Diff of the two buildlogs: -- --- b1/build.log 2021-04-08 14:10:43.671270318 +0000 +++ b2/build.log 2021-04-08 14:11:34.521280417 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 8 02:06:13 -12 2021 -I: pbuilder-time-stamp: 1617890773 +I: Current time: Thu May 12 10:33:53 +14 2022 +I: pbuilder-time-stamp: 1652301233 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Feb 14 18:47:23 2019 -12 +gpgv: Signature made Fri Feb 15 20:47:23 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -37,136 +37,170 @@ dpkg-source: info: applying fix_tempfile_name_sharing.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/51634/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10921/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/10921/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10921/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='8caa504bcb0a44d6aedfd0beff66f563' - 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='51634' - PS1='# ' - PS2='> ' + INVOCATION_ID=8d0a89bf14294a5bb82ae80af82a2cf6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=10921 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.U1SASTOSkb/pbuilderrc_SLG5 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.U1SASTOSkb/b1 --logfile b1/build.log t-coffee_12.00.7fb08c2-4.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.U1SASTOSkb/pbuilderrc_7qWo --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.U1SASTOSkb/b2 --logfile b2/build.log t-coffee_12.00.7fb08c2-4.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos1-amd64 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.4-amd64 #1 SMP Debian 5.10.19-1~bpo10+1 (2021-03-13) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Apr 6 20:23 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/51634/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 May 12 10:33 sh -> bash + lrwxrwxrwx 1 root root 4 May 11 04:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/10921/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -235,7 +269,7 @@ Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Fetched 19.0 MB in 0s (58.5 MB/s) +Fetched 19.0 MB in 0s (75.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -390,7 +424,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/t-coffee-12.00.7fb08c2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package t-coffee dpkg-buildpackage: info: source version 12.00.7fb08c2-4 dpkg-buildpackage: info: source distribution unstable @@ -417,27 +451,28 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/t-coffee-12.00.7fb08c2' dh_auto_build -- USER_BIN=../bin/ FCC="gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" 'CC=$(CXX)' all - cd t_coffee_source && make -j15 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" CC=\$\(CXX\) all + cd t_coffee_source && make -j16 "INSTALL=install --strip-program=true" USER_BIN=../bin/ "FCC=gfortran -g -O2 -ffile-prefix-map=/build/t-coffee-12.00.7fb08c2=. -fstack-protector-strong" CC=\$\(CXX\) all make[2]: Entering directory '/build/t-coffee-12.00.7fb08c2/t_coffee_source' + CC dp_lib/CUSTOM_evaluate_for_struc.c CC dev_lib/dev1.c + CC dp_lib/evaluate_for_domain.c CC dp_lib/evaluate.c - CC dp_lib/CUSTOM_evaluate_for_struc.c CC dp_lib/evaluate_dirichlet.c - CC dp_lib/evaluate_for_domain.c - CC dp_lib/evaluate_for_struc.c CC dp_lib/fsa_dp.c + CC dp_lib/evaluate_for_struc.c CC dp_lib/pavie_dp.c + CC dp_lib/util_domain_dp_drivers.c CC dp_lib/showpair.c CC dp_lib/util_domain_dp.c - CC dp_lib/util_domain_dp_drivers.c CC dp_lib/util_dp_cdna_fasta_nw.c CC dp_lib/util_dp_clean_maln.c CC dp_lib/util_dp_drivers.c CC dp_lib/util_dp_est.c + CC dp_lib/util_dp_fasta_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dev_lib/dev1.c:33: + from dp_lib/util_domain_dp.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -489,7 +524,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate_for_domain.c:33: + from dp_lib/showpair.c:32: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -541,19 +576,57 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate_dirichlet.c:33: + from dp_lib/util_domain_dp_drivers.c:33: +./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_4_TCOFFEE "x3dna" + ^ +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from dp_lib/fsa_dp.c:33: +./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_4_TCOFFEE "x3dna" + ^ +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ ./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_type "RNA_secondarystructure_predictor" ^ +./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ^ +./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ^ +./programmes_define.h:380: warning: "x3dna" redefined + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:380: warning: "x3dna" redefined + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ./programmes_define.h:380: warning: "x3dna" redefined #define x3dna-ssr_type "RNA_secondarystructure_predictor" ./programmes_define.h:379: note: this is the location of the previous definition #define x3dna-ssr_4_TCOFFEE "x3dna" +./programmes_define.h:379: note: this is the location of the previous definition + #define x3dna-ssr_4_TCOFFEE "x3dna" + +./programmes_define.h:379: note: this is the location of the previous definition + #define x3dna-ssr_4_TCOFFEE "x3dna" + +./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + ^ +./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + ^ ./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ^ @@ -563,76 +636,84 @@ ./programmes_define.h:380: note: this is the location of the previous definition #define x3dna-ssr_type "RNA_secondarystructure_predictor" +./programmes_define.h:381: warning: "x3dna" redefined + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:381: warning: "x3dna" redefined + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:380: note: this is the location of the previous definition + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:380: note: this is the location of the previous definition + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + ^ +./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + ^ ./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" ^ ./programmes_define.h:382: warning: "x3dna" redefined #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" +./programmes_define.h:382: warning: "x3dna" redefined + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:381: note: this is the location of the previous definition + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:382: warning: "x3dna" redefined + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + ./programmes_define.h:381: note: this is the location of the previous definition #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" ./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_mode "saracoffee" ^ -./programmes_define.h:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" +./programmes_define.h:381: note: this is the location of the previous definition + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" +./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_mode "saracoffee" ^ -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:383: note: this is the location of the previous definition +./programmes_define.h:383: warning: "x3dna" redefined #define x3dna-ssr_mode "saracoffee" -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from dp_lib/util_dp_clean_maln.c:33: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" +./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_mode "saracoffee" ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" +./programmes_define.h:383: warning: "x3dna" redefined + #define x3dna-ssr_mode "saracoffee" -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" +./programmes_define.h:382: note: this is the location of the previous definition + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" +./programmes_define.h:383: warning: "x3dna" redefined + #define x3dna-ssr_mode "saracoffee" -./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name +./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_update_action "never" ^ -./programmes_define.h:382: warning: "x3dna" redefined +./programmes_define.h:382: note: this is the location of the previous definition #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" -./programmes_define.h:381: note: this is the location of the previous definition - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" +./programmes_define.h:384: warning: "x3dna" redefined + #define x3dna-ssr_update_action "never" -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_mode "saracoffee" +./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_update_action "never" ^ -./programmes_define.h:383: warning: "x3dna" redefined +./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - ./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_update_action "never" ^ @@ -642,10 +723,16 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +./programmes_define.h:384: warning: "x3dna" redefined + #define x3dna-ssr_update_action "never" + +./programmes_define.h:383: note: this is the location of the previous definition + #define x3dna-ssr_mode "saracoffee" + In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/showpair.c:32: + from dp_lib/evaluate.