sw.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ - CC dp_lib/util_dp_generic_fasta_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': dp_lib/util_dp_drivers.c:382:31: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 382 | sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); @@ -743,11 +779,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_generic_fasta_nw.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': dp_lib/util_dp_drivers.c:921:25: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 921 | sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); @@ -761,8 +792,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_gotoh_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c +In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_fasta_sw.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC dp_lib/util_dp_generic_fasta_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': dp_lib/util_dp_drivers.c:1854:80: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] 1854 | sprintf ( command, "t_coffee -other_pg tc_generic_method.pl -mode=%s -method=%s %s %s%s %s %s%s -tmpdir=%s %s %s", M->executable, M->executable2, M->param1,M->in_flag,infile,M->param2,M->out_flag,outfile,get_tmp_4_tcoffee(),db,M->param); @@ -777,13 +813,22 @@ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_nw.c:34: + from dp_lib/util_dp_generic_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC dp_lib/util_dp_gotoh_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c CC dp_lib/util_dp_gotoh_sw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c In file included from ./io_lib_header.h:33, + from dp_lib/util_dp_gotoh_nw.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ + CC dp_lib/util_dp_mm_nw.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c +In file included from ./io_lib_header.h:33, from dp_lib/util_dp_gotoh_sw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol @@ -792,35 +837,20 @@ dp_lib/util_dp_gotoh_sw.c:391:42: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 391 | fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_mm_nw.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': -dp_lib/util_dp_drivers.c:3717:25: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ CC dp_lib/util_dp_sim.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c + CC dp_lib/util_dp_ssec_pwaln.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC dp_lib/util_dp_ssec_pwaln.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c dp_lib/util_dp_sim.c: In function 'int addnode(int, int, int, int, int, int, int)': dp_lib/util_dp_sim.c:173:16: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 173 | register int d; @@ -1001,6 +1031,19 @@ dp_lib/util_dp_sim.c:912:27: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 912 | register int c, e, d, s; | ^ +dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': +dp_lib/util_dp_drivers.c:3717:25: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 3717 | sprintf ( dp_mode, "%s", CL->dp_mode); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)' at dp_lib/util_dp_drivers.c:3717:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, from dp_lib/util_dp_ssec_pwaln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1008,22 +1051,24 @@ | ^~~~~~~ CC dp_lib/util_dp_suboptimal_nw.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c - CC dp_lib/util_graph_maln.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c In file included from ./io_lib_header.h:33, from dp_lib/util_dp_suboptimal_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC dp_lib/util_graph_maln.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c + CC fastal/diagonal.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c + CC fastal/fastal.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c In file included from ./io_lib_header.h:33, - from dp_lib/util_graph_maln.c:33: + from fastal/diagonal.c:31: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/diagonal.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c In file included from ./io_lib_header.h:33, - from fastal/diagonal.c:31: + from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -1040,17 +1085,11 @@ fastal/diagonal.c:441:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 441 | fgets(line, 300, diag_f); | ~~~~~^~~~~~~~~~~~~~~~~~~ - CC fastal/fastal.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c - CC fastal/fastal_opt_parsing.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c In file included from ./io_lib_header.h:33, from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC fastal/iteration.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': fastal/fastal.c:1924:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1924 | system(blast_command); @@ -1127,49 +1166,19 @@ fastal/fastal.c:3643:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3643 | fgets(aligned_sequence, alignment_length+3, edit_seq_file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC fastal/fastal_opt_parsing.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c + CC fastal/iteration.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c + CC fastal/parttree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c In file included from ./io_lib_header.h:33, - from fastal/iteration.c:34: + from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ -fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': -fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 185 | fgets(line, LINE_LENGTH , alignment_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': -fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 310 | fgets(line, LINE_LENGTH , alignment_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 435 | system(command); - | ~~~~~~^~~~~~~~~ -fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': -fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': -fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 563 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 565 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 567 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 569 | fgets(line, LINE_LENGTH , edit_file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC fastal/parttree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c In file included from ./io_lib_header.h:33, - from fastal/parttree.c:36: + from fastal/iteration.