Diff of the two buildlogs: -- --- b1/build.log 2024-07-14 15:51:08.177790460 +0000 +++ b2/build.log 2024-07-14 15:52:24.738535109 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Aug 16 10:13:27 -12 2025 -I: pbuilder-time-stamp: 1755382407 +I: Current time: Mon Jul 15 05:51:10 +14 2024 +I: pbuilder-time-stamp: 1720972270 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ 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.hvnO2X54/trustedkeys.kbx': General error -gpgv: Signature made Fri May 1 08:11:31 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.kuxQxVtz/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 @@ -31,135 +31,166 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/671806/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2314433/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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 +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jul 15 05:51 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2314433/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2314433/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - 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=42 ' - DISTRIBUTION='bullseye' - 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/reproducible-path + 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=20 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='71460e959b4343e79fd542b7def4d2ae' - 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='671806' - PS1='# ' - PS2='> ' + INVOCATION_ID=14518ebc56c44543b0954f2d24b099d2 + 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=2314433 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.qCDgu6ii/pbuilderrc_WQNI --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qCDgu6ii/b1 --logfile b1/build.log poa_2.0+20060928-8.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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/r-b-build.qCDgu6ii/pbuilderrc_srjm --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qCDgu6ii/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://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Mar 27 2022 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 Mar 27 2024 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 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 69032 Mar 27 2024 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98048 Apr 9 2022 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 Mar 27 2024 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 Mar 27 2024 more - -rwsr-xr-x 1 root root 55528 Mar 27 2024 mount - -rwxr-xr-x 1 root root 18664 Mar 27 2024 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 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 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 Aug 9 03:46 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 Mar 27 2024 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Jan 19 2024 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 Mar 27 2024 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Mar 27 2024 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/671806/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Mar 28 2022 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 Mar 29 00:09 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 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98048 Apr 10 2022 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 Mar 29 00:09 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 Mar 29 00:09 more + -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount + -rwxr-xr-x 1 root root 18664 Mar 29 00:09 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 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 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 9 Jul 15 05:51 sh -> /bin/bash + -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 Mar 29 00:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Jan 20 23:59 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 Mar 29 00:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/2314433/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -226,7 +257,7 @@ 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 2s (9174 kB/s) +Fetched 18.3 MB in 0s (62.0 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 ... 19711 files and directories currently installed.) @@ -366,7 +397,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/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 +I: user script /srv/workspace/pbuilder/2314433/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/2314433/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/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 @@ -376,7 +411,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/poa-2.0+20060928' @@ -389,7 +424,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/poa-2.0+20060928' dh_auto_build -- poa - make -j42 "INSTALL=install --strip-program=true" poa + make -j20 "INSTALL=install --strip-program=true" poa make[2]: Entering directory '/build/reproducible-path/poa-2.0+20060928' gcc -g -O2 -fdebug-prefix-map=/build/reproducible-path/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/reproducible-path/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 @@ -417,80 +452,22 @@ black_flag.c:109:3: note: in expansion of macro 'CALLOC' 109 | CALLOC(Program_name,len,char); | ^~~~~~ +fasta_format.c: In function 'read_fasta': default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +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 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=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -seq_util.c:170:3: note: in expansion of macro 'CALLOC' - 170 | CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_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 -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=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -seq_util.c:171:3: note: in expansion of macro 'CALLOC' - 171 | CALLOC (m->gap_penalty_y, m->max_gap_length+2, LPOScore_T); - | ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' - 41 | CALLOC (node_type, 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 -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 msa_format.h:17, from msa_format.c:17: msa_format.c: In function 'read_clustal': -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 -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:42:3: note: in expansion of macro 'CALLOC' - 42 | CALLOC (refs_from_right, 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 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -505,34 +482,6 @@ | | | 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 -align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' - 43 | CALLOC (tmp, 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 -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:44:3: note: in expansion of macro 'CALLOC' - 44 | CALLOC (left_links, len, 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 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -541,53 +490,34 @@ msa_format.c:171:7: note: in expansion of macro 'REALLOC' 171 | REALLOC (seq_titles, n_seqs, char *); | ^~~~~~~ -In file included from lpo.h:6, - from main.c:3: -main.c: In function 'main': 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 -main.c:183:3: note: in expansion of macro 'CALLOC' - 183 | CALLOC (input_seqs, max_input_seqs, 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 +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: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); - | ^~~~~~ +seq_util.c:170:3: note: in expansion of macro 'CALLOC' + 170 | CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_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 -In file included from buildup_lpo.c:3: -buildup_lpo.c: In function 'clip_unaligned_ends': -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)); \ | ~^ @@ -599,8 +529,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 */ +seq_util.c:171:3: note: in expansion of macro 'CALLOC' + 171 | CALLOC (m->gap_penalty_y, m->max_gap_length+2, LPOScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -616,33 +546,38 @@ msa_format.c:176:7: note: in expansion of macro 'REALLOC' 176 | REALLOC (aln_lengths, n_seqs, int); | ^~~~~~~ -In file included from create_seq.c:3: -create_seq.c: In function 'create_seq': -align_lpo_po2.c: In function 'trace_back_lpo_alignment': +In file included from lpo.h:6, + from main.c:3: +main.c: In function 'main': 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=] +./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); +main.c:183:3: note: in expansion of macro 'CALLOC' + 183 | CALLOC (input_seqs, max_input_seqs, LPOSequence_T *); | ^~~~~~ +In file included from align_lpo2.c:2: +align_lpo2.c: In function 'get_seq_left_and_final': +./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 -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*/ +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)); \ @@ -650,6 +585,24 @@ | | | 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:66:3: note: in expansion of macro 'CALLOC' + 66 | CALLOC (x_left, len_x, LPOLetterLink_T *); + | ^~~~~~ +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:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -670,63 +623,20 @@ | | | int | %ld -In file included from lpo_format.c:3: -lpo_format.c: In function 'read_lpo': -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: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:121:3: note: in expansion of macro 'CALLOC' - 121 | CALLOC (y_al, len_y, LPOLetterRef_T); - | ^~~~~~ 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 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:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:39: 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_format.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC(seq,1,LPOSequence_T); - | ^~~~~~ +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)); \ | ~^ @@ -746,93 +656,91 @@ ./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' 212 | (sprintf MESSAGE,\ | ^~~~~~~ -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); - | ^~~~~~~ main.c:225:59: note: format string is defined here 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", | ~^ | | | 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 +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:71:3: note: in expansion of macro 'CALLOC' - 71 | CALLOC(seq->letter,length,LPOLetter_T); +align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' + 96 | CALLOC (x_al, len_x, LPOLetterRef_T); | ^~~~~~ -align_lpo_po2.c: In function 'align_lpo_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 +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); + | ^~~~~~~ +In file included from lpo.h:6, + from main.c:3: +./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +main.c:254:2: note: in expansion of macro 'REALLOC' + 254 | REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); + | ^~~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 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_lpo2.c:97:3: note: in expansion of macro 'CALLOC' + 97 | CALLOC (y_al, len_y, LPOLetterRef_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:155:37: 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.h:6, - from main.c:3: -./default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +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 -main.c:254:2: note: in expansion of macro 'REALLOC' - 254 | REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); - | ^~~~~~~ -./default.h:196:39: note: format string is defined here +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 -In file included from lpo.c:3: -lpo.c: In function 'lpo_init': +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_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' - 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); +align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' + 185 | CALLOC (next_gap_array, max_gap_length + 2, int); | ^~~~~~ -buildup_lpo.c: In function 'read_seqpair_scorefile': default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -844,19 +752,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' - 327 | CALLOC (adj_score, nseq, int); +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)); \ + | ~^ + | | + | 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 -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); +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)); \ @@ -865,23 +776,14 @