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -749,7 +836,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/CUSTOM_evaluate_for_struc.c:33: + from dp_lib/evaluate_dirichlet.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -801,7 +888,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_domain_dp.c:33: + from dev_lib/dev1.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -905,7 +992,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_domain_dp_drivers.c:33: + from dp_lib/evaluate_for_struc.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1009,7 +1096,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/fsa_dp.c:33: + from dp_lib/util_dp_fasta_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1061,7 +1148,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate_for_struc.c:34: + from dp_lib/util_dp_drivers.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1113,7 +1200,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_drivers.c:33: + from dp_lib/evaluate_for_domain.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1165,7 +1252,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/evaluate.c:34: + from dp_lib/util_dp_clean_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1215,75 +1302,79 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from dp_lib/pavie_dp.c:33: + from dp_lib/showpair.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_drivers.c:33: + from dp_lib/util_domain_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/CUSTOM_evaluate_for_struc.c:33: + from dp_lib/util_domain_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/showpair.c:32: + from dp_lib/evaluate_dirichlet.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_clean_maln.c:33: + from dp_lib/pavie_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_struc.c:34: + from dp_lib/CUSTOM_evaluate_for_struc.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_dirichlet.c:33: + from dp_lib/fsa_dp.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/fsa_dp.c:33: + from dev_lib/dev1.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 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_dp_est.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp_drivers.c: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 typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_domain_dp.c:33: + from dp_lib/evaluate_for_struc.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate_for_domain.c:33: + from dp_lib/evaluate.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dev_lib/dev1.c:33: + from dp_lib/util_dp_fasta_nw.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/evaluate.c:34: + from dp_lib/util_dp_drivers.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ +dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': +dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] + fprintf (stdout, "Process positions\n", i); + ^~~~~~~~~~~~~~~~~~~~~ dp_lib/evaluate_dirichlet.c: In function 'Mixture* read_dirichlet(char*)': dp_lib/evaluate_dirichlet.c:317:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%f\n", &f); @@ -1308,78 +1399,30 @@ dp_lib/pavie_dp.c:1081:14: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system (command); ~~~~~~~^~~~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ dp_lib/pavie_dp.c: In function 'Alignment* pavie_seq2pavie_msa(Sequence*, char*, char*)': 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] fscanf (fp, "%s", mat); ~~~~~~~^~~~~~~~~~~~~~~ -dev_lib/dev1.c: In function 'void aln2hitMat(Alignment*, char*)': -dev_lib/dev1.c:89:19: warning: too many arguments for format [-Wformat-extra-args] - fprintf (stdout, "Process positions\n", i); - ^~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_fasta_nw.c -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from dp_lib/util_dp_fasta_nw.c:34: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - ^ -./programmes_define.h:382: warning: "x3dna" redefined - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:381: note: this is the location of the previous definition - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_mode "saracoffee" - ^ -./programmes_define.h:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - - CC dp_lib/util_dp_fasta_sw.c +dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': +dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] + 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); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ +dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] +dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] +dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_fasta_nw.c:34: + from dp_lib/evaluate_for_domain.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration 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 + typedef struct ALNcol + ^~~~~~~ + CC dp_lib/util_dp_fasta_sw.c + CC dp_lib/util_dp_generic_fasta_nw.c + CC dp_lib/util_dp_gotoh_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1432,6 +1475,16 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': +dp_lib/evaluate.c:809:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d ", &res); + ~~~~~~~^~~~~~~~~~~~~~~~~ +dp_lib/evaluate.c:814:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%f %f", &sseq, &mseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/evaluate.c:819:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%f %f", &sseq, &mseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] chdir (dir); @@ -1511,70 +1564,6 @@ dp_lib/util_dp_drivers.c:2256:6: warning: ignoring return value of 'int atoi(const char*)', declared with attribute warn_unused_result [-Wunused-result] atoi(strtok (seq,SEPARATORS)); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ -dp_lib/evaluate.c: In function 'Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)': -dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 4 has type 'int' [-Wformat=] - 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); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ -dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 5 has type 'double' [-Wformat=] -dp_lib/evaluate.c:2956:22: warning: format '%f' expects argument of type 'double', but argument 6 has type 'int' [-Wformat=] -dp_lib/evaluate.c:2956:22: warning: format '%d' expects argument of type 'int', but argument 7 has type 'double' [-Wformat=] -dp_lib/evaluate.c: In function 'Alignment* fork_triplet_coffee_evaluate_output(Alignment*, Constraint_list*, int)': -dp_lib/evaluate.c:809:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d ", &res); - ~~~~~~~^~~~~~~~~~~~~~~~~ -dp_lib/evaluate.c:814:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%f %f", &sseq, &mseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/evaluate.c:819:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%f %f", &sseq, &mseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': -dp_lib/evaluate.c:7511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%f %c %*s",&v1, &c1 ); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC dp_lib/util_dp_generic_fasta_nw.c - CC dp_lib/util_dp_gotoh_nw.c - CC dp_lib/util_dp_gotoh_sw.c - CC dp_lib/util_dp_mm_nw.c - CC dp_lib/util_dp_sim.c - CC dp_lib/util_dp_ssec_pwaln.c - CC dp_lib/util_dp_suboptimal_nw.c -dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': -dp_lib/util_dp_drivers.c:382:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c:373:22: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -dp_lib/util_dp_drivers.c:386:40: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1627,6 +1616,10 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +dp_lib/evaluate.c: In function 'float** initialise_aa_physico_chemical_property_table(int*)': +dp_lib/evaluate.c:7511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%f %c %*s",&v1, &c1 ); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ dp_lib/pavie_dp.c: In function 'char** output_pavie_mat_list(int***, double*, char**, int, char*, int, char**)': dp_lib/pavie_dp.c:1078:26: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf ( command, "cp %s %s", mat_name[a], latest); @@ -1648,10 +1641,15 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 + typedef struct ALNcol + ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_mm_nw.c:33: + from dp_lib/util_dp_gotoh_nw.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1700,7 +1698,19 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC dp_lib/util_graph_maln.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 + typedef struct ALNcol + ^~~~~~~ + CC 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 + typedef struct ALNcol + ^~~~~~~ + CC dp_lib/util_dp_mm_nw.c + CC dp_lib/util_dp_sim.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1753,10 +1763,12 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC dp_lib/util_dp_ssec_pwaln.c + CC dp_lib/util_dp_suboptimal_nw.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_ssec_pwaln.c:33: + from dp_lib/util_dp_mm_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1805,6 +1817,7 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" + CC dp_lib/util_graph_maln.