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ @@ -1211,8 +1220,44 @@ fastal/parttree.c:962:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 962 | fgets(line, LINE_LENGTH, ktup_f); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c: In function 'void split_set(FILE*, Fastal_profile*, Fastal_profile*, char*, int, int*, char*)': +fastal/iteration.c:185:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 185 | fgets(line, LINE_LENGTH , alignment_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c: In function 'void iterate(Fastal_param*, void*, char*, char*, int)': +fastal/iteration.c:310:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 310 | fgets(line, LINE_LENGTH , alignment_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:435:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 435 | system(command); + | ~~~~~~^~~~~~~~~ +fastal/iteration.c: In function 'void write_iterated_aln(char*, char*, char*, char*, int*, int, char*, int*, int)': +fastal/iteration.c:501:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 501 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:504:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 504 | fgets(alnline, ALNLINE_LENGTH , old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:535:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 535 | fgets(alnline, ALNLINE_LENGTH, old_aln_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c: In function 'void edit2seq_pattern(FILE*, char*, char*)': +fastal/iteration.c:563:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 563 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:565:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 565 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:567:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 567 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/iteration.c:569:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 569 | fgets(line, LINE_LENGTH , edit_file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC fastal/scoring.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c + CC fastal/tree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c In file included from ./io_lib_header.h:33, from fastal/scoring.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1252,6 +1297,11 @@ fastal/scoring.c:585:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 585 | fgets(line, LINE_LENGTH, result); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from fastal/tree.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ fastal/scoring.c: In function 'int complete_agreement_score(char*, const char*)': fastal/scoring.c:624:49: warning: '%s' directive writing up to 499 bytes into a region of size 200 [-Wformat-overflow=] 624 | sprintf(ref_file_name, "%s/%s",directory, dp->d_name); @@ -1267,17 +1317,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC fastal/tree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c -In file included from ./io_lib_header.h:33, - from fastal/tree.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ CC io_lib/io_func.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c CC io_lib/pb_util_read_seq_util.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c + CC io_lib/pb_util_read_sequence.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_seq_util.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1340,8 +1385,6 @@ io_lib/io_func.c:971:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 971 | fscanf (fp, "%s %f %f %f", html_code[classC], &ps_code[classC][0], &ps_code[classC][1],&ps_code[classC][2]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC io_lib/pb_util_read_sequence.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c In file included from ./io_lib_header.h:33, from io_lib/pb_util_read_sequence.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1391,6 +1434,8 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC km_coffee/Stack.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c io_lib/tree_util.c: In function 'tnode* tree_scan(Alignment*, NT_node, char*, char*)': io_lib/tree_util.c:836:26: warning: too many arguments for format [-Wformat-extra-args] 836 | fprintf (stdout, "Process positions\n", i); @@ -1403,6 +1448,8 @@ io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void [-Wreturn-type] 2317 | } | ^ + CC km_coffee/Vector.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c io_lib/tree_util.c: In function 'int node_sort(char*, NT_node)': io_lib/tree_util.c:6273:1: warning: no return statement in function returning non-void [-Wreturn-type] 6273 | } @@ -1444,8 +1491,6 @@ io_lib/tree_util.c:9947:46: note: declared here 9947 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ - CC km_coffee/Stack.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c io_lib/tree_util.c: In function 'FILE* create_tree(NT_node, NT_node, int*, int*, int*, tnode***, FILE*)': io_lib/tree_util.c:3973:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 3973 | fscanf(fp,"%f",&dist); @@ -1457,8 +1502,6 @@ io_lib/tree_util.c:9772:1: warning: control reaches end of non-void function [-Wreturn-type] 9772 | } | ^ - CC km_coffee/Vector.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c CC km_coffee/classes.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c CC km_coffee/km_coffee.c @@ -1572,26 +1615,10 @@ | char* CC km_coffee/kmeans.