Diff of the two buildlogs: -- --- b1/build.log 2020-08-12 19:02:24.802017548 +0000 +++ b2/build.log 2020-08-12 19:03:29.992006787 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Aug 12 07:01:29 -12 2020 -I: pbuilder-time-stamp: 1597258889 +I: Current time: Wed Sep 15 15:25:34 +14 2021 +I: pbuilder-time-stamp: 1631669134 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 '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Thu Sep 27 07:55:06 2018 -12 +gpgv: Signature made Fri Sep 28 09:55:06 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,136 +29,170 @@ dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/8311/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1734/tmp/hooks/D01_modify_environment starting +debug: Running on codethink-sled11-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1734/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1734/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='8311' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1734 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.RYLlkm8cCc/pbuilderrc_ifyq --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RYLlkm8cCc/b1 --logfile b1/build.log poa_2.0+20060928-7.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.RYLlkm8cCc/pbuilderrc_uhG0 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.RYLlkm8cCc/b2 --logfile b2/build.log poa_2.0+20060928-7.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink-sled12-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 - -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 34808 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 34808 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14264 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 35576 Feb 28 2019 cat - -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown - -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp - -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash - -rwxr-xr-x 1 root root 97136 Feb 28 2019 date - -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93752 Feb 28 2019 df - -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir - -rwxr-xr-x 1 root root 75984 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 31368 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 27256 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 174304 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 89656 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln - -rwxr-xr-x 1 root root 52544 Jul 26 2018 login - -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 38840 Jan 9 2019 more - -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138736 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 35560 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm - -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 10 20:26 sh -> dash - -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty - -rwsr-xr-x 1 root root 59424 Jan 9 2019 su - -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync - -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar - -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch - -rwxr-xr-x 1 root root 27256 Feb 28 2019 true - -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount - -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34824 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/8311/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 34808 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 34808 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14264 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 35576 Mar 1 2019 cat + -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown + -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp + -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash + -rwxr-xr-x 1 root root 97136 Mar 1 2019 date + -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93752 Mar 1 2019 df + -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir + -rwxr-xr-x 1 root root 75984 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 31368 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 27256 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 174304 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 89656 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln + -rwxr-xr-x 1 root root 52544 Jul 27 2018 login + -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 38840 Jan 10 2019 more + -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138736 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 35560 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm + -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 15 15:25 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 14 04:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty + -rwsr-xr-x 1 root root 59424 Jan 10 2019 su + -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync + -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar + -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch + -rwxr-xr-x 1 root root 27256 Mar 1 2019 true + -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount + -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34824 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/1734/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +261,7 @@ Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] -Fetched 18.6 MB in 1s (19.4 MB/s) +Fetched 18.6 MB in 2s (8289 