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -1858,29 +1871,19 @@ #define x3dna-ssr_mode "saracoffee" 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 - typedef struct ALNcol - ^~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ -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 typedef struct ALNcol ^~~~~~~ In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_ssec_pwaln.c:33: + from dp_lib/util_dp_mm_nw.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_suboptimal_nw.c:33: + from dp_lib/util_graph_maln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -1929,26 +1932,10 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -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 - typedef struct ALNcol - ^~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': -dp_lib/util_dp_drivers.c:920:22: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] - sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_dp_gotoh_nw.c:34: + from dp_lib/util_dp_ssec_pwaln.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2000,7 +1987,7 @@ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from dp_lib/util_graph_maln.c:33: + from dp_lib/util_dp_suboptimal_nw.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2054,36 +2041,16 @@ fread ( &k, sizeof (TRACE_TYPE), 1, long_trace); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 - typedef struct ALNcol - ^~~~~~~ -In file included from ./io_lib_header.h:33, - from dp_lib/util_dp_gotoh_nw.c:34: + from dp_lib/util_dp_sim.c:32: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ + CC fastal/diagonal.c In file included from ./io_lib_header.h:33, from dp_lib/util_graph_maln.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': -dp_lib/util_dp_drivers.c:1854:22: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] - 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); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 6067) into a destination of size 1000 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC fastal/diagonal.c - CC fastal/fastal.c - CC fastal/iteration.c - CC fastal/fastal_opt_parsing.c - CC fastal/parttree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2136,62 +2103,39 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +In file included from ./io_lib_header.h:33, + from fastal/diagonal.c:31: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ + CC fastal/fastal.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 + typedef struct ALNcol + ^~~~~~~ +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 + typedef struct ALNcol + ^~~~~~~ +fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': +fastal/diagonal.c:434:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(blast_command); + ~~~~~~^~~~~~~~~~~~~~~ +fastal/diagonal.c:439:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:440:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/diagonal.c:441:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from fastal/iteration.c:34: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - ^ -./programmes_define.h:382: warning: "x3dna" redefined - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:381: note: this is the location of the previous definition - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_mode "saracoffee" - ^ -./programmes_define.h:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from fastal/parttree.c:36: + from fastal/fastal.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2240,24 +2184,87 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" - CC fastal/scoring.c - CC fastal/tree.c - CC io_lib/io_func.c -In file included from ./io_lib_header.h:33, - from fastal/diagonal.c:31: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ - CC io_lib/pb_util_read_seq_util.c +dp_lib/util_dp_drivers.c: In function 'Constraint_list* method2pw_cl(TC_method*, Constraint_list*)': +dp_lib/util_dp_drivers.c:382:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( mat, "%s", (strm(m, "default"))?"dna_idmat":m); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c:373:22: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( mat, "%s", (strm(m, "default"))?"blosum62mt":m); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c:386:40: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + if ( M->matrix[0])sprintf ( mat, "%s", M->matrix); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./io_lib_header.h:33, - from fastal/iteration.c:34: + from fastal/fastal.c:34: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Alignment* realign_block(Alignment*, int, int, char*)': +dp_lib/util_dp_drivers.c:920:22: warning: ' -infile=' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] + sprintf ( command, "%s -infile=%s -outfile=%s %s", script,seq_name, aln_name, TO_NULL_DEVICE); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 38 or more bytes (assuming 1037) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC fastal/fastal_opt_parsing.c + CC fastal/iteration.c + CC fastal/parttree.c + CC fastal/scoring.c + CC fastal/tree.c +fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': +fastal/fastal.c:1924:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(blast_command); + ~~~~~~^~~~~~~~~~~~~~~ +fastal/fastal.c:1929:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1930:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1931:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1976:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(blast_command); + ~~~~~~^~~~~~~~~~~~~~~ +fastal/fastal.c:1980:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1981:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:1982:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 300, diag_f); + ~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from io_lib/pb_util_read_seq_util.c:34: + from fastal/iteration.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2306,28 +2313,61 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -In file included from ./io_lib_header.h:33, - from fastal/parttree.c:36: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ -fastal/diagonal.c: In function 'int seq_pair2blast_diagonal2(char*, char*, Diagonal**, int*, int, int, int)': -fastal/diagonal.c:434:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] +fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': +fastal/fastal.c:2115:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(blast_command); ~~~~~~^~~~~~~~~~~~~~~ -fastal/diagonal.c:439:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:440:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/diagonal.c:441:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': +fastal/fastal.c:2262:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] + system(blast_command); + ~~~~~~^~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': +fastal/fastal.c:3201:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets (line, LINE_LENGTH , seq_file); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': +fastal/fastal.c:3323:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, profile_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3326:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, profile_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3329:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, profile_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3331:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, profile_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3333:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, profile_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3352:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH , profile_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': +fastal/fastal.c:3502:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets (line, LINE_LENGTH , sequence_file); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c: In function 'void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)': +fastal/fastal.c:3575:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH , edit_file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3577:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH , edit_file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3579:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH , edit_file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3581:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH , edit_file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/fastal.c:3643:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(aligned_sequence, alignment_length+3, edit_seq_file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from fastal/scoring.c:37: + from fastal/parttree.c:36: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2376,10 +2416,15 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +In file included from ./io_lib_header.h:33, + from fastal/iteration.c:34: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from fastal/fastal.c:34: + from fastal/scoring.c:37: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2481,7 +2526,7 @@ #define x3dna-ssr_mode "saracoffee" In file included from ./io_lib_header.h:33, - from io_lib/pb_util_read_seq_util.c:34: + from fastal/parttree.c:36: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ @@ -2519,6 +2564,46 @@ fastal/iteration.c:569:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH , edit_file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC io_lib/io_func.c +fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': +fastal/parttree.c:695:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 500, aln_f); + ~~~~~^~~~~~~~~~~~~~~~~~ +fastal/parttree.c:701:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, 500, aln_f); + ~~~~~^~~~~~~~~~~~~~~~~~ +fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': +fastal/parttree.c:848:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, tables_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c:859:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, tables_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c: In function 'int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)': +fastal/parttree.c:891:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, ktup_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c:903:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, ktup_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c:906:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, ktup_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c:912:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, ktup_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c: In function 'int euclidean_dist_half(FILE*, long int, short int*, short int*, int)': +fastal/parttree.c:951:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, ktup_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +fastal/parttree.c:962:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line, LINE_LENGTH, ktup_f); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 + typedef struct ALNcol + ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -2571,69 +2656,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -fastal/parttree.c: In function 'int** make_distance_matrix_sim(FILE*, long int*, int*, int, int**)': -fastal/parttree.c:695:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 500, aln_f); - ~~~~~^~~~~~~~~~~~~~~~~~ -fastal/parttree.c:701:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 500, aln_f); - ~~~~~^~~~~~~~~~~~~~~~~~ -fastal/parttree.c: In function 'void get_table(short int*, FILE*, long int)': -fastal/parttree.c:848:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, tables_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c:859:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, tables_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c: In function 'int euclidean_dist(FILE*, long int, long int, short int*, short int*, int)': -fastal/parttree.c:891:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, ktup_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c:903:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, ktup_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c:906:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, ktup_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c:912:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, ktup_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c: In function 'int euclidean_dist_half(FILE*, long int, short int*, short int*, int)': -fastal/parttree.c:951:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, ktup_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/parttree.c:962:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, ktup_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC io_lib/pb_util_read_sequence.c - CC io_lib/tree_util.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 - typedef struct ALNcol - ^~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'void getstr(char*, char*)': -io_lib/pb_util_read_seq_util.c:269:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(outstr, 100, stdin); - ~~~~~^~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'double getreal(char*, double, double, double)': -io_lib/pb_util_read_seq_util.c:280:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, MAXLINE, stdin); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_seq_util.c: In function 'int getint(char*, int, int, int)': -io_lib/pb_util_read_seq_util.c:305:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, MAXLINE, stdin); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ fastal/scoring.c: In function 'double calculate_sum_of_pairs_score_affine(char*, int**, double, double)': fastal/scoring.c:76:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, alignment_file); @@ -2668,11 +2690,38 @@ fastal/scoring.c:585:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINE_LENGTH, result); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC km_coffee/Stack.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 + typedef struct ALNcol + ^~~~~~~ +In file included from ./io_lib_header.h:33, + from io_lib/io_func.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +io_lib/io_func.c: In function 'int output_raw_score(Alignment*, Alignment*, char*)': +io_lib/io_func.c:1235:17: warning: converting to non-pointer type 'int' from NULL [-Wconversion-null] + if (!A)return NULL; + ^~~~ +io_lib/io_func.c: In function 'int aln2compressed_ps(Alignment*, char*)': +io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +io_lib/io_func.c: In function 'int** read_matrice(char*)': +io_lib/io_func.c:511:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "\n"); + ~~~~~~~^~~~~~~~~~~ +io_lib/io_func.c: In function 'void get_rgb_values(int, Color*)': +io_lib/io_func.c:971:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + 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_seq_util.c + CC io_lib/pb_util_read_sequence.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from io_lib/pb_util_read_sequence.c:35: + from io_lib/pb_util_read_seq_util.c:34: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -2721,145 +2770,26 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +dp_lib/util_dp_drivers.c: In function 'Constraint_list* seq_msa(TC_method*, char*, Constraint_list*)': +dp_lib/util_dp_drivers.c:1854:22: warning: '%s' directive writing up to 500 bytes into a region of size between 445 and 945 [-Wformat-overflow=] + 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); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 71 or more bytes (assuming 6067) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 - typedef struct ALNcol - ^~~~~~~ -In file included from ./io_lib_header.h:33, - from io_lib/io_func.c: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 typedef struct ALNcol ^~~~~~~ -fastal/fastal.c: In function 'int seq_pair2blast_diagonal(char*, char*, int**, int*, int, int, int)': -fastal/fastal.c:1924:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(blast_command); - ~~~~~~^~~~~~~~~~~~~~~ -fastal/fastal.c:1929:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1930:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1931:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1976:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(blast_command); - ~~~~~~^~~~~~~~~~~~~~~ -fastal/fastal.c:1980:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1981:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:1982:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, 300, diag_f); - ~~~~~^~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'int seq_pair2blat_diagonal(char*, char*, int**, int*, int, int, int)': -fastal/fastal.c:2115:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(blast_command); - ~~~~~~^~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'int seq_pair2blastz_diagonal(char*, char*, int**, int*, int, int, int)': -fastal/fastal.c:2262:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] - system(blast_command); - ~~~~~~^~~~~~~~~~~~~~~ - CC km_coffee/Vector.c -fastal/fastal.c: In function 'void file_pos2profile(FILE*, long int, Fastal_profile*, int, Fastal_param*)': -fastal/fastal.c:3201:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets (line, LINE_LENGTH , seq_file); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void profile_file2profile(Fastal_profile*, FILE*, long int, Fastal_param*)': -fastal/fastal.c:3323:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, profile_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3326:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, profile_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3329:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, profile_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3331:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, profile_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3333:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH, profile_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3352:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH , profile_f); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void edit_seq2aligned_seq(char*, FILE*, long int, FILE*)': -fastal/fastal.c:3502:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets (line, LINE_LENGTH , sequence_file); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c: In function 'void edit2alignment(FILE*, long int*, FILE*, long