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c -io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': -io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - 4597 | sprintf (index, "%d", i); - | ^~ -io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] - 4597 | sprintf (index, "%d", i); - | ^~~~ -In file included from /usr/include/stdio.h:906, - from io_lib/tree_util.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ CC t_coffee_lib/t_coffee.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c + CC util_lib/aln_compare.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c In file included from ./io_lib_header.h:33, from t_coffee_lib/t_coffee.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -1605,6 +1632,11 @@ t_coffee_lib/t_coffee.c:7172:57: warning: too many arguments for format [-Wformat-extra-args] 7172 | else { w=seq2dpa_weight (S, "longuest");fprintf ( le, "default longuest\n", dpa_weight);} | ^~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/aln_compare.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ t_coffee_lib/t_coffee.c: In function 'int run_other_pg(int, char**)': t_coffee_lib/t_coffee.c:6139:30: warning: control reaches end of non-void function [-Wreturn-type] 6139 | unpack_all_perl_script (argv[0]+strlen ("unpack_")); @@ -1613,13 +1645,6 @@ t_coffee_lib/t_coffee.c:6816:1: warning: control reaches end of non-void function [-Wreturn-type] 6816 | } | ^ - CC util_lib/aln_compare.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c -In file included from ./io_lib_header.h:33, - from util_lib/aln_compare.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ In file included from /usr/include/string.h:535, from t_coffee_lib/t_coffee.c:32: In function 'char* strcpy(char*, const char*)', @@ -1634,6 +1659,33 @@ 79 | return __builtin___strcpy_chk (__dest, __src, __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:79:33: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' + CC util_lib/aln_convertion_util.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c + CC util_lib/hsearch.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c +In file included from ./io_lib_header.h:33, + from util_lib/aln_convertion_util.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +io_lib/tree_util.c: In function 'Sequence* get_nexus(char*)': +io_lib/tree_util.c:4597:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + 4597 | sprintf (index, "%d", i); + | ^~ +io_lib/tree_util.c:4597:39: note: directive argument in the range [1, 2147483647] + 4597 | sprintf (index, "%d", i); + | ^~~~ +In file included from /usr/include/stdio.h:906, + from io_lib/tree_util.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Sequence* get_nexus(char*)' at io_lib/tree_util.c:4597:17: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 5 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': t_coffee_lib/t_coffee.c:5662:66: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] 5662 | sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); @@ -1649,13 +1701,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ - CC util_lib/aln_convertion_util.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c -In file included from ./io_lib_header.h:33, - from util_lib/aln_convertion_util.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ util_lib/aln_convertion_util.c: In function 'int trim_aln_file(char*, char*, char*, char*)': util_lib/aln_convertion_util.c:3105:62: warning: NULL used in arithmetic [-Wpointer-arith] 3105 | while ((get_next_fasta_sequence(fp, &name, &comment,&seq)!=NULL)) @@ -1664,6 +1709,11 @@ util_lib/aln_convertion_util.c:4511:1: warning: no return statement in function returning non-void [-Wreturn-type] 4511 | } | ^ +In file included from ./io_lib_header.h:33, + from util_lib/hsearch.c:35: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': util_lib/aln_convertion_util.c:7762:1: warning: no return statement in function returning non-void [-Wreturn-type] 7762 | } @@ -1678,18 +1728,11 @@ util_lib/aln_convertion_util.c:7547:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 7547 | fgets ( line, VERY_LONG_STRING,fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/hsearch.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c CC util_lib/random.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c CC util_lib/reformat.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c In file included from ./io_lib_header.h:33, - from util_lib/hsearch.c:35: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -In file included from ./io_lib_header.h:33, from util_lib/reformat.c:35: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol @@ -1698,8 +1741,6 @@ util_lib/reformat.c:7551:1: warning: no return statement in function returning non-void [-Wreturn-type] 7551 | } | ^ - CC util_lib/reformat_struc.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': util_lib/reformat.c:14453:1: warning: no return statement in function returning non-void [-Wreturn-type] 14453 | } @@ -1837,11 +1878,6 @@ util_lib/reformat.c:6511:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 6511 | fscanf (fp, "%s %d", name,&i); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/reformat_struc.c:34: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14294:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 14294 | fscanf ( fp, "%s ", buf); @@ -1869,6 +1905,13 @@ util_lib/reformat.c:14525:19: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 14525 | fgets ( sbuf, VERY_LONG_STRING, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/reformat_struc.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c +In file included from ./io_lib_header.h:33, + from util_lib/reformat_struc.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': util_lib/reformat_struc.c:125:25: warning: too many arguments for format [-Wformat-extra-args] 125 | fprintf (out, "ATOM ", lw[1]);//ATOM @@ -2007,6 +2050,21 @@ util_lib/util.c:10533:1: warning: control reaches end of non-void function [-Wreturn-type] 10533 | } | ^ + CC util_lib/util_aln_analyze.