Diff of the two buildlogs: -- --- b1/build.log 2021-06-27 11:54:22.662799041 +0000 +++ b2/build.log 2021-06-27 11:55:56.635254343 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 26 23:52:46 -12 2021 -I: pbuilder-time-stamp: 1624794766 +I: Current time: Sun Jul 31 08:17:25 +14 2022 +I: pbuilder-time-stamp: 1659205045 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 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/11156/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/47116/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/47116/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/47116/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='44ce6e4f48844d41aa5eeaf0aba5e0fb' - 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='11156' - PS1='# ' - PS2='> ' + INVOCATION_ID=bcacc2ef5ae747a79433447b763aa46e + 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=47116 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.9oMfnB50Zn/pbuilderrc_bweW --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9oMfnB50Zn/b1 --logfile b1/build.log poa_2.0+20060928-7.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.9oMfnB50Zn/pbuilderrc_M9iB --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.9oMfnB50Zn/b2 --logfile b2/build.log poa_2.0+20060928-7.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 ionos11-amd64 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) 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 Jun 20 20:26 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/11156/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 Jul 31 08:17 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 25 04:47 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/47116/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 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 1s (25.8 MB/s) +Fetched 19.0 MB in 1s (28.5 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.) @@ -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 @@ -392,7 +426,7 @@ fakeroot debian/rules clean dh clean dh_auto_clean - make -j15 clean + make -j16 clean make[1]: Entering directory '/build/poa-2.0+20060928' rm -f align_score.o main.o 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 poa liblpo.a poa_doc libbflag.a make[1]: Leaving directory '/build/poa-2.0+20060928' @@ -405,7 +439,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/poa-2.0+20060928' dh_auto_build -- poa - make -j15 "INSTALL=install --strip-program=true" poa + make -j16 "INSTALL=install --strip-program=true" poa make[2]: Entering directory '/build/poa-2.0+20060928' 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_score.o align_score.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 main.o main.c @@ -420,11 +454,33 @@ 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 heaviest_bundle.o heaviest_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 lpo_format.o lpo_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 create_seq.o create_seq.c +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); + ^~~~~~ 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 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); + ^~~~~~ +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); + ^~~~~~ In file included from lpo.h:6, from main.c:3: main.c: In function 'main': +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 ./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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -456,136 +512,15 @@ main.c:254:2: note: in expansion of macro 'REALLOC' REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); ^~~~~~~ -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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' - CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ - ^~~~~~ -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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' - CALLOC(score,len,LPOScore_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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' - CALLOC(contains_pos,nsource_seq,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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' - CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ - ^~~~~~ 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 -heaviest_bundle.c: In function 'assign_sequence_bundle_id': -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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' - CALLOC(bundle_count,seq->nsource_seq,int); - ^~~~~~ -In file included from lpo_format.c:3: -lpo_format.c: In function 'read_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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:60:3: note: in expansion of macro 'CALLOC' - CALLOC(seq,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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:71:3: note: in expansion of macro 'CALLOC' - CALLOC(seq->letter,length,LPOLetter_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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -default.h:241:5: note: in expansion of macro 'CALLOC' - CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - ^~~~~~ -lpo_format.c:72:3: note: in expansion of macro 'GETMEM' - GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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:245:5: note: in expansion of macro 'REALLOC' - REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - ^~~~~~~ -lpo_format.c:72:3: note: in expansion of macro 'GETMEM' - GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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_format.c:73:3: note: in expansion of macro 'CALLOC' - CALLOC(pos_count,nsource_seq,int); - ^~~~~~ -lpo_format.c: In function 'read_lpo_select': -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_format.c:159:3: note: in expansion of macro 'CALLOC' - CALLOC(seq,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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:170:3: note: in expansion of macro 'CALLOC' - CALLOC(seq->letter,length,LPOLetter_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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -default.h:241:5: note: in expansion of macro 'CALLOC' - CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - ^~~~~~ -lpo_format.c:171:3: note: in expansion of macro 