int*, int, int, char*, int, FILE*, int, FILE*)': -fastal/fastal.c:3575:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH , edit_file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3577:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH , edit_file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3579:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH , edit_file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3581:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line, LINE_LENGTH , edit_file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fastal/fastal.c:3643:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(aligned_sequence, alignment_length+3, edit_seq_file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_sequence.c: In function 'void get_clustal_seq(char*, char*, int*, char*, int)': -io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ - ~~~~~^~~~~~~~~~~~~~~~~~~~ -io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - for(i=1;id_name); @@ -2919,10 +2867,42 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +io_lib/pb_util_read_sequence.c: In function 'void get_clustal_seq(char*, char*, int*, char*, int)': +io_lib/pb_util_read_sequence.c:144:7: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets(line,MAXLINE+1,fin); /* read the title line...ignore it */ + ~~~~~^~~~~~~~~~~~~~~~~~~~ +io_lib/pb_util_read_sequence.c:149:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + for(i=1;idp_mode); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ -util_lib/aln_convertion_util.c: In function 'Alignment* aln2conservation(Alignment*, int, char*)': -util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -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 - typedef struct ALNcol - ^~~~~~~ - CC util_lib/util.c CC util_lib/util_aln_analyze.c - CC util_lib/util_analyse_constraints_list.c -util_lib/aln_convertion_util.c: In function 'Alignment* aln2N_replicate(Alignment*, char*, char*)': -util_lib/aln_convertion_util.c:7697:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/reformat.c: In function 'int output_suchard_aln(char*, Alignment*)': -util_lib/reformat.c:7441:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': -util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] - fprintf (out, "ATOM ", lw[1]);//ATOM - ^~~~~~~~ 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:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) @@ -3508,6 +3531,58 @@ util_lib/reformat.c:11754:29: warning: null argument where non-null required (argument 1) [-Wnonnull] int shuf=atoi (ACTION(1)); ^ +In file included from ./define_header.h:31, + from ./io_lib/io_structures.h:33, + from ./io_lib_header.h:30, + from util_lib/util.c:52: +./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_4_TCOFFEE "x3dna" + ^ +./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + ^ +./programmes_define.h:380: warning: "x3dna" redefined + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:379: note: this is the location of the previous definition + #define x3dna-ssr_4_TCOFFEE "x3dna" + +./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + ^ +./programmes_define.h:381: warning: "x3dna" redefined + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:380: note: this is the location of the previous definition + #define x3dna-ssr_type "RNA_secondarystructure_predictor" + +./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + ^ +./programmes_define.h:382: warning: "x3dna" redefined + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:381: note: this is the location of the previous definition + #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" + +./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_mode "saracoffee" + ^ +./programmes_define.h:383: warning: "x3dna" redefined + #define x3dna-ssr_mode "saracoffee" + +./programmes_define.h:382: note: this is the location of the previous definition + #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" + +./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name + #define x3dna-ssr_update_action "never" + ^ +./programmes_define.h:384: warning: "x3dna" redefined + #define x3dna-ssr_update_action "never" + +./programmes_define.h:383: note: this is the location of the previous definition + #define x3dna-ssr_mode "saracoffee" + util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ @@ -3523,25 +3598,6 @@ util_lib/reformat.c:11978:77: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+1)&& !strm (ACTION(na+1), "def"))max=atof(ACTION(na+1)); ^ -util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': -util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:378:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%*s" ); - ~~~~~~~^~~~~~~~~~~~~ -util_lib/reformat_struc.c:416:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c:11979:77: warning: null argument where non-null required (argument 1) [-Wnonnull] if (ACTION(na+2)&& !strm (ACTION(na+2), "def"))enb=atoi(ACTION(na+2)); ^ @@ -3590,6 +3646,11 @@ util_lib/reformat.c:12266:37: note: in expansion of macro 'ATOI_ACTION' D1->A=aln2conservation ( D1->A, ATOI_ACTION (1), ACTION (2)); ^~~~~~~~~~~ +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 + typedef struct ALNcol + ^~~~~~~ util_lib/reformat.c:43:58: warning: null argument where non-null required (argument 1) [-Wnonnull] #define ATOI_ACTION(x) ((ACTION(x)!=NULL)?(atoi(ACTION(x))):0) ^ @@ -3695,45 +3756,14 @@ util_lib/reformat.c:13620:8: note: in expansion of macro 'ATOI_ACTION' p3=ATOI_ACTION(5); ^~~~~~~~~~~ -util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': -util_lib/reformat.c:14324:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': -util_lib/reformat.c:1321:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ -util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': -util_lib/reformat.c:1360:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ -util_lib/reformat.c: In function 'Alignment* quick_read_aln(char*)': -util_lib/reformat.c:1402:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ -util_lib/reformat.c: In function 'int read_nameseq(char*, char***, char***, char***)': -util_lib/reformat.c:1416:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "#NAMESEQ_01\n"); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:1417:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "# %d\n", &nseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:1427:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d %d ", &l1, &l2); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:1430:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/reformat.c:1435:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d ", &l1); - ~~~~~~~^~~~~~~~~~~~~~~~ -util_lib/reformat.c:1437:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets (com[0][nseq],l1, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat_struc.c: In function 'void bfactor2x_in_pdb(char*, char*, float*)': +util_lib/reformat_struc.c:125:18: warning: too many arguments for format [-Wformat-extra-args] + fprintf (out, "ATOM ", lw[1]);//ATOM + ^~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from util_lib/util.c:52: + from util_lib/util_aln_analyze.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -3782,6 +3812,60 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +util_lib/reformat.c: In function 'int output_header_mat(int**, char*)': +util_lib/reformat.c:14324:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +util_lib/reformat_struc.c: In function 'Ca_trace* simple_read_ca_trace(char*)': +util_lib/reformat_struc.c:370:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:372:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:378:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%*s %*s %c %*c %d %*f %*f %*f\n",&res,&res_num); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat_struc.c:405:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:407:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%*s" ); + ~~~~~~~^~~~~~~~~~~~~ +util_lib/reformat_struc.c:416:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%*s %s %s %*c %d %f %f %f\n",A->type, A->res,&A->res_num, &A->x, &A->y, &A->z); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c: In function 'Sequence* quick_read_seq(char*)': +util_lib/reformat.c:1321:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ +util_lib/reformat.c: In function 'Alignment* quick_read_aln_static(char*)': +util_lib/reformat.c:1360:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ +util_lib/reformat.c: In function 'Alignment* quick_read_aln(char*)': +util_lib/reformat.c:1402:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ +util_lib/reformat.c: In function 'int read_nameseq(char*, char***, char***, char***)': +util_lib/reformat.c:1416:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "#NAMESEQ_01\n"); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:1417:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "# %d\n", &nseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:1427:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d %d ", &l1, &l2); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:1430:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%s %s\n", nam[0][nseq], seq[0][nseq]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/reformat.c:1435:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d ", &l1); + ~~~~~~~^~~~~~~~~~~~~~~~ +util_lib/reformat.c:1437:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets (com[0][nseq],l1, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int read_nameseq_old(char*, char***, char***, char***)': util_lib/reformat.c:1461:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "#NAMESEQ_01\n"); @@ -3857,72 +3941,15 @@ util_lib/reformat.c:4602:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%s",name); ~~~~~~~^~~~~~~~~~~~~~~ -In file included from ./define_header.h:31, - from ./io_lib/io_structures.h:33, - from ./io_lib_header.h:30, - from util_lib/util_analyse_constraints_list.c:33: -./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_4_TCOFFEE "x3dna" - ^ -./programmes_define.h:380:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - ^ -./programmes_define.h:380: warning: "x3dna" redefined - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:379: note: this is the location of the previous definition - #define x3dna-ssr_4_TCOFFEE "x3dna" - -./programmes_define.h:381:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - ^ -./programmes_define.h:381: warning: "x3dna" redefined - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:380: note: this is the location of the previous definition - #define x3dna-ssr_type "RNA_secondarystructure_predictor" - -./programmes_define.h:382:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - ^ -./programmes_define.h:382: warning: "x3dna" redefined - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:381: note: this is the location of the previous definition - #define x3dna-ssr_ADDRESS "http://x3dna.bio.columbia.edu/" - -./programmes_define.h:383:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_mode "saracoffee" - ^ -./programmes_define.h:383: warning: "x3dna" redefined - #define x3dna-ssr_mode "saracoffee" - -./programmes_define.h:382: note: this is the location of the previous definition - #define x3dna-ssr_source "http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz" - -./programmes_define.h:384:14: warning: ISO C++11 requires whitespace after the macro name - #define x3dna-ssr_update_action "never" - ^ -./programmes_define.h:384: warning: "x3dna" redefined - #define x3dna-ssr_update_action "never" - -./programmes_define.h:383: note: this is the location of the previous definition - #define x3dna-ssr_mode "saracoffee" - +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 + typedef struct ALNcol + ^~~~~~~ util_lib/reformat.c: In function 'int fscanf_seq_name(FILE*, char*)': util_lib/reformat.c:5636:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s", name); ~~~~~~~^~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c: In function 'Alignment* extract_aln3(Alignment*, char*)': -util_lib/aln_convertion_util.c:7459:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:7478:31: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - if ( c=='#' || c=='!')fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:7482:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/reformat.c: In function 'int get_amps_seq_name(char**, char*)': util_lib/reformat.c:5989:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] {fscanf (fp, "%*d >%s", name[nseq++]); @@ -3942,6 +3969,19 @@ util_lib/reformat.c:6423:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf (fp, "%s %d", name,&i); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from ./io_lib_header.h:33, + from util_lib/util.c:52: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + 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] + } + ^ +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] + } + ^ util_lib/reformat.c: In function 'int** read_blast_matrix(char*)': util_lib/reformat.c:14165:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf ( fp, "%s ", buf); @@ -3969,10 +4009,27 @@ util_lib/reformat.c:14396:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets ( sbuf, VERY_LONG_STRING, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int cherry(int, char**)': +util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ + CC util_lib/util_analyse_constraints_list.c +util_lib/util.c: In function 'int dump_nfc(char*, char*)': +util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +util_lib/util.c: In function 'int set_nproc(int)': +util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +util_lib/util.c: In function 'char* vremove3(char*, char*)': +util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, - from util_lib/util_aln_analyze.c:33: + from util_lib/util_analyse_constraints_list.c:33: ./programmes_define.h:379:14: warning: ISO C++11 requires whitespace after the macro name #define x3dna-ssr_4_TCOFFEE "x3dna" ^ @@ -4021,23 +4078,128 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +util_lib/util.c: In function 'FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))': +util_lib/util.c:281:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread( rra, size, len,fp); /*rra=ra[--l]*/ + ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:286:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread( rra, size, len,fp); /*rra=ra[ir]*/ + ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:289:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread( rrb, size, len,fp); /*rrb=ra[0]*/ + ~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:306:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread (ra_j, size, len, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:311:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread (ra_j_1, size, len, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': +dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( dp_mode, "%s", CL->dp_mode); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))': +util_lib/util.c:420:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread ( key2, el_size, entry_len,fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': +util_lib/util.c:847:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%d",&list[n[0]++]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int quantile(int, char**)': +util_lib/util.c:1321:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%s %s\n", s1, s2); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int** input_array_int(char*)': +util_lib/util.c:1805:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d\n", &len); + ~~~~~~~^~~~~~~~~~~~~~~~~~ +util_lib/util.c:1809:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(fp, "%d ", &len2); + ~~~~~~^~~~~~~~~~~~~~~~~~ +util_lib/util.c:1812:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(fp, "%d ", &array[a][b]); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c:1813:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "\n"); + ~~~~~~~^~~~~~~~~~ In file included from ./io_lib_header.h:33, from util_lib/util_analyse_constraints_list.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util.c:52: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ +util_lib/util.c: In function 'int perl_strstr(char*, char*)': +util_lib/util.c:2468:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d", &r); + ~~~~~~~^~~~~~~~~~~~~~ +util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': +util_lib/util.c:4439:19: warning: control reaches end of non-void function [-Wreturn-type] + printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); + ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC util_lib/util_constraints_list.c +util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': +util_lib/util.c:5760:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%s\n",list[n]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'char* redirect_stderr(char*)': +util_lib/util.c:6300:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + freopen(stderr_file, "w", stderr); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'char* redirect_stdout(char*)': +util_lib/util.c:6343:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + freopen(stdout_file, "w", stdout); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': +t_coffee_lib/t_coffee.c:5621:32: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] + sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); + ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from t_coffee_lib/t_coffee.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)': +util_lib/util.c:7554:2: warning: second parameter of 'va_start' not last named argument [-Wvarargs] + va_start (ap, usage); + ^~~~~~~~ +util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': +util_lib/util.c:7821:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line, VERY_LONG_STRING,fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': +util_lib/util.c:7841:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%s", string); + ~~~~~~~^~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': +util_lib/util.c:8228:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line, lline,fp); + ~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util.c:8258:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line, lline,fp); + ~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int check_for_update(char*)': +util_lib/util.c:8345:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "Version_%f", &new_version); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util.c: In function 'int check_internet_connection(int)': +util_lib/util.c:8437:10: warning: control reaches end of non-void function [-Wreturn-type] + myexit (EXIT_FAILURE); + ~~~~~~~^~~~~~~~~~~~~~ CC util_lib/util_declare.