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c +In file included from ./io_lib_header.h:33, + from util_lib/util_aln_analyze.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ +util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] + 713 | } + | ^ +util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': +util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] + 4480 | } + | ^ util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': util_lib/aln_convertion_util.c:12147:32: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 12147 | sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); @@ -2035,6 +2093,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': +util_lib/reformat.c:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] +13639 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); + | ^~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from util_lib/reformat.c:27: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) into a destination of size 1000 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': +util_lib/reformat.c:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] +11638 | sprintf (type, "%s", ACTION (2)); + | ^~ util_lib/util.c: In function 'char* get_cache_4_tcoffee()': util_lib/util.c:5385:42: warning: '/cache/' directive writing 7 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 5385 | else sprintf ( cache_4_tcoffee, "%s/cache/", get_dir_4_tcoffee()); @@ -2106,68 +2183,26 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': -util_lib/reformat.c:13639:34: warning: ' -method ' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] -13639 | sprintf ( command, "%s -method %s -aln %s -tree %s -dmatrix %s -weightfile %s %s",method_4_msa_weights, action_list[1],aln_name, tree_name, dist_matrix_name,weight_name, TO_NULL_DEVICE); - | ^~~~~~~~~ In file included from /usr/include/stdio.h:906, - from util_lib/reformat.c:27: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)' at util_lib/reformat.c:13639:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output 64 or more bytes (assuming 3059) into a destination of size 1000 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -util_lib/reformat.c: In function 'void modify_data(Sequence_data_struc*, Sequence_data_struc*, Sequence_data_struc*, char**, int, Action_data_struc*)': -util_lib/reformat.c:11638:32: warning: '%s' directive argument is null [-Wformat-overflow=] -11638 | sprintf (type, "%s", ACTION (2)); - | ^~ - CC util_lib/util_aln_analyze.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c -In file included from ./io_lib_header.h:33, - from util_lib/util_aln_analyze.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ -util_lib/util_aln_analyze.c: In function 'Alignment* sar_analyze(Alignment*, Alignment*, char*)': -util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void [-Wreturn-type] - 713 | } - | ^ -util_lib/util_aln_analyze.c: In function 'Alignment* or_scan(Alignment*, Alignment*, char*)': -util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void [-Wreturn-type] - 4480 | } - | ^ -util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': -util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] - 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); - | ^~ -util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': -util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); - | ^~~~~~~~~ + from util_lib/util_aln_analyze.c:27: In function 'int sprintf(char*, const char*, ...)', - inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, - inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7, - inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10018:11: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 + inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4598:11, + inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': -util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); - | ^~~~~~~~~ +util_lib/util_aln_analyze.c: In function 'Alignment* or_sar(Alignment*, Alignment*, char*, int)': +util_lib/util_aln_analyze.c:4599:23: warning: 'COMBINED' directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] + 4599 | sprintf ( N->mode, "COMBINED"); + | ^~~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, - inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7, - inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10019:11: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 + inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4599:11, + inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin_sprintf' output 9 bytes into a destination of size 0 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, @@ -2183,8 +2218,6 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC util_lib/util_declare.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c In file included from ./io_lib_header.h:33, from util_lib/util_constraints_list.c:37: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -2202,11 +2235,6 @@ util_lib/util_constraints_list.c:2851:40: warning: too many arguments for format [-Wformat-extra-args] 2851 | x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); | ^~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_declare.c:37: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - 30 | typedef struct ALNcol - | ^~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': util_lib/util_constraints_list.c:582:19: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 582 | chdir (tdir); @@ -2243,6 +2271,10 @@ util_lib/util_constraints_list.c:4053:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 4053 | fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'FILE* display_output_filename(FILE*, char*, char*, char*, int)': +util_lib/util.c:8658:68: warning: '%s' directive argument is null [-Wformat-overflow=] + 8658 | fprintf ( io, "\n\t#### File Type= %-15s