'GETMEM' - GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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:245:5: note: in expansion of macro 'REALLOC' - REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - ^~~~~~~ -lpo_format.c:171:3: note: in expansion of macro 'GETMEM' - GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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_format.c:172:3: note: in expansion of macro 'CALLOC' - CALLOC(pos_count,nsource_seq,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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:196:3: note: in expansion of macro 'CALLOC' - CALLOC(iseq_compact,nsource_seq,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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:197:3: note: in expansion of macro 'CALLOC' - CALLOC(last_pos,nsource_seq,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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:198:3: note: in expansion of macro 'CALLOC' - CALLOC(match_pos,nsource_seq,int); - ^~~~~~ +fasta_format.c: In function 'read_fasta': In file included from msa_format.h:17, from msa_format.c:17: msa_format.c: In function 'read_clustal': +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: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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -630,43 +565,6 @@ msa_format.c:185:5: note: in expansion of macro 'REALLOC' REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); ^~~~~~~ -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_format.c:229:3: note: in expansion of macro 'CALLOC' - CALLOC(link_list,seq->length,int); /*TEMPORARY DATA FOR COMPACTION MAPPING */ - ^~~~~~ -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_format.c:230:3: note: in expansion of macro 'CALLOC' - CALLOC(pos_compact,seq->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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo_format.c:231:3: note: in expansion of macro 'CALLOC' - CALLOC(ring_old,seq->length,int); - ^~~~~~ -lpo_format.c: In function 'xlate_lpo_to_al': -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_format.c:353:3: note: in expansion of macro 'CALLOC' - CALLOC(seq_pos,seq->nsource_seq,char *); /* ALLOCATE MAP ARRAY*/ - ^~~~~~ -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_format.c:354:3: note: in expansion of macro 'CALLOC' - CALLOC(p,seq->nsource_seq*nring,char); - ^~~~~~ -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_format.c:374:5: note: in expansion of macro 'CALLOC' - CALLOC(include_in_save,nring,char); /* BLANK FLAGS: WHAT RINGS TO SHOW*/ - ^~~~~~ msa_format.c: In function 'read_pir': 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)); \ @@ -731,19 +629,6 @@ msa_format.c:326:5: note: in expansion of macro 'CALLOC' CALLOC (column_ids[i], max_aln_length, int); ^~~~~~ -lpo_format.c: In function 'read_lpo': -lpo_format.c:61:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile,"VERSION=%s",version); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:62:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile," NAME=%[^\n]",name); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:63:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile," TITLE=%[^\n]",title); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:86:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile,"%*[ \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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -756,6 +641,14 @@ msa_format.c:334:3: note: in expansion of macro 'CALLOC' CALLOC (consens_row, max_aln_length, char); ^~~~~~ +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=] + fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' + CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ + ^~~~~~ 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -792,22 +685,22 @@ msa_format.c:398:5: note: in expansion of macro 'REALLOC' REALLOC (curr_seq->sequence, len+1, char); ^~~~~~~ -lpo_format.c: In function 'read_lpo_select': -lpo_format.c:160:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile,"VERSION=%s",version); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:161:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile," NAME=%[^\n]",name); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:162:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile," TITLE=%[^\n]",title); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:185:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf(ifile,"%*[ \t]"); - ^~~~~~~~~~~~~~~~~~~~~~~ +buildup_lpo.c: In function 'read_seqpair_scorefile': +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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' + CALLOC (adj_score, nseq, int); + ^~~~~~ msa_format.c:404:5: warning: implicit declaration of function 'build_seq_to_po_index' [-Wimplicit-function-declaration] build_seq_to_po_index (lposeq); ^~~~~~~~~~~~~~~~~~~~~ +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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' + CALLOC (score_list, max_nscore, SeqPairScore_T); + ^~~~~~ In file included from msa_format.h:17, from msa_format.c:17: default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -822,40 +715,67 @@ msa_format.c:407:5: note: in expansion of macro 'CALLOC' CALLOC (al_y, lposeq->length, 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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:353:2: note: in expansion of macro 'REALLOC' + REALLOC (score_list, max_nscore, SeqPairScore_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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:374:2: note: in expansion of macro 'REALLOC' + REALLOC (score_list, max_nscore, SeqPairScore_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: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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:394:2: note: in expansion of macro 'REALLOC' + REALLOC (score_list, max_nscore, SeqPairScore_T); + ^~~~~~~ In file included from msa_format.h:17, from msa_format.c:17: msa_format.c: In function 'filter_sequence_set': +buildup_lpo.c: In function 'buildup_progressive_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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +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 */ + ^~~~~~ 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:485:3: note: in expansion