Diff of the two buildlogs: -- --- b1/build.log 2021-11-03 11:48:43.945572133 +0000 +++ b2/build.log 2021-11-03 11:49:39.135672407 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Nov 2 23:47:31 -12 2021 -I: pbuilder-time-stamp: 1635940051 +I: Current time: Wed Dec 7 08:11:46 +14 2022 +I: pbuilder-time-stamp: 1670350306 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./poa_2.0+20060928-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.aGs3uGsa/trustedkeys.kbx': General error -gpgv: Signature made Fri May 1 08:11:31 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.ggIXnVb7/trustedkeys.kbx': General error +gpgv: Signature made Sat May 2 10:11:31 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,135 +30,169 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1709621/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1666642/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/1666642/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1666642/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='668aa9da2af243dab3ccfbace88b480c' - 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='1709621' - PS1='# ' - PS2='> ' + INVOCATION_ID=e308dd8f926f4bf8bd57c1a6d4079a0a + 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=1666642 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.Wf6hWaAjUH/pbuilderrc_Mwey --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Wf6hWaAjUH/b1 --logfile b1/build.log poa_2.0+20060928-8.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.Wf6hWaAjUH/pbuilderrc_6oXZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Wf6hWaAjUH/b2 --logfile b2/build.log poa_2.0+20060928-8.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 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more - -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Oct 20 23:41 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/1709621/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 2021 more + -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount + -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 7 08:11 sh -> bash + lrwxrwxrwx 1 root root 4 Nov 24 08:05 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 2021 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1666642/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -225,7 +259,7 @@ Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] -Fetched 18.3 MB in 1s (32.8 MB/s) +Fetched 18.3 MB in 1s (31.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) @@ -365,7 +399,8 @@ Building tag database... -> Finished parsing the build-deps 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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../poa_2.0+20060928-8_source.changes +hostname: Name or service not known +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 && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../poa_2.0+20060928-8_source.changes dpkg-buildpackage: info: source package poa dpkg-buildpackage: info: source version 2.0+20060928-8 dpkg-buildpackage: info: source distribution unstable @@ -375,7 +410,7 @@ 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' @@ -388,7 +423,7 @@ 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 -fdebug-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 -fdebug-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 @@ -403,10 +438,9 @@ gcc -g -O2 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 -fdebug-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 black_flag.c:4: black_flag.c: In function 'black_flag_init_args': +gcc -g -O2 -fdebug-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 default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -486,7 +520,12 @@ | | | int | %ld -gcc -g -O2 -fdebug-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 +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] + 48 | stringptr_cat_pos(&tmp_seq,line,&length); + | ^~~~~~~~~~~~~~~~~ + | stringptr_cat +gcc -g -O2 -fdebug-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=] @@ -517,15 +556,213 @@ | | | int | %ld -In file included from align_lpo2.c:2: -align_lpo2.c: In function 'get_seq_left_and_final': +gcc -g -O2 -fdebug-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 msa_format.h:17, + from msa_format.c:17: +msa_format.c: In function 'read_clustal': +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:169:7: note: in expansion of macro 'REALLOC' + 169 | REALLOC (seq_names, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:171:7: note: in expansion of macro 'REALLOC' + 171 | REALLOC (seq_titles, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:174:7: note: in expansion of macro 'REALLOC' + 174 | REALLOC (aln_mat, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:176:7: note: in expansion of macro 'REALLOC' + 176 | REALLOC (aln_lengths, n_seqs, int); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 185 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ + | ~~~~~ + | | + | size_t {aka long unsigned int} +default.h:184:22: note: in definition of macro 'REALLOC' + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +default.h:184:68: note: format string is defined here + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +msa_format.c:185:5: note: in expansion of macro 'REALLOC' + 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); + | ^~~~~~~ +default.h:196:34: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:185:5: note: in expansion of macro 'REALLOC' + 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +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=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:248:7: note: in expansion of macro 'REALLOC' + 248 | REALLOC (seq_names, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:250:7: note: in expansion of macro 'REALLOC' + 250 | REALLOC (seq_titles, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:252:7: note: in expansion of macro 'REALLOC' + 252 | REALLOC (aln_mat, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:254:7: note: in expansion of macro 'REALLOC' + 254 | REALLOC (aln_lengths, n_seqs, int); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 185 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ + | ~~~~~ +default.h:184:22: note: in definition of macro 'REALLOC' + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +default.h:184:68: note: format string is defined here + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +msa_format.c:268:7: note: in expansion of macro 'REALLOC' + 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); + | ^~~~~~~ +default.h:196:34: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:268:7: note: in expansion of macro 'REALLOC' + 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC (is_final_node_x, len_x, int); +msa_format.c:318:3: note: in expansion of macro 'CALLOC' + 318 | CALLOC (column_ids, n_seqs+1, int *); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -538,8 +775,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' - 66 | CALLOC (x_left, len_x, LPOLetterLink_T *); +msa_format.c:319:3: note: in expansion of macro 'CALLOC' + 319 | CALLOC (res_ids, n_seqs+1, int *); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -552,24 +789,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' - 70 | CALLOC (x_left[i], 1, LPOLetterLink_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -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=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' - 96 | CALLOC (x_al, len_x, LPOLetterRef_T); - | ^~~~~~ +msa_format.c:326:5: note: in expansion of macro 'CALLOC' + 326 | CALLOC (column_ids[i], max_aln_length, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -581,24 +803,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' - 97 | CALLOC (y_al, len_y, LPOLetterRef_T); - | ^~~~~~ +msa_format.c:327:5: note: in expansion of macro 'CALLOC' + 327 | CALLOC (res_ids[i], max_aln_length, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC(seq,1,LPOSequence_T); +msa_format.c:334:3: note: in expansion of macro 'CALLOC' + 334 | CALLOC (consens_row, max_aln_length, char); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -611,8 +831,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:71:3: note: in expansion of macro 'CALLOC' - 71 | CALLOC(seq->letter,length,LPOLetter_T); +msa_format.c:347:3: note: in expansion of macro 'CALLOC' + 347 | CALLOC (lposeq, 1, LPOSequence_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -625,11 +845,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:241:5: note: in expansion of macro 'CALLOC' - 241 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -lpo_format.c:72:3: note: in expansion of macro 'GETMEM' - 72 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); +msa_format.c:351:3: note: in expansion of macro 'CALLOC' + 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -642,12 +859,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:245:5: note: in expansion of macro 'REALLOC' - 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -lpo_format.c:72:3: note: in expansion of macro 'GETMEM' - 72 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); - | ^~~~~~ +msa_format.c:369:3: note: in expansion of macro 'REALLOC' + 369 | REALLOC (lposeq->sequence, len+1, char); + | ^~~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ @@ -659,38 +873,56 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:73:3: note: in expansion of macro 'CALLOC' - 73 | CALLOC(pos_count,nsource_seq,int); - | ^~~~~~ +msa_format.c:375:5: note: in expansion of macro 'CALLOC' + 375 | CALLOC (curr_seq, 1, LPOSequence_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:159:3: note: in expansion of macro 'CALLOC' - 159 | CALLOC(seq,1,LPOSequence_T); - | ^~~~~~ +msa_format.c:380:5: note: in expansion of macro 'CALLOC' + 380 | CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:398:5: note: in expansion of macro 'REALLOC' + 398 | REALLOC (curr_seq->sequence, len+1, char); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +msa_format.c:404:5: warning: implicit declaration of function 'build_seq_to_po_index' [-Wimplicit-function-declaration] + 404 | build_seq_to_po_index (lposeq); + | ^~~~~~~~~~~~~~~~~~~~~ +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:170:3: note: in expansion of macro 'CALLOC' - 170 | CALLOC(seq->letter,length,LPOLetter_T); - | ^~~~~~ +msa_format.c:406:5: note: in expansion of macro 'CALLOC' + 406 | CALLOC (al_x, len, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -702,42 +934,28 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:241:5: note: in expansion of macro 'CALLOC' - 241 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ +msa_format.c:407:5: note: in expansion of macro 'CALLOC' + 407 | CALLOC (al_y, lposeq->length, int); | ^~~~~~ -lpo_format.c:171:3: note: in expansion of macro 'GETMEM' - 171 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); - | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -default.h:245:5: note: in expansion of macro 'REALLOC' - 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -lpo_format.c:171:3: note: in expansion of macro 'GETMEM' - 171 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); - | ^~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld +msa_format.c:428:5: warning: implicit declaration of function 'fuse_ring_identities' [-Wimplicit-function-declaration] + 428 | 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': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:172:3: note: in expansion of macro 'CALLOC' - 172 | CALLOC(pos_count,nsource_seq,int); +msa_format.c:485:3: note: in expansion of macro 'CALLOC' + 485 | CALLOC (keep_seq, n_seqs, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -745,13 +963,15 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:196:3: note: in expansion of macro 'CALLOC' - 196 | CALLOC(iseq_compact,nsource_seq,int); +align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC (is_final_node_x, len_x, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -764,8 +984,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:197:3: note: in expansion of macro 'CALLOC' - 197 | CALLOC(last_pos,nsource_seq,int); +align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' + 66 | CALLOC (x_left, len_x, LPOLetterLink_T *); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -778,22 +998,23 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:198:3: note: in expansion of macro 'CALLOC' - 198 | CALLOC(match_pos,nsource_seq,int); - | ^~~~~~ +align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' + 70 | CALLOC (x_left[i], 1, LPOLetterLink_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:229:3: note: in expansion of macro 'CALLOC' - 229 | CALLOC(link_list,seq->length,int); /*TEMPORARY DATA FOR COMPACTION MAPPING */ +align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' + 96 | CALLOC (x_al, len_x, LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -806,8 +1027,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:230:3: note: in expansion of macro 'CALLOC' - 230 | CALLOC(pos_compact,seq->length,int); +align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' + 97 | CALLOC (y_al, len_y, LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -815,13 +1036,14 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:231:3: note: in expansion of macro 'CALLOC' - 231 | CALLOC(ring_old,seq->length,int); +align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' + 185 | CALLOC (next_gap_array, max_gap_length + 2, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -829,19 +1051,13 @@ | | | int | %ld -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] - 48 | stringptr_cat_pos(&tmp_seq,line,&length); - | ^~~~~~~~~~~~~~~~~ - | stringptr_cat -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:353:3: note: in expansion of macro 'CALLOC' - 353 | CALLOC(seq_pos,seq->nsource_seq,char *); /* ALLOCATE MAP ARRAY*/ +align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' + 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -854,8 +1070,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:354:3: note: in expansion of macro 'CALLOC' - 354 | CALLOC(p,seq->nsource_seq*nring,char); +align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' + 199 | CALLOC (move, len_y, DPMove_T *); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -868,8 +1084,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:374:5: note: in expansion of macro 'CALLOC' - 374 | CALLOC(include_in_save,nring,char); /* BLANK FLAGS: WHAT RINGS TO SHOW*/ +align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' + 201 | CALLOC (move[i], len_x, DPMove_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -877,14 +1093,13 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' - 185 | CALLOC (next_gap_array, max_gap_length + 2, int); +align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' + 204 | CALLOC (init_col_score, len_y+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -897,8 +1112,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' - 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); +align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' + 207 | CALLOC (curr_score, len_x+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -911,8 +1126,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' - 199 | CALLOC (move, len_y, DPMove_T *); +align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' + 209 | CALLOC (prev_score, len_x+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -920,27 +1135,15 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' - 201 | CALLOC (move[i], len_x, DPMove_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' - 204 | CALLOC (init_col_score, len_y+1, DPScore_T); +buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' + 146 | CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -948,13 +1151,14 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' - 207 | CALLOC (curr_score, len_x+1, DPScore_T); +buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' + 327 | CALLOC (adj_score, nseq, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -967,8 +1171,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' - 209 | CALLOC (prev_score, len_x+1, DPScore_T); +buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' + 330 | CALLOC (score_list, max_nscore, SeqPairScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -976,170 +1180,14 @@ | | | int | %ld -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] - 61 | fscanf(ifile,"VERSION=%s",version); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:62:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 62 | fscanf(ifile," NAME=%[^\n]",name); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:63:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 63 | fscanf(ifile," TITLE=%[^\n]",title); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:86:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 86 | 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] - 160 | fscanf(ifile,"VERSION=%s",version); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:161:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 161 | fscanf(ifile," NAME=%[^\n]",name); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:162:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 162 | fscanf(ifile," TITLE=%[^\n]",title); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:185:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 185 | fscanf(ifile,"%*[ \t]"); - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from msa_format.h:17, - from msa_format.c:17: -msa_format.c: In function 'read_clustal': -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:169:7: note: in expansion of macro 'REALLOC' - 169 | REALLOC (seq_names, n_seqs, char *); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:171:7: note: in expansion of macro 'REALLOC' - 171 | REALLOC (seq_titles, n_seqs, char *); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:174:7: note: in expansion of macro 'REALLOC' - 174 | REALLOC (aln_mat, n_seqs, char *); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:176:7: note: in expansion of macro 'REALLOC' - 176 | REALLOC (aln_lengths, n_seqs, int); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 185 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ - | ~~~~~ - | | - | size_t {aka long unsigned int} -default.h:184:22: note: in definition of macro 'REALLOC' - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -default.h:184:68: note: format string is defined here - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -msa_format.c:185:5: note: in expansion of macro 'REALLOC' - 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ -default.h:196:34: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:185:5: note: in expansion of macro 'REALLOC' - 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -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=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:248:7: note: in expansion of macro 'REALLOC' - 248 | REALLOC (seq_names, n_seqs, char *); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:250:7: note: in expansion of macro 'REALLOC' - 250 | REALLOC (seq_titles, n_seqs, char *); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:252:7: note: in expansion of macro 'REALLOC' - 252 | REALLOC (aln_mat, n_seqs, char *); - | ^~~~~~~ +buildup_lpo.c:353:2: note: in expansion of macro 'REALLOC' + 353 | REALLOC (score_list, max_nscore, SeqPairScore_T); + | ^~~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ @@ -1151,63 +1199,37 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:254:7: note: in expansion of macro 'REALLOC' - 254 | REALLOC (aln_lengths, n_seqs, int); - | ^~~~~~~ +buildup_lpo.c:374:2: note: in expansion of macro 'REALLOC' + 374 | REALLOC (score_list, max_nscore, SeqPairScore_T); + | ^~~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 185 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ - | ~~~~~ -default.h:184:22: note: in definition of macro 'REALLOC' - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -default.h:184:68: note: format string is defined here - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -msa_format.c:268:7: note: in expansion of macro 'REALLOC' - 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ -default.h:196:34: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:268:7: note: in expansion of macro 'REALLOC' - 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ +buildup_lpo.c:394:2: note: in expansion of macro 'REALLOC' + 394 | REALLOC (score_list, max_nscore, SeqPairScore_T); + | ^~~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -msa_format.c: In function 'lpo_from_aln_mat': +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:318:3: note: in expansion of macro 'CALLOC' - 318 | CALLOC (column_ids, n_seqs+1, int *); +buildup_lpo.c:445:3: note: in expansion of macro 'CALLOC' + 445 | CALLOC(seq_cluster,nseq,int); /* MAPS SEQS (or CLUSTERS) TO CLUSTER THEY'RE IN */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1220,8 +1242,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:319:3: note: in expansion of macro 'CALLOC' - 319 | CALLOC (res_ids, n_seqs+1, int *); +buildup_lpo.c:446:3: note: in expansion of macro 'CALLOC' + 446 | CALLOC(seq_id_in_cluster,nseq,int); /* INDEXES SEQS (or CLUSTERS) WITHIN EACH CLUSTER */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1234,9 +1256,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:326:5: note: in expansion of macro 'CALLOC' - 326 | CALLOC (column_ids[i], max_aln_length, int); - | ^~~~~~ +buildup_lpo.c:447:3: note: in expansion of macro 'CALLOC' + 447 | CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1248,22 +1270,24 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:327:5: note: in expansion of macro 'CALLOC' - 327 | CALLOC (res_ids[i], max_aln_length, int); - | ^~~~~~ +buildup_lpo.c:448:3: note: in expansion of macro 'CALLOC' + 448 | CALLOC(initial_nseq,nseq,int); /* COUNTS SEQS INITIALLY IN EACH CLUSTER (not updated w/ merges) */ + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:334:3: note: in expansion of macro 'CALLOC' - 334 | CALLOC (consens_row, max_aln_length, char); +lpo.c:15:3: note: in expansion of macro 'CALLOC' + 15 | CALLOC(seq->letter,seq->length,LPOLetter_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1271,14 +1295,6 @@ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:347:3: note: in expansion of macro 'CALLOC' - 347 | CALLOC (lposeq, 1, LPOSequence_T); - | ^~~~~~ 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=] @@ -1342,28 +1358,37 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' - 71 | CALLOC (left_links[i], 1, LPOLetterLink_T); - | ^~~~~~ +buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' + 538 | CALLOC (perm, nseq_tot, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' + 71 | CALLOC (left_links[i], 1, LPOLetterLink_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:351:3: note: in expansion of macro 'CALLOC' - 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); +align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' + 120 | CALLOC (x_al, len_x, LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1371,74 +1396,43 @@ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:369:3: note: in expansion of macro 'REALLOC' - 369 | REALLOC (lposeq->sequence, len+1, char); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:375:5: note: in expansion of macro 'CALLOC' - 375 | CALLOC (curr_seq, 1, LPOSequence_T); - | ^~~~~~ +align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' + 121 | CALLOC (y_al, len_y, LPOLetterRef_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:380:5: note: in expansion of macro 'CALLOC' - 380 | CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); - | ^~~~~~ +align_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' + 