Format= %-15s Name= %s",type, format, name ); + | ^~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1286:28: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 1286 | sprintf ( buf, "%s %s %s%s %s %s%s %s", m->executable, m->param1, m->in_flag, seq,m->param2, m->out_flag,aln, m->param); @@ -2258,32 +2290,64 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:906, - from util_lib/util_aln_analyze.c:27: +util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': +util_lib/util.c:5400:44: warning: '/mcoffee/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + 5400 | else sprintf ( mcoffee_4_tcoffee, "%s/mcoffee/", get_dir_4_tcoffee()); + | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4598:11, - inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] + inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5400:20, + inlined from 'char* get_mcoffee_4_tcoffee()' at util_lib/util.c:5392:7, + inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10018:11: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -util_lib/util_aln_analyze.c: In function 'Alignment* or_sar(Alignment*, Alignment*, char*, int)': -util_lib/util_aln_analyze.c:4599:23: warning: 'COMBINED' directive writing 8 bytes into a region of size 0 [-Wformat-overflow=] - 4599 | sprintf ( N->mode, "COMBINED"); - | ^~~~~~~~ +util_lib/util.c: In function 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)': +util_lib/util.c:5413:44: warning: '/methods/' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + 5413 | else sprintf ( methods_4_tcoffee, "%s/methods/", get_dir_4_tcoffee()); + | ^~~~~~~~~ In function 'int sprintf(char*, const char*, ...)', - inlined from 'ORP* combine_n_predictions(ORP**, Alignment*, Alignment*)' at util_lib/util_aln_analyze.c:4599:11, - inlined from 'Alignment* or_sar(Alignment*, Alignment*, char*, int)' at util_lib/util_aln_analyze.c:4560:29: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin_sprintf' output 9 bytes into a destination of size 0 + inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5413:20, + inlined from 'char* get_methods_4_tcoffee()' at util_lib/util.c:5405:7, + inlined from 'char** _Z23standard_initialisationPPcPi.part.0(char**, int*)' at util_lib/util.c:10019:11: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': +util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': +util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ + CC util_lib/util_declare.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c CC util_lib/util_domain_constraints_list.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c In file included from ./io_lib_header.h:33, @@ -2291,6 +2355,11 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/util_declare.c:37: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 30 | typedef struct ALNcol + | ^~~~~~~ CC util_lib/util_dps.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c CC util_lib/util_job_handling.c @@ -2300,13 +2369,13 @@ ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ - CC util_lib/util_make_tree.c -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c In file included from ./io_lib_header.h:33, from util_lib/util_job_handling.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 30 | typedef struct ALNcol | ^~~~~~~ + CC util_lib/util_make_tree.c +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/t-coffee-13.45.0.4846264+really13.41.0.28bdc39+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O0 -fsigned-char -O3 -Wno-write-strings -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c In file included from ./io_lib_header.h:33, from util_lib/util_make_tree.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration @@ -2418,32 +2487,6 @@ util_lib/util_make_tree.c:2119:12: warning: ignoring return value of 'int chdir(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 2119 | chdir (cdir); | ~~~~~~~~~^~~~~~ -util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': -util_lib/util_constraints_list.c:4922:26: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 4922 | sprintf ( mode, "%s", (CL && in_mode==NULL)?CL->distance_matrix_mode:in_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4922:10: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)': -util_lib/util_constraints_list.c:4923:30: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - 4923 | sprintf ( sim_mode, "%s", (CL && in_sim_mode==NULL)?CL->distance_matrix_sim_mode:in_sim_mode); - | ^~ -In function 'int sprintf(char*, const char*, ...)', - inlined from 'Distance_matrix* cl2distance_matrix(Constraint_list*, Alignment*, char*, char*, int)' at util_lib/util_constraints_list.c:4923:10: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'Job_TC* method2job_list(char*, Sequence*, char*, char*, Distance_matrix*, Constraint_list*)': util_lib/util_constraints_list.c:694:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] 694 | sprintf ( aln_mode, "%s", method->aln_mode); @@ -2515,8 +2558,8 @@ dh_gencontrol -O--sourcedirectory=t_coffee_source dh_md5sums -O--sourcedirectory=t_coffee_source dh_builddeb -O--sourcedirectory=t_coffee_source -dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb'. dpkg-deb: building package 't-coffee' in '../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb'. +dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.deb'. dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../t-coffee_13.45.0.4846264+really13.41.0.28bdc39+dfsg-1_armhf.changes @@ -2525,12 +2568,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/25824/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25824/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/23078 and its subdirectories -I: Current time: Mon May 29 14:34:22 -12 2023 -I: pbuilder-time-stamp: 1685414062 +I: removing directory /srv/workspace/pbuilder/25824 and its subdirectories +I: Current time: Tue May 30 16:42:36 +14 2023 +I: pbuilder-time-stamp: 1685414556