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) @@ -382,7 +416,7 @@ 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/poa-2.0+20060928/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/poa-2.0+20060928/ && 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 poa dpkg-buildpackage: info: source version 2.0+20060928-7 dpkg-buildpackage: info: source distribution unstable @@ -415,62 +449,113 @@ gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o msa_format.o msa_format.c gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align_lpo2.o align_lpo2.c gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align_lpo_po2.o align_lpo_po2.c -In file included from black_flag.c:4: -black_flag.c: In function 'black_flag_init_args': +In file included from align_lpo_po2.c:2: +align_lpo_po2.c: In function 'get_lpo_stats': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -black_flag.c:109:3: note: in expansion of macro 'CALLOC' - CALLOC(Program_name,len,char); +align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' + CALLOC (node_type, len, int); ^~~~~~ -In file included from lpo.h:6, - from main.c:3: -main.c: In function 'main': -./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -main.c:183:3: note: in expansion of macro 'CALLOC' - CALLOC (input_seqs, max_input_seqs, LPOSequence_T *); +align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' + CALLOC (refs_from_right, len, int); ^~~~~~ -./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -main.c:221:2: note: in expansion of macro 'REALLOC' - REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); - ^~~~~~~ -In file included from ./default.h:16, - from lpo.h:6, - from main.c:3: -main.c:225:30: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'FILE *' {aka 'struct _IO_FILE *'} [-Wformat=] - WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - po_list_file),"$Revision: 1.2.2.9 $"); - ~~~~~~~~~~~~ -./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' - (sprintf MESSAGE,\ - ^~~~~~~ -In file included from lpo.h:6, - from main.c:3: -./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -main.c:254:2: note: in expansion of macro 'REALLOC' - REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); - ^~~~~~~ -In file included from seq_util.c:2: -seq_util.c: In function 'read_score_matrix': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -seq_util.c:170:3: note: in expansion of macro 'CALLOC' - CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_T); +align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' + CALLOC (tmp, len, int); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -seq_util.c:171:3: note: in expansion of macro 'CALLOC' - CALLOC (m->gap_penalty_y, m->max_gap_length+2, LPOScore_T); +align_lpo_po2.c:44:3: note: in expansion of macro 'CALLOC' + CALLOC (left_links, len, LPOLetterLink_T *); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' + CALLOC (left_links[i], 1, LPOLetterLink_T); + ^~~~~~ +align_lpo_po2.c: In function 'trace_back_lpo_alignment': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' + CALLOC (x_al, len_x, LPOLetterRef_T); ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' + CALLOC (y_al, len_y, LPOLetterRef_T); + ^~~~~~ +align_lpo_po2.c: In function 'align_lpo_po': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' + CALLOC (next_gap_array, max_gap_length + 2, int); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' + CALLOC (next_perp_gap_array, max_gap_length + 2, int); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' + CALLOC (move, len_y, DPMove_T *); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' + CALLOC (move[i], len_x, DPMove_T); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' + CALLOC (init_col_score, len_y+1, DPScore_T); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' + CALLOC (score_rows, len_y+1, DPScore_T *); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' + CALLOC (score_rows[-1], len_x+1, DPScore_T); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo_po2.c:312:5: note: in expansion of macro 'CALLOC' + CALLOC (score_rows[i], len_x+1, DPScore_T); + ^~~~~~ +align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] + fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + ~~^ ~~~~~~~~~ + %d +align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] + fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + ~~^ ~~~~~~~~~ + %d +fasta_format.c: In function 'read_fasta': +fasta_format.c:48:2: warning: implicit declaration of function 'stringptr_cat_pos'; did you mean 'stringptr_cat'? [-Wimplicit-function-declaration] + stringptr_cat_pos(&tmp_seq,line,&length); + ^~~~~~~~~~~~~~~~~ + stringptr_cat In file included from msa_format.h:17, from msa_format.c:17: msa_format.c: In function 'read_clustal': @@ -492,6 +577,14 @@ msa_format.c:174:7: note: in expansion of macro 'REALLOC' REALLOC (aln_mat, n_seqs, char *); ^~~~~~~ +In file included from align_lpo2.c:2: +align_lpo2.c: In function 'get_seq_left_and_final': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' + CALLOC (is_final_node_x, len_x, int); + ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -519,6 +612,31 @@ REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); ^~~~~~~ msa_format.c: In function 'read_pir': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' + CALLOC (x_left, len_x, LPOLetterLink_T *); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' + CALLOC (x_left[i], 1, LPOLetterLink_T); + ^~~~~~ +align_lpo2.c: In function 'trace_back_lpo_alignment': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' + CALLOC (x_al, len_x, LPOLetterRef_T); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' + CALLOC (y_al, len_y, LPOLetterRef_T); + ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -563,82 +681,91 @@ msa_format.c:268:7: note: in expansion of macro 'REALLOC' REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); ^~~~~~~ -msa_format.c: In function 'lpo_from_aln_mat': +align_lpo2.c: In function 'align_lpo': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:318:3: note: in expansion of macro 'CALLOC' - CALLOC (column_ids, n_seqs+1, int *); +align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' + CALLOC (next_gap_array, max_gap_length + 2, int); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:319:3: note: in expansion of macro 'CALLOC' - CALLOC (res_ids, n_seqs+1, int *); +align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' + CALLOC (next_perp_gap_array, max_gap_length + 2, int); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:326:5: note: in expansion of macro 'CALLOC' - CALLOC (column_ids[i], max_aln_length, int); - ^~~~~~ +align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' + CALLOC (move, len_y, DPMove_T *); + ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:327:5: note: in expansion of macro 'CALLOC' - CALLOC (res_ids[i], max_aln_length, int); +align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' + CALLOC (move[i], len_x, DPMove_T); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:334:3: note: in expansion of macro 'CALLOC' - CALLOC (consens_row, max_aln_length, char); +align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' + CALLOC (init_col_score, len_y+1, DPScore_T); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:347:3: note: in expansion of macro 'CALLOC' - CALLOC (lposeq, 1, LPOSequence_T); +align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' + CALLOC (curr_score, len_x+1, DPScore_T); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -msa_format.c:351:3: note: in expansion of macro 'CALLOC' - CALLOC (lposeq->sequence, max_aln_length+1, char); +align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' + CALLOC (prev_score, len_x+1, DPScore_T); ^~~~~~ -In file included from align_lpo2.c:2: -align_lpo2.c: In function 'get_seq_left_and_final': +msa_format.c: In function 'lpo_from_aln_mat': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' - CALLOC (is_final_node_x, len_x, int); +msa_format.c:318:3: note: in expansion of macro 'CALLOC' + CALLOC (column_ids, n_seqs+1, int *); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' - CALLOC (x_left, len_x, LPOLetterLink_T *); +msa_format.c:319:3: note: in expansion of macro 'CALLOC' + CALLOC (res_ids, n_seqs+1, int *); ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' - CALLOC (x_left[i], 1, LPOLetterLink_T); - ^~~~~~ -align_lpo2.c: In function 'trace_back_lpo_alignment': +msa_format.c:326:5: note: in expansion of macro 'CALLOC' + CALLOC (column_ids[i], max_aln_length, int); + ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' - CALLOC (x_al, len_x, LPOLetterRef_T); +msa_format.c:327:5: note: in expansion of macro 'CALLOC' + CALLOC (res_ids[i], max_aln_length, int); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +msa_format.c:334:3: note: in expansion of macro 'CALLOC' + CALLOC (consens_row, max_aln_length, char); ^~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o buildup_lpo.o buildup_lpo.c default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' - CALLOC (y_al, len_y, LPOLetterRef_T); +msa_format.c:347:3: note: in expansion of macro 'CALLOC' + CALLOC (lposeq, 1, LPOSequence_T); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +msa_format.c:351:3: note: in expansion of macro 'CALLOC' + CALLOC (lposeq->sequence, max_aln_length+1, char); ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ @@ -658,6 +785,14 @@ msa_format.c:380:5: note: in expansion of macro 'CALLOC' CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); ^~~~~~ +In file included from black_flag.c:4: +black_flag.c: In function 'black_flag_init_args': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +black_flag.c:109:3: note: in expansion of macro 'CALLOC' + CALLOC(Program_name,len,char); + ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -681,52 +816,23 @@ msa_format.c:407:5: note: in expansion of macro 'CALLOC' CALLOC (al_y, lposeq->length, int); ^~~~~~ -align_lpo2.c: In function 'align_lpo': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' - CALLOC (next_gap_array, max_gap_length + 2, int); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' - CALLOC (next_perp_gap_array, max_gap_length + 2, int); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' - CALLOC (move, len_y, DPMove_T *); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' - CALLOC (move[i], len_x, DPMove_T); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' - CALLOC (init_col_score, len_y+1, DPScore_T); - ^~~~~~ +In file included from seq_util.c:2: +seq_util.c: In function 'read_score_matrix': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' - CALLOC (curr_score, len_x+1, DPScore_T); +seq_util.c:170:3: note: in expansion of macro 'CALLOC' + CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_T); ^~~~~~ +msa_format.c:428:5: warning: implicit declaration of function 'fuse_ring_identities' [-Wimplicit-function-declaration] + fuse_ring_identities (lposeq->length, lposeq->letter, + ^~~~~~~~~~~~~~~~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' - CALLOC (prev_score, len_x+1, DPScore_T); +seq_util.c:171:3: note: in expansion of macro 'CALLOC' + CALLOC (m->gap_penalty_y, m->max_gap_length+2, LPOScore_T); ^~~~~~ -msa_format.c:428:5: warning: implicit declaration of function 'fuse_ring_identities' [-Wimplicit-function-declaration] - fuse_ring_identities (lposeq->length, lposeq->letter, - ^~~~~~~~~~~~~~~~~~~~ In file included from msa_format.h:17, from msa_format.c:17: msa_format.c: In function 'filter_sequence_set': @@ -736,113 +842,41 @@ msa_format.c:485:3: note: in expansion of macro 'CALLOC' CALLOC (keep_seq, n_seqs, int); ^~~~~~ -In file included from align_lpo_po2.c:2: -align_lpo_po2.c: In function 'get_lpo_stats': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' - CALLOC (node_type, len, int); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' - CALLOC (refs_from_right, len, int); - ^~~~~~ -fasta_format.c: In function 'read_fasta': -fasta_format.c:48:2: warning: implicit declaration of function 'stringptr_cat_pos'; did you mean 'stringptr_cat'? [-Wimplicit-function-declaration] - stringptr_cat_pos(&tmp_seq,line,&length); - ^~~~~~~~~~~~~~~~~ - stringptr_cat -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' - CALLOC (tmp, len, int); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:44:3: note: in expansion of macro 'CALLOC' - CALLOC (left_links, len, LPOLetterLink_T *); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' - CALLOC (left_links[i], 1, LPOLetterLink_T); - ^~~~~~ -align_lpo_po2.c: In function 'trace_back_lpo_alignment': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' - CALLOC (x_al, len_x, LPOLetterRef_T); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' - CALLOC (y_al, len_y, LPOLetterRef_T); - ^~~~~~ -align_lpo_po2.c: In function 'align_lpo_po': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' - CALLOC (next_gap_array, max_gap_length + 2, int); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' - CALLOC (next_perp_gap_array, max_gap_length + 2, int); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' - CALLOC (move, len_y, DPMove_T *); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' - CALLOC (move[i], len_x, DPMove_T); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' - CALLOC (init_col_score, len_y+1, DPScore_T); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' - CALLOC (score_rows, len_y+1, DPScore_T *); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +In file included from lpo.h:6, + from main.c:3: +main.c: In function 'main': +./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' - CALLOC (score_rows[-1], len_x+1, DPScore_T); +main.c:183:3: note: in expansion of macro 'CALLOC' + CALLOC (input_seqs, max_input_seqs, LPOSequence_T *); ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:312:5: note: in expansion of macro 'CALLOC' - CALLOC (score_rows[i], len_x+1, DPScore_T); - ^~~~~~ -align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] - fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); - ~~^ ~~~~~~~~~ - %d -align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] - fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); - ~~^ ~~~~~~~~~ - %d +./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +main.c:221:2: note: in expansion of macro 'REALLOC' + REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); + ^~~~~~~ +In file included from ./default.h:16, + from lpo.h:6, + from main.c:3: +main.c:225:30: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'FILE *' {aka 'struct _IO_FILE *'} [-Wformat=] + WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + po_list_file),"$Revision: 1.2.2.9 $"); + ~~~~~~~~~~~~ +./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' + (sprintf MESSAGE,\ + ^~~~~~~ +In file included from lpo.h:6, + from main.c:3: +./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +main.c:254:2: note: in expansion of macro 'REALLOC' + REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); + ^~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o buildup_lpo.o buildup_lpo.c In file included from buildup_lpo.c:3: buildup_lpo.c: In function 'clip_unaligned_ends': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -889,6 +923,7 @@ buildup_lpo.c:445:3: note: in expansion of macro 'CALLOC' CALLOC(seq_cluster,nseq,int); /* MAPS SEQS (or CLUSTERS) TO CLUSTER THEY'RE IN */ ^~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo.o lpo.c default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -907,7 +942,6 @@ buildup_lpo.c:448:3: note: in expansion of macro 'CALLOC' CALLOC(initial_nseq,nseq,int); /* COUNTS SEQS INITIALLY IN EACH CLUSTER (not updated w/ merges) */ ^~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo.o lpo.c default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1002,8 +1036,6 @@ lpo.c:427:3: note: in expansion of macro 'CALLOC' CALLOC(do_fuse,len_y,char); /* MARK POSITIONS TO FUSE seq_y TO seq_x */ ^~~~~~ -In file included from heaviest_bundle.c:3: -heaviest_bundle.c: In function 'heaviest_bundle': lpo.c: In function 'copy_fuse_lpo_remap': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1036,6 +1068,27 @@ lpo.c:564:3: note: in expansion of macro 'CALLOC' CALLOC(x_to_y,holder_x->length,LPOLetterRef_T); ^~~~~~ +lpo.c: In function 'fuse_lpo_remap': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +lpo.c:618:3: note: in expansion of macro 'CALLOC' + CALLOC(new_x,len_x,LPOLetterRef_T); + ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +lpo.c:619:3: note: in expansion of macro 'CALLOC' + CALLOC(new_y,len_y,LPOLetterRef_T); + ^~~~~~ +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +lpo.c:622:3: note: in expansion of macro 'REALLOC' + REALLOC(seq_x,new_len,LPOLetter_T); /* EXPAND seq_x TO HOLD FUSED LPO */ + ^~~~~~~ +In file included from heaviest_bundle.c:3: +heaviest_bundle.c: In function 'heaviest_bundle': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1067,25 +1120,6 @@ heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' CALLOC(bundle_count,seq->nsource_seq,int); ^~~~~~ -lpo.c: In function 'fuse_lpo_remap': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo.c:618:3: note: in expansion of macro 'CALLOC' - CALLOC(new_x,len_x,LPOLetterRef_T); - ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo.c:619:3: note: in expansion of macro 'CALLOC' - CALLOC(new_y,len_y,LPOLetterRef_T); - ^~~~~~ -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo.c:622:3: note: in expansion of macro 'REALLOC' - REALLOC(seq_x,new_len,LPOLetter_T); /* EXPAND seq_x TO HOLD FUSED LPO */ - ^~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo_format.o lpo_format.c In file included from lpo_format.c:3: lpo_format.c: In function 'read_lpo': @@ -1245,6 +1279,7 @@ ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o create_seq.o create_seq.c gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o remove_bundle.o remove_bundle.c +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o numeric_data.o numeric_data.c In file included from create_seq.c:3: create_seq.c: In function 'create_seq': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -1287,8 +1322,6 @@ remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ ^~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o numeric_data.o numeric_data.c -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stringptr.o stringptr.c In file included from ./lpo.h:6, from numeric_data.c:3: numeric_data.c: In function 'new_numeric_data': @@ -1301,6 +1334,26 @@ numeric_data.c:18:3: note: in expansion of macro 'REBUFF' REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); ^~~~~~ +./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +./default.h:215:5: note: in expansion of macro 'REALLOC' + REALLOC(memptr,(NUM)+(BUF),ATYPE); \ + ^~~~~~~ +numeric_data.c:18:3: note: in expansion of macro 'REBUFF' + REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); + ^~~~~~ +./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +numeric_data.c:25:3: note: in expansion of macro 'CALLOC' + CALLOC(data->data,source_seq->length,double); /* ALLOCATE THE ARRAY */ + ^~~~~~ +numeric_data.c: In function 'read_numeric_data': +numeric_data.c:139:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile," %lf",data->data+j); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stringptr.o stringptr.c In file included from stringptr.c:2: stringptr.c: In function 'stringptr_cat_pos': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -1386,21 +1439,6 @@ stringptr.c:67:3: note: in expansion of macro 'GETMEM' GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); ^~~~~~ -./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -./default.h:215:5: note: in expansion of macro 'REALLOC' - REALLOC(memptr,(NUM)+(BUF),ATYPE); \ - ^~~~~~~ -numeric_data.c:18:3: note: in expansion of macro 'REBUFF' - REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); - ^~~~~~ -./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -numeric_data.c:25:3: note: in expansion of macro 'CALLOC' - CALLOC(data->data,source_seq->length,double); /* ALLOCATE THE ARRAY */ - ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1410,10 +1448,6 @@ stringptr.c:67:3: note: in expansion of macro 'GETMEM' GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); ^~~~~~ -numeric_data.c: In function 'read_numeric_data': -numeric_data.c:139:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile," %lf",data->data+j); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f liblpo.a ar rc liblpo.a black_flag.o seq_util.o fasta_format.o msa_format.o align_lpo2.o align_lpo_po2.o buildup_lpo.o lpo.o heaviest_bundle.o lpo_format.o create_seq.o remove_bundle.o numeric_data.o stringptr.o ranlib liblpo.a @@ -1440,7 +1474,7 @@ aligned (1394 nodes, 1413 edges) to (217 nodes, 216 edges): best local score = 437 @ (1274 215) Fusing cluster 3 (MATK_HUMAN, nseq=1) --> 0 (ABL1_HUMAN, nseq=3)... score -1.00 aligned (1532 nodes, 1601 edges) to (507 nodes, 506 edges): best local score = 1212 @ (654 470) -...Wrote 4 sequences to CLUSTAL file /tmp/tmp.WEGT9zW9YZ... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.LARnJTwIrE... X-Gap Penalties (Open, Aff1, Aff2; LTrunc, LDecay): 12 6 6 16 0 X-Gap Penalties (0, 1, 2, ...): 12 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 ... Y-Gap Penalties (Open, Aff1, Aff2; LTrunc, LDecay): 12 6 6 16 0 @@ -1483,12 +1517,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/1734/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1734/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/8311 and its subdirectories -I: Current time: Wed Aug 12 07:02:23 -12 2020 -I: pbuilder-time-stamp: 1597258943 +I: removing directory /srv/workspace/pbuilder/1734 and its subdirectories +I: Current time: Wed Sep 15 15:26:26 +14 2021 +I: pbuilder-time-stamp: 1631669186