227 | CALLOC (next_gap_array, max_gap_length + 2, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:398:5: note: in expansion of macro 'REALLOC' - 398 | REALLOC (curr_seq->sequence, len+1, char); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -msa_format.c:404:5: warning: implicit declaration of function 'build_seq_to_po_index' [-Wimplicit-function-declaration] - 404 | build_seq_to_po_index (lposeq); - | ^~~~~~~~~~~~~~~~~~~~~ -In file included from msa_format.h:17, - from msa_format.c:17: +lpo.c: In function 'build_seq_to_po_index': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:406:5: note: in expansion of macro 'CALLOC' - 406 | CALLOC (al_x, len, int); +lpo.c:157:5: note: in expansion of macro 'CALLOC' + 157 | CALLOC(seq->source_seq[i].seq_to_po,seq->source_seq[i].length,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1446,16 +1440,13 @@ | | | int | %ld -In file included from buildup_lpo.c:3: -buildup_lpo.c: In function 'clip_unaligned_ends': -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' - 120 | CALLOC (x_al, len_x, LPOLetterRef_T); +align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' + 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1468,23 +1459,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' - 121 | CALLOC (y_al, len_y, LPOLetterRef_T); - | ^~~~~~ +lpo.c:158:5: note: in expansion of macro 'CALLOC' + 158 | CALLOC(seq->source_seq[i].po_to_seq,seq->length,int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' - 227 | CALLOC (next_gap_array, max_gap_length + 2, int); +align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' + 254 | CALLOC (move, len_y, DPMove_T *); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1497,9 +1487,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' - 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); - | ^~~~~~ +lpo.c:159:5: note: in expansion of macro 'CALLOC' + 159 | CALLOC(seq->source_seq[i].sequence,seq->source_seq[i].length+1,char); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1511,36 +1501,58 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' - 254 | CALLOC (move, len_y, DPMove_T *); - | ^~~~~~ +align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' + 256 | CALLOC (move[i], len_x, DPMove_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +lpo.c: In function 'save_lpo_source': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' - 256 | CALLOC (move[i], len_x, DPMove_T); +default.h:212:5: note: in expansion of macro 'CALLOC' + 212 | CALLOC(memptr,BUF,ATYPE) } \ | ^~~~~~ +lpo.c:189:3: note: in expansion of macro 'REBUFF' + 189 | REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +default.h:215:5: note: in expansion of macro 'REALLOC' + 215 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ + | ^~~~~~~ +lpo.c:189:3: note: in expansion of macro 'REBUFF' + 189 | REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, + | ^~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' - 259 | CALLOC (init_col_score, len_y+1, DPScore_T); +lpo.c:213:3: note: in expansion of macro 'CALLOC' + 213 | CALLOC(list,nsource_seq,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1548,13 +1560,14 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' - 262 | CALLOC (score_rows, len_y+1, DPScore_T *); +lpo.c:238:3: note: in expansion of macro 'CALLOC' + 238 | CALLOC(list->more,1,LPOLetterLink_T); /* ADD ENTRY TO LINKED LIST */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1562,47 +1575,43 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' - 264 | CALLOC (score_rows[-1], len_x+1, DPScore_T); - | ^~~~~~ +lpo.c:252:7: note: in expansion of macro 'CALLOC' + 252 | CALLOC(new_s->more,1,LPOLetterSource_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +lpo.c: In function 'reindex_lpo_source_seqs': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:407:5: note: in expansion of macro 'CALLOC' - 407 | CALLOC (al_y, lposeq->length, int); - | ^~~~~~ +lpo.c:270:3: note: in expansion of macro 'CALLOC' + 270 | CALLOC (map, len, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -msa_format.c:428:5: warning: implicit declaration of function 'fuse_ring_identities' [-Wimplicit-function-declaration] - 428 | 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': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:485:3: note: in expansion of macro 'CALLOC' - 485 | CALLOC (keep_seq, n_seqs, int); +lpo.c:271:3: note: in expansion of macro 'CALLOC' + 271 | CALLOC (invmap, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1610,13 +1619,15 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' - 146 | CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ +heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' + 27 | CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1624,14 +1635,13 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' - 327 | CALLOC (adj_score, nseq, int); +heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' + 28 | CALLOC(score,len,LPOScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1639,23 +1649,27 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' - 330 | CALLOC (score_list, max_nscore, SeqPairScore_T); +heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' + 29 | CALLOC(contains_pos,nsource_seq,int); | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:15:3: note: in expansion of macro 'CALLOC' - 15 | CALLOC(seq->letter,seq->length,LPOLetter_T); +align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' + 259 | CALLOC (init_col_score, len_y+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1663,117 +1677,71 @@ | | | int | %ld +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=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +lpo.c:427:3: note: in expansion of macro 'CALLOC' + 427 | CALLOC(do_fuse,len_y,char); /* MARK POSITIONS TO FUSE seq_y TO seq_x */ + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -buildup_lpo.c:353:2: note: in expansion of macro 'REALLOC' - 353 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -buildup_lpo.c:374:2: note: in expansion of macro 'REALLOC' - 374 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -lpo.c: In function 'build_seq_to_po_index': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:157:5: note: in expansion of macro 'CALLOC' - 157 | CALLOC(seq->source_seq[i].seq_to_po,seq->source_seq[i].length,int); - | ^~~~~~ +align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' + 262 | CALLOC (score_rows, len_y+1, DPScore_T *); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -buildup_lpo.c:394:2: note: in expansion of macro 'REALLOC' - 394 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:158:5: note: in expansion of macro 'CALLOC' - 158 | CALLOC(seq->source_seq[i].po_to_seq,seq->length,int); - | ^~~~~~ +align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' + 264 | CALLOC (score_rows[-1], len_x+1, DPScore_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:312:5: note: in expansion of macro 'CALLOC' - 312 | CALLOC (score_rows[i], len_x+1, DPScore_T); - | ^~~~~~ +lpo.c:500:3: note: in expansion of macro 'CALLOC' + 500 | CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] - 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); - | ~~^ ~~~~~~~~~ - | | | - | long int int - | %d -align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] - 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); - | ~~^ ~~~~~~~~~ - | | | - | long int int - | %d -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:159:5: note: in expansion of macro 'CALLOC' - 159 | CALLOC(seq->source_seq[i].sequence,seq->source_seq[i].length+1,char); +align_lpo_po2.c:312:5: note: in expansion of macro 'CALLOC' + 312 | CALLOC (score_rows[i], len_x+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1786,8 +1754,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:445:3: note: in expansion of macro 'CALLOC' - 445 | CALLOC(seq_cluster,nseq,int); /* MAPS SEQS (or CLUSTERS) TO CLUSTER THEY'RE IN */ +lpo.c:501:3: note: in expansion of macro 'CALLOC' + 501 | CALLOC(new_x,len_x,LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1800,8 +1768,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:446:3: note: in expansion of macro 'CALLOC' - 446 | CALLOC(seq_id_in_cluster,nseq,int); /* INDEXES SEQS (or CLUSTERS) WITHIN EACH CLUSTER */ +lpo.c:502:3: note: in expansion of macro 'CALLOC' + 502 | CALLOC(new_y,len_y,LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1809,25 +1777,40 @@ | | | int | %ld -lpo.c: In function 'save_lpo_source': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:212:5: note: in expansion of macro 'CALLOC' - 212 | CALLOC(memptr,BUF,ATYPE) } \ - | ^~~~~~ -lpo.c:189:3: note: in expansion of macro 'REBUFF' - 189 | REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, +lpo.c:505:3: note: in expansion of macro 'CALLOC' + 505 | CALLOC(new_lpo,new_len,LPOLetter_T); /* ALLOCATE NEW LINEARIZED PO */ | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] + 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + | ~~^ ~~~~~~~~~ + | | | + | long int int + | %d +align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] + 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + | ~~^ ~~~~~~~~~ + | | | + | long int int + | %d +lpo.c: In function 'copy_lpo': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:447:3: note: in expansion of macro 'CALLOC' - 447 | CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ +heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' + 67 | CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1835,6 +1818,15 @@ | | | int | %ld +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=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' + 90 | CALLOC(bundle_count,seq->nsource_seq,int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1846,8 +1838,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:448:3: note: in expansion of macro 'CALLOC' - 448 | CALLOC(initial_nseq,nseq,int); /* COUNTS SEQS INITIALLY IN EACH CLUSTER (not updated w/ merges) */ +lpo.c:564:3: note: in expansion of macro 'CALLOC' + 564 | CALLOC(x_to_y,holder_x->length,LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1855,31 +1847,15 @@ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -default.h:215:5: note: in expansion of macro 'REALLOC' - 215 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ - | ^~~~~~~ -lpo.c:189:3: note: in expansion of macro 'REBUFF' - 189 | REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, - | ^~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -lpo.c: In function 'save_lpo_source_list': +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:213:3: note: in expansion of macro 'CALLOC' - 213 | CALLOC(list,nsource_seq,int); +lpo_format.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC(seq,1,LPOSequence_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1887,15 +1863,15 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' - 538 | CALLOC (perm, nseq_tot, int); - | ^~~~~~ -lpo.c: In function 'add_lpo_link': +lpo.c:618:3: note: in expansion of macro 'CALLOC' + 618 | CALLOC(new_x,len_x,LPOLetterRef_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1907,8 +1883,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:238:3: note: in expansion of macro 'CALLOC' - 238 | CALLOC(list->more,1,LPOLetterLink_T); /* ADD ENTRY TO LINKED LIST */ +lpo_format.c:71:3: note: in expansion of macro 'CALLOC' + 71 | CALLOC(seq->letter,length,LPOLetter_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1916,29 +1892,30 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:252:7: note: in expansion of macro 'CALLOC' - 252 | CALLOC(new_s->more,1,LPOLetterSource_T); - | ^~~~~~ +lpo.c:619:3: note: in expansion of macro 'CALLOC' + 619 | CALLOC(new_y,len_y,LPOLetterRef_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'reindex_lpo_source_seqs': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:270:3: note: in expansion of macro 'CALLOC' - 270 | CALLOC (map, len, int); +default.h:241:5: note: in expansion of macro 'CALLOC' + 241 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~ +lpo_format.c:72:3: note: in expansion of macro 'GETMEM' + 72 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1946,13 +1923,44 @@ | | | int | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +lpo.c:622:3: note: in expansion of macro 'REALLOC' + 622 | REALLOC(seq_x,new_len,LPOLetter_T); /* EXPAND seq_x TO HOLD FUSED LPO */ + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +default.h:245:5: note: in expansion of macro 'REALLOC' + 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +lpo_format.c:72:3: note: in expansion of macro 'GETMEM' + 72 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); + | ^~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:271:3: note: in expansion of macro 'CALLOC' - 271 | CALLOC (invmap, len, int); +lpo_format.c:73:3: note: in expansion of macro 'CALLOC' + 73 | CALLOC(pos_count,nsource_seq,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1960,14 +1968,18 @@ | | | int | %ld -lpo.c: In function 'reindex_lpo_fusion': +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:427:3: note: in expansion of macro 'CALLOC' - 427 | CALLOC(do_fuse,len_y,char); /* MARK POSITIONS TO FUSE seq_y TO seq_x */ +default.h:212:5: note: in expansion of macro 'CALLOC' + 212 | CALLOC(memptr,BUF,ATYPE) } \ + | ^~~~~~ +create_seq.c:29:3: note: in expansion of macro 'REBUFF' + 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1975,14 +1987,31 @@ | | | int | %ld -lpo.c: In function 'copy_fuse_lpo_remap': +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +default.h:215:5: note: in expansion of macro 'REALLOC' + 215 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ + | ^~~~~~~ +create_seq.c:29:3: note: in expansion of macro 'REBUFF' + 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ + | ^~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:500:3: note: in expansion of macro 'CALLOC' - 500 | CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ +lpo_format.c:159:3: note: in expansion of macro 'CALLOC' + 159 | CALLOC(seq,1,LPOSequence_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1995,8 +2024,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:501:3: note: in expansion of macro 'CALLOC' - 501 | CALLOC(new_x,len_x,LPOLetterRef_T); +lpo_format.c:170:3: note: in expansion of macro 'CALLOC' + 170 | CALLOC(seq->letter,length,LPOLetter_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2009,8 +2038,11 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:502:3: note: in expansion of macro 'CALLOC' - 502 | CALLOC(new_y,len_y,LPOLetterRef_T); +default.h:241:5: note: in expansion of macro 'CALLOC' + 241 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~ +lpo_format.c:171:3: note: in expansion of macro 'GETMEM' + 171 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2018,13 +2050,30 @@ | | | int | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +default.h:245:5: note: in expansion of macro 'REALLOC' + 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +lpo_format.c:171:3: note: in expansion of macro 'GETMEM' + 171 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); + | ^~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:505:3: note: in expansion of macro 'CALLOC' - 505 | CALLOC(new_lpo,new_len,LPOLetter_T); /* ALLOCATE NEW LINEARIZED PO */ +lpo_format.c:172:3: note: in expansion of macro 'CALLOC' + 172 | CALLOC(pos_count,nsource_seq,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2032,15 +2081,13 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' - 27 | CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ +lpo_format.c:196:3: note: in expansion of macro 'CALLOC' + 196 | CALLOC(iseq_compact,nsource_seq,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2053,8 +2100,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' - 28 | CALLOC(score,len,LPOScore_T); +lpo_format.c:197:3: note: in expansion of macro 'CALLOC' + 197 | CALLOC(last_pos,nsource_seq,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2067,8 +2114,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' - 29 | CALLOC(contains_pos,nsource_seq,int); +lpo_format.c:198:3: note: in expansion of macro 'CALLOC' + 198 | CALLOC(match_pos,nsource_seq,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2076,13 +2123,15 @@ | | | int | %ld +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' - 67 | CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ +remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' + 16 | CALLOC(link,1,LPOLetterLink_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2090,14 +2139,14 @@ | | | int | %ld -lpo.c: In function 'copy_lpo': +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:564:3: note: in expansion of macro 'CALLOC' - 564 | CALLOC(x_to_y,holder_x->length,LPOLetterRef_T); +remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' + 59 | CALLOC(source,1,LPOLetterSource_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2105,14 +2154,14 @@ | | | int | %ld -lpo.c: In function 'fuse_lpo_remap': +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:618:3: note: in expansion of macro 'CALLOC' - 618 | CALLOC(new_x,len_x,LPOLetterRef_T); +remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' + 128 | CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2125,8 +2174,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:619:3: note: in expansion of macro 'CALLOC' - 619 | CALLOC(new_y,len_y,LPOLetterRef_T); +lpo_format.c:229:3: note: in expansion of macro 'CALLOC' + 229 | CALLOC(link_list,seq->length,int); /*TEMPORARY DATA FOR COMPACTION MAPPING */ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2134,32 +2183,13 @@ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -lpo.c:622:3: note: in expansion of macro 'REALLOC' - 622 | REALLOC(seq_x,new_len,LPOLetter_T); /* EXPAND seq_x TO HOLD FUSED LPO */ - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:212:5: note: in expansion of macro 'CALLOC' - 212 | CALLOC(memptr,BUF,ATYPE) } \ - | ^~~~~~ -create_seq.c:29:3: note: in expansion of macro 'REBUFF' - 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ +lpo_format.c:230:3: note: in expansion of macro 'CALLOC' + 230 | CALLOC(pos_compact,seq->length,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2167,32 +2197,13 @@ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -default.h:215:5: note: in expansion of macro 'REALLOC' - 215 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ - | ^~~~~~~ -create_seq.c:29:3: note: in expansion of macro 'REBUFF' - 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ - | ^~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' - 16 | CALLOC(link,1,LPOLetterLink_T); +lpo_format.c:231:3: note: in expansion of macro 'CALLOC' + 231 | CALLOC(ring_old,seq->length,int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2200,14 +2211,14 @@ | | | int | %ld -remove_bundle.c: In function 'compact_sources': +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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' - 59 | CALLOC(source,1,LPOLetterSource_T); +lpo_format.c:353:3: note: in expansion of macro 'CALLOC' + 353 | CALLOC(seq_pos,seq->nsource_seq,char *); /* ALLOCATE MAP ARRAY*/ | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2215,14 +2226,13 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' - 128 | CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ +lpo_format.c:354:3: note: in expansion of macro 'CALLOC' + 354 | CALLOC(p,seq->nsource_seq*nring,char); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2230,21 +2240,33 @@ | | | int | %ld -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=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' - 90 | CALLOC(bundle_count,seq->nsource_seq,int); - | ^~~~~~ +lpo_format.c:374:5: note: in expansion of macro 'CALLOC' + 374 | CALLOC(include_in_save,nring,char); /* BLANK FLAGS: WHAT RINGS TO SHOW*/ + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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] + 61 | fscanf(ifile,"VERSION=%s",version); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:62:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 62 | fscanf(ifile," NAME=%[^\n]",name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:63:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 63 | fscanf(ifile," TITLE=%[^\n]",title); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:86:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 86 | fscanf(ifile,"%*[ \t]"); + | ^~~~~~~~~~~~~~~~~~~~~~~ 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=] @@ -2278,6 +2300,70 @@ | | | int | %ld +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] + 160 | fscanf(ifile,"VERSION=%s",version); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:161:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 161 | fscanf(ifile," NAME=%[^\n]",name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:162:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 162 | fscanf(ifile," TITLE=%[^\n]",title); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:185:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 185 | fscanf(ifile,"%*[ \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=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +./default.h:212:5: note: in expansion of macro 'CALLOC' + 212 | CALLOC(memptr,BUF,ATYPE) } \ + | ^~~~~~ +numeric_data.c:18:3: note: in expansion of macro 'REBUFF' + 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); + | ^~~~~~ +./default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +./default.h:215:5: note: in expansion of macro 'REALLOC' + 215 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ + | ^~~~~~~ +numeric_data.c:18:3: note: in expansion of macro 'REBUFF' + 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); + | ^~~~~~ +./default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +numeric_data.c:25:3: note: in expansion of macro 'CALLOC' + 25 | CALLOC(data->data,source_seq->length,double); /* ALLOCATE THE ARRAY */ + | ^~~~~~ +./default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -2409,57 +2495,6 @@ | | | int | %ld -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=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -./default.h:212:5: note: in expansion of macro 'CALLOC' - 212 | CALLOC(memptr,BUF,ATYPE) } \ - | ^~~~~~ -numeric_data.c:18:3: note: in expansion of macro 'REBUFF' - 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); - | ^~~~~~ -./default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -./default.h:215:5: note: in expansion of macro 'REALLOC' - 215 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ - | ^~~~~~~ -numeric_data.c:18:3: note: in expansion of macro 'REBUFF' - 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); - | ^~~~~~ -./default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -numeric_data.c:25:3: note: in expansion of macro 'CALLOC' - 25 | CALLOC(data->data,source_seq->length,double); /* ALLOCATE THE ARRAY */ - | ^~~~~~ -./default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld 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] 139 | fscanf(ifile," %lf",data->data+j); @@ -2490,7 +2525,7 @@ 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.k6m1ibghuU... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.l75pxtziAB... 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 @@ -2531,12 +2566,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1666642/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1666642/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/1709621 and its subdirectories -I: Current time: Tue Nov 2 23:48:43 -12 2021 -I: pbuilder-time-stamp: 1635940123 +I: removing directory /srv/workspace/pbuilder/1666642 and its subdirectories +I: Current time: Wed Dec 7 08:12:39 +14 2022 +I: pbuilder-time-stamp: 1670350359