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 - typedef struct ALNcol - ^~~~~~~ +util_lib/util.c: In function 'int km_main(int, char**)': +util_lib/util.c:10370:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ + CC util_lib/util_domain_constraints_list.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4090,14 +4252,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -util_lib/util.c: In function 'int cherry(int, char**)': -util_lib/util.c:1009:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -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] - } - ^ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4150,144 +4304,12 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -util_lib/util.c: In function 'int dump_nfc(char*, char*)': -util_lib/util.c:4455:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -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 - typedef struct ALNcol - ^~~~~~~ -util_lib/util.c: In function 'int set_nproc(int)': -util_lib/util.c:5488:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -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] - } - ^ -util_lib/util.c: In function 'char* vremove3(char*, char*)': -util_lib/util.c:6920:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ - CC util_lib/util_domain_constraints_list.c -dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': -dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( dp_mode, "%s", CL->dp_mode); - ^~~~ -In file included from /usr/include/stdio.h:873, - from dp_lib/util_dp_drivers.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'FILE* hsort_file(FILE*, int, int, size_t, int, int, int (*)(const void*, const void*, int, int, size_t), void* (*)(void*, void*, size_t))': -util_lib/util.c:281:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread( rra, size, len,fp); /*rra=ra[--l]*/ - ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:286:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread( rra, size, len,fp); /*rra=ra[ir]*/ - ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:289:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread( rrb, size, len,fp); /*rrb=ra[0]*/ - ~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:306:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread (ra_j, size, len, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:311:11: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread (ra_j_1, size, len, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'void* bsearch_file(const void*, int*, int, int, FILE*, int, int, size_t, int (*)(const void*, const void*, int, int, size_t))': -util_lib/util.c:420:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread ( key2, el_size, entry_len,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + CC util_lib/util_dps.c 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 typedef struct ALNcol ^~~~~~~ -util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': -util_lib/util_constraints_list.c:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] - } - ^ -util_lib/util.c: In function 'FILE* get_number_list_in_file(FILE*, int*, int*, int*)': -util_lib/util.c:847:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%d",&list[n[0]++]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int quantile(int, char**)': -util_lib/util.c:1321:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%s %s\n", s1, s2); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int** input_array_int(char*)': -util_lib/util.c:1805:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d\n", &len); - ~~~~~~~^~~~~~~~~~~~~~~~~~ -util_lib/util.c:1809:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(fp, "%d ", &len2); - ~~~~~~^~~~~~~~~~~~~~~~~~ -util_lib/util.c:1812:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(fp, "%d ", &array[a][b]); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c:1813:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "\n"); - ~~~~~~~^~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)': -util_lib/util_constraints_list.c:2225:28: warning: too many arguments for format [-Wformat-extra-args] - fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Constraint_list* read_constraint_list_file(Constraint_list*, char*)': -util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] - x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); - ^~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int perl_strstr(char*, char*)': -util_lib/util.c:2468:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d", &r); - ~~~~~~~^~~~~~~~~~~~~~ -util_lib/util.c: In function 'int printf_system_direct_check(char*, ...)': -util_lib/util.c:4439:19: warning: control reaches end of non-void function [-Wreturn-type] - printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); - ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'char* count_strings_in_file(char*, char*)': -util_lib/util.c:5760:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%s\n",list[n]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'char* redirect_stderr(char*)': -util_lib/util.c:6300:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - freopen(stderr_file, "w", stderr); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'char* redirect_stdout(char*)': -util_lib/util.c:6343:12: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - freopen(stdout_file, "w", stdout); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)': -util_lib/util.c:7554:2: warning: second parameter of 'va_start' not last named argument [-Wvarargs] - va_start (ap, usage); - ^~~~~~~~ -util_lib/util.c: In function 'char** get_parameter(char*, int*, char*)': -util_lib/util.c:7821:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, VERY_LONG_STRING,fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'FILE* set_fp_id(FILE*, char*)': -util_lib/util.c:7841:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%s", string); - ~~~~~~~^~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int** get_file_block_pattern(char*, int*, int)': -util_lib/util.c:8228:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, lline,fp); - ~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/util.c:8258:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line, lline,fp); - ~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int check_for_update(char*)': -util_lib/util.c:8345:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "Version_%f", &new_version); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util.c: In function 'int check_internet_connection(int)': -util_lib/util.c:8437:10: warning: control reaches end of non-void function [-Wreturn-type] - myexit (EXIT_FAILURE); - ~~~~~~~^~~~~~~~~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4340,53 +4362,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -util_lib/util.c: In function 'int km_main(int, char**)': -util_lib/util.c:10370:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ -util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': -util_lib/util_constraints_list.c:582:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] - chdir (tdir); - ~~~~~~^~~~~~ -util_lib/util_constraints_list.c:585:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] - chdir (cdir); - ~~~~~~^~~~~~ -util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': -util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line,LONG_STRING, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'TC_method* method_file2TC_method(char*)': -util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets ( line,LONG_STRING, fp); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -In file included from ./io_lib_header.h:33, - from util_lib/util_domain_constraints_list.c:33: -./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration - typedef struct ALNcol - ^~~~~~~ - CC util_lib/util_dps.c -util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': -util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - if ( c=='C')fscanf( fp, "PU %d\n", &cpu); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)': -util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d\n", &max_nseq); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%*s %d %*s\n", &l); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fgets (line , 200 , fp); - ~~~~~~^~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': -util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); - ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - CC util_lib/util_job_handling.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4440,10 +4415,33 @@ #define x3dna-ssr_mode "saracoffee" 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 + typedef struct ALNcol + ^~~~~~~ +In file included from ./io_lib_header.h:33, from util_lib/util_dps.c:33: ./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration typedef struct ALNcol ^~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* unfreeze_constraint_list(Constraint_list*)': +util_lib/util_constraints_list.c:1312:1: warning: no return statement in function returning non-void [-Wreturn-type] + } + ^ +In file included from ./io_lib_header.h:33, + from util_lib/util_domain_constraints_list.c:33: +./io_lib/tree_util.h:30:1: warning: 'typedef' was ignored in this declaration + typedef struct ALNcol + ^~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* fork_read_n_constraint_list(char**, int, char*, char*, char*, char*, FILE*, Constraint_list*, char*, int)': +util_lib/util_constraints_list.c:2225:28: warning: too many arguments for format [-Wformat-extra-args] + fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* read_constraint_list_file(Constraint_list*, char*)': +util_lib/util_constraints_list.c:2852:19: warning: too many arguments for format [-Wformat-extra-args] + x=sscanf (buf, "%s %d %d %d %d %d",arg, &length, &r1,&r2,&we,&cons,&misc); + ^~~~~~~~~~~~~~~~~~~ + CC util_lib/util_job_handling.c CC util_lib/util_make_tree.c In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, @@ -4497,22 +4495,6 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" -t_coffee_lib/t_coffee.c: In function 'int batch_main(int, char**)': -t_coffee_lib/t_coffee.c:5621:32: warning: '%s' directive writing up to 999 bytes into a region of size between 982 and 991 [-Wformat-overflow=] - sprintf ( split_name, "%s.split.%d.%s", F->name, b,split_format); - ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from t_coffee_lib/t_coffee.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1018) into a destination of size 1000 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - typedef struct ALNcol - ^~~~~~~ In file included from ./define_header.h:31, from ./io_lib/io_structures.h:33, from ./io_lib_header.h:30, @@ -4565,6 +4547,47 @@ ./programmes_define.h:383: note: this is the location of the previous definition #define x3dna-ssr_mode "saracoffee" +util_lib/util_constraints_list.c: In function 'Job_TC* submit_lib_job(Job_TC*)': +util_lib/util_constraints_list.c:582:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] + chdir (tdir); + ~~~~~~^~~~~~ +util_lib/util_constraints_list.c:585:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] + chdir (cdir); + ~~~~~~^~~~~~ +util_lib/util_constraints_list.c: In function 'char* method_file_tag2value(char*, char*)': +util_lib/util_constraints_list.c:1151:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line,LONG_STRING, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'TC_method* method_file2TC_method(char*)': +util_lib/util_constraints_list.c:1194:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets ( line,LONG_STRING, fp); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +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 + typedef struct ALNcol + ^~~~~~~ +util_lib/util_constraints_list.c: In function 'int read_cpu_in_list(char*)': +util_lib/util_constraints_list.c:2600:20: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + if ( c=='C')fscanf( fp, "PU %d\n", &cpu); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'int read_seq_in_list(char*, int*, char***, char***, Genomic_info**)': +util_lib/util_constraints_list.c:2918:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d\n", &max_nseq); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:2923:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%*s %d %*s\n", &l); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:2955:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( fp, "%s %d %s\n", name, &seq_len, sequence); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:2980:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fgets (line , 200 , fp); + ~~~~~~^~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c: In function 'Constraint_list* nfork_relax_constraint_list_4gp(Constraint_list*)': +util_lib/util_constraints_list.c:4054:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf (fp, "%d ", &CL->residue_index[s][r][a+WE]); + ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -4672,6 +4695,17 @@ util_lib/util_make_tree.c:2118:12: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir (cdir); ~~~~~~~~~^~~~~~ +dp_lib/util_dp_drivers.c: In function 'Alignment* stack_progressive_aln(Alignment*, Constraint_list*, int, int)': +dp_lib/util_dp_drivers.c:3717:24: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( dp_mode, "%s", CL->dp_mode); + ^~~~ +In file included from /usr/include/stdio.h:873, + from dp_lib/util_dp_drivers.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util_constraints_list.c: In function 'char* make_aln_command(TC_method*, char*, char*)': util_lib/util_constraints_list.c:1287:17: warning: '%s' directive writing up to 999 bytes into a region of size between 499 and 999 [-Wformat-overflow=] 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); @@ -4727,6 +4761,27 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': +util_lib/aln_convertion_util.c:12082:26: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] + sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); + ^~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from util_lib/aln_convertion_util.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +util_lib/aln_convertion_util.c:12076:26: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] + sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:873, + from util_lib/aln_convertion_util.c:27: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function 'char* long_tmpnam_2(char*)': util_lib/util.c:6808:16: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf (buf, "%s/%s%d%s",tmpdir,root2, file++,set_file2remove_extension (NULL, GET)); @@ -4760,23 +4815,23 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c: In function 'float** get_weight(Alignment*, Sequence*, char*)': -util_lib/aln_convertion_util.c:12082:26: warning: ' -w ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] - sprintf ( command, "%s %s -w %s", program, seq_name, weight_name); - ^~~~~~~~~~~~~ +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:695:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( aln_mode, "%s", method->aln_mode); + ^~~~ In file included from /usr/include/stdio.h:873, - from util_lib/aln_convertion_util.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 1005) into a destination of size 1000 + from util_lib/util_constraints_list.c:29: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/aln_convertion_util.c:12076:26: warning: ' -i ' directive writing 4 bytes into a region of size between 0 and 999 [-Wformat-overflow=] - sprintf ( command, "%s %s -i %s -w %s", program, seq_name, aln_name, weight_name); - ^~~~~~~~~~~~~~~~~~~ +util_lib/util_constraints_list.c:696:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] + sprintf ( out_mode, "%s", method->out_mode); + ^~~~ In file included from /usr/include/stdio.h:873, - from util_lib/aln_convertion_util.c:27: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output 10 or more bytes (assuming 1009) into a destination of size 1000 + from util_lib/util_constraints_list.c:29: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); @@ -4795,27 +4850,6 @@ util_lib/reformat.c:11528:24: warning: '%s' directive argument is null [-Wformat-overflow=] sprintf (type, "%s", ACTION (2)); ^~~~ -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:695:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( aln_mode, "%s", method->aln_mode); - ^~~~ -In file included from /usr/include/stdio.h:873, - from util_lib/util_constraints_list.c:29: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -util_lib/util_constraints_list.c:696:23: warning: '%s' directive writing up to 500 bytes into a region of size 100 [-Wformat-overflow=] - sprintf ( out_mode, "%s", method->out_mode); - ^~~~ -In file included from /usr/include/stdio.h:873, - from util_lib/util_constraints_list.c:29: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 1 and 501 bytes into a destination of size 100 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Linking... /usr/bin/ld: dp_lib/util_dp_drivers.o: in function `hh_pair(TC_method*, char*, Constraint_list*)': ./t_coffee_source/dp_lib/util_dp_drivers.c:1160: warning: the use of `tmpnam' is dangerous, better use `mkstemp' @@ -4861,8 +4895,8 @@ 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' in '../t-coffee_12.00.7fb08c2-4_amd64.deb'. dpkg-deb: building package 't-coffee-dbgsym' in '../t-coffee-dbgsym_12.00.7fb08c2-4_amd64.deb'. +dpkg-deb: building package 't-coffee' in '../t-coffee_12.00.7fb08c2-4_amd64.deb'. dpkg-deb: building package 't-coffee-examples' in '../t-coffee-examples_12.00.7fb08c2-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../t-coffee_12.00.7fb08c2-4_amd64.changes @@ -4870,12 +4904,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/10921/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10921/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/51634 and its subdirectories -I: Current time: Thu Apr 8 02:10:43 -12 2021 -I: pbuilder-time-stamp: 1617891043 +I: removing directory /srv/workspace/pbuilder/10921 and its subdirectories +I: Current time: Thu May 12 10:34:41 +14 2022 +I: pbuilder-time-stamp: 1652301281