of macro 'CALLOC' CALLOC (keep_seq, n_seqs, int); ^~~~~~ -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); +buildup_lpo.c:446:3: note: in expansion of macro 'CALLOC' + CALLOC(seq_id_in_cluster,nseq,int); /* INDEXES SEQS (or CLUSTERS) WITHIN EACH CLUSTER */ ^~~~~~ -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); +buildup_lpo.c:447:3: note: in expansion of macro 'CALLOC' + CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ ^~~~~~ 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); +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) */ ^~~~~~ +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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' + CALLOC (perm, nseq_tot, int); + ^~~~~~ 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=] @@ -889,51 +809,45 @@ align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' CALLOC (y_al, len_y, LPOLetterRef_T); ^~~~~~ -In file included from buildup_lpo.c:3: -buildup_lpo.c: In function 'clip_unaligned_ends': -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 align_lpo_po2.c:2: +align_lpo_po2.c: In function 'get_lpo_stats': +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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' - CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ +align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' + CALLOC (next_gap_array, max_gap_length + 2, int); ^~~~~~ -buildup_lpo.c: In function 'read_seqpair_scorefile': 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' - CALLOC (adj_score, nseq, int); +align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' + CALLOC (node_type, len, 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); +align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' + CALLOC (refs_from_right, 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' - CALLOC (score_list, max_nscore, SeqPairScore_T); +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:186:3: note: in expansion of macro 'CALLOC' - CALLOC (next_perp_gap_array, max_gap_length + 2, int); +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: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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:353:2: note: in expansion of macro 'REALLOC' - REALLOC (score_list, max_nscore, SeqPairScore_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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -952,12 +866,6 @@ align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' CALLOC (init_col_score, len_y+1, DPScore_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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:374:2: note: in expansion of macro 'REALLOC' - REALLOC (score_list, max_nscore, SeqPairScore_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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -970,144 +878,137 @@ align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' CALLOC (prev_score, len_x+1, DPScore_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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:394:2: note: in expansion of macro 'REALLOC' - REALLOC (score_list, max_nscore, SeqPairScore_T); - ^~~~~~~ -buildup_lpo.c: In function 'buildup_progressive_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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -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 */ +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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:446:3: note: in expansion of macro 'CALLOC' - CALLOC(seq_id_in_cluster,nseq,int); /* INDEXES SEQS (or CLUSTERS) WITHIN EACH CLUSTER */ +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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:447:3: note: in expansion of macro 'CALLOC' - CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ +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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -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) */ +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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' - CALLOC (perm, nseq_tot, int); - ^~~~~~ -In file included from create_seq.c:3: -create_seq.c: In function 'create_seq': +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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -default.h:212:5: note: in expansion of macro 'CALLOC' - CALLOC(memptr,BUF,ATYPE) } \ +align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' + CALLOC (move[i], len_x, DPMove_T); ^~~~~~ -create_seq.c:29:3: note: in expansion of macro 'REBUFF' - REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ - ^~~~~~ -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); \ - ^~~~~~~ -create_seq.c:29:3: note: in expansion of macro 'REBUFF' - REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ - ^~~~~~ -In file included from remove_bundle.c:4: -remove_bundle.c: In function 'compact_links': -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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' - CALLOC(link,1,LPOLetterLink_T); +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:41:3: note: in expansion of macro 'CALLOC' - CALLOC (node_type, len, int); +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:42:3: note: in expansion of macro 'CALLOC' - CALLOC (refs_from_right, len, int); +align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' + CALLOC (score_rows[-1], len_x+1, DPScore_T); ^~~~~~ -remove_bundle.c: In function 'compact_sources': 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); +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 +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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' + CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ ^~~~~~ 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' - CALLOC(source,1,LPOLetterSource_T); +heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' + CALLOC(score,len,LPOScore_T); ^~~~~~ -In file included from ./lpo.h:6, - from numeric_data.c:3: -numeric_data.c: In function 'new_numeric_data': -./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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -./default.h:212:5: note: in expansion of macro 'CALLOC' - CALLOC(memptr,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); +heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' + CALLOC(contains_pos,nsource_seq,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 *); +heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' + CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ ^~~~~~ -./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); +heaviest_bundle.c: In function 'assign_sequence_bundle_id': +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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' + CALLOC(bundle_count,seq->nsource_seq,int); ^~~~~~ -remove_bundle.c: In function 'remove_bundle': +In file included from remove_bundle.c:4: +remove_bundle.c: In function 'compact_links': 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' - CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ +remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' + CALLOC(link,1,LPOLetterLink_T); ^~~~~~ -./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +remove_bundle.c: In function 'compact_sources': +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 */ +remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' + CALLOC(source,1,LPOLetterSource_T); ^~~~~~ +remove_bundle.c: In function 'remove_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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' - CALLOC (left_links[i], 1, LPOLetterLink_T); - ^~~~~~ +remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' + CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ + ^~~~~~ In file included from lpo.c:3: lpo.c: In function 'lpo_init': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -1145,77 +1046,83 @@ lpo.c:189:3: note: in expansion of macro 'REBUFF' REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, ^~~~~~ -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); +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); \ + ^~~~~~~ +lpo.c:189:3: note: in expansion of macro 'REBUFF' + REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, ^~~~~~ -align_lpo_po2.c: In function 'align_lpo_po': +lpo.c: In function 'save_lpo_source_list': 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); +lpo.c:213:3: note: in expansion of macro 'CALLOC' + CALLOC(list,nsource_seq,int); ^~~~~~ +In file included from create_seq.c:3: +create_seq.c: In function 'create_seq': +In file included from lpo_format.c:3: +lpo_format.c: In function 'read_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_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' - CALLOC (next_perp_gap_array, max_gap_length + 2, int); +lpo_format.c:60:3: note: in expansion of macro 'CALLOC' + CALLOC(seq,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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' - CALLOC (move, len_y, DPMove_T *); +lpo_format.c:71:3: note: in expansion of macro 'CALLOC' + CALLOC(seq->letter,length,LPOLetter_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:241:5: note: in expansion of macro 'CALLOC' + CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ ^~~~~~ +lpo_format.c:72:3: note: in expansion of macro 'GETMEM' + GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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:245:5: note: in expansion of macro 'REALLOC' + REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + ^~~~~~~ +lpo_format.c:72:3: note: in expansion of macro 'GETMEM' + GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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); +lpo_format.c:73:3: note: in expansion of macro 'CALLOC' + CALLOC(pos_count,nsource_seq,int); ^~~~~~ +lpo_format.c: In function 'read_lpo_select': 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 *); +lpo_format.c:159:3: note: in expansion of macro 'CALLOC' + CALLOC(seq,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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' - CALLOC (score_rows[-1], len_x+1, DPScore_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); \ - ^~~~~~~ -lpo.c:189:3: note: in expansion of macro 'REBUFF' - REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, +lpo_format.c:170:3: note: in expansion of macro 'CALLOC' + CALLOC(seq->letter,length,LPOLetter_T); ^~~~~~ -lpo.c: In function 'save_lpo_source_list': 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:213:3: note: in expansion of macro 'CALLOC' - CALLOC(list,nsource_seq,int); +default.h:241:5: note: in expansion of macro 'CALLOC' + CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + ^~~~~~ +lpo_format.c:171:3: note: in expansion of macro 'GETMEM' + GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); ^~~~~~ In file included from stringptr.c:2: stringptr.c: In function 'stringptr_cat_pos': @@ -1225,13 +1132,6 @@ stringptr.c:30:3: note: in expansion of macro 'CALLOC' CALLOC(s2_temp,s2_len,char); /* ALLOCATE TEMP STORAGE */ ^~~~~~ -lpo.c: In function 'add_lpo_link': -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:238:3: note: in expansion of macro 'CALLOC' - CALLOC(list->more,1,LPOLetterLink_T); /* ADD ENTRY TO LINKED LIST */ - ^~~~~~ 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1241,6 +1141,13 @@ stringptr.c:40:3: note: in expansion of macro 'GETMEM' GETMEM(s1->p,total_len, ^~~~~~ +lpo.c: In function 'add_lpo_link': +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:238:3: note: in expansion of macro 'CALLOC' + CALLOC(list->more,1,LPOLetterLink_T); /* ADD ENTRY TO LINKED LIST */ + ^~~~~~ lpo.c: In function 'add_lpo_sources': 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)); \ @@ -1255,6 +1162,83 @@ lpo.c:270:3: note: in expansion of macro 'CALLOC' CALLOC (map, 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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +lpo.c:271:3: note: in expansion of macro 'CALLOC' + CALLOC (invmap, len, int); + ^~~~~~ +lpo.c: In function 'reindex_lpo_fusion': +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: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 ./lpo.h:6, + from numeric_data.c:3: +numeric_data.c: In function 'new_numeric_data': +./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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +./default.h:212:5: note: in expansion of macro 'CALLOC' + CALLOC(memptr,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: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 */ + ^~~~~~ +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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +lpo.c:500:3: note: in expansion of macro 'CALLOC' + CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ + ^~~~~~ +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:501:3: 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:502:3: note: in expansion of macro 'CALLOC' + CALLOC(new_y,len_y,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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +default.h:212:5: note: in expansion of macro 'CALLOC' + CALLOC(memptr,BUF,ATYPE) } \ + ^~~~~~ +create_seq.c:29:3: note: in expansion of macro 'REBUFF' + REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ + ^~~~~~ +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:245:5: note: in expansion of macro 'REALLOC' + REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + ^~~~~~~ +lpo_format.c:171:3: note: in expansion of macro 'GETMEM' + GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1267,13 +1251,18 @@ 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:271:3: note: in expansion of macro 'CALLOC' - CALLOC (invmap, len, int); +lpo_format.c:172:3: note: in expansion of macro 'CALLOC' + CALLOC(pos_count,nsource_seq,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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +default.h:215:5: note: in expansion of macro 'REALLOC' + REALLOC(memptr,(NUM)+(BUF),ATYPE); \ + ^~~~~~~ +create_seq.c:29:3: note: in expansion of macro 'REBUFF' + REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ ^~~~~~ -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); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ stringptr.c: In function 'stringptr_cpy': default.h:147:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ @@ -1286,6 +1275,12 @@ 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: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_format.c:196:3: note: in expansion of macro 'CALLOC' + CALLOC(iseq_compact,nsource_seq,int); + ^~~~~~ default.h:154:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ @@ -1313,6 +1308,18 @@ 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: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_format.c:197:3: note: in expansion of macro 'CALLOC' + CALLOC(last_pos,nsource_seq,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)); \ + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ +lpo_format.c:198:3: note: in expansion of macro 'CALLOC' + CALLOC(match_pos,nsource_seq,int); + ^~~~~~ default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1342,46 +1349,28 @@ stringptr.c:67:3: note: in expansion of macro 'GETMEM' GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); ^~~~~~ -lpo.c: In function 'reindex_lpo_fusion': -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:427:3: note: in expansion of macro 'CALLOC' - CALLOC(do_fuse,len_y,char); /* MARK POSITIONS TO FUSE seq_y TO seq_x */ - ^~~~~~ 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 -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)); \ - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo.c:500:3: note: in expansion of macro 'CALLOC' - CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ +lpo_format.c:229:3: note: in expansion of macro 'CALLOC' + CALLOC(link_list,seq->length,int); /*TEMPORARY DATA FOR COMPACTION MAPPING */ ^~~~~~ 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:501:3: note: in expansion of macro 'CALLOC' - CALLOC(new_x,len_x,LPOLetterRef_T); +lpo_format.c:230:3: note: in expansion of macro 'CALLOC' + CALLOC(pos_compact,seq->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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ -lpo.c:502:3: note: in expansion of macro 'CALLOC' - CALLOC(new_y,len_y,LPOLetterRef_T); +lpo_format.c:231:3: note: in expansion of macro 'CALLOC' + CALLOC(ring_old,seq->length,int); ^~~~~~ +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); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1414,6 +1403,51 @@ lpo.c:622:3: note: in expansion of macro 'REALLOC' REALLOC(seq_x,new_len,LPOLetter_T); /* EXPAND seq_x TO HOLD FUSED LPO */ ^~~~~~~ +lpo_format.c: In function 'xlate_lpo_to_al': +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_format.c:353:3: note: in expansion of macro 'CALLOC' + CALLOC(seq_pos,seq->nsource_seq,char *); /* ALLOCATE MAP ARRAY*/ + ^~~~~~ +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_format.c:354:3: note: in expansion of macro 'CALLOC' + CALLOC(p,seq->nsource_seq*nring,char); + ^~~~~~ +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_format.c:374:5: note: in expansion of macro 'CALLOC' + CALLOC(include_in_save,nring,char); /* BLANK FLAGS: WHAT RINGS TO SHOW*/ + ^~~~~~ +lpo_format.c: In function 'read_lpo': +lpo_format.c:61:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile,"VERSION=%s",version); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:62:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile," NAME=%[^\n]",name); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:63:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile," TITLE=%[^\n]",title); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:86:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile,"%*[ \t]"); + ^~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c: In function 'read_lpo_select': +lpo_format.c:160:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile,"VERSION=%s",version); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:161:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile," NAME=%[^\n]",name); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:162:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile," TITLE=%[^\n]",title); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:185:5: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf(ifile,"%*[ \t]"); + ^~~~~~~~~~~~~~~~~~~~~~~ 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.Lh50Uk0gwN... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.fh6Sfjexwp... 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/47116/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/47116/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/11156 and its subdirectories -I: Current time: Sat Jun 26 23:54:22 -12 2021 -I: pbuilder-time-stamp: 1624794862 +I: removing directory /srv/workspace/pbuilder/47116 and its subdirectories +I: Current time: Sun Jul 31 08:18:56 +14 2022 +I: pbuilder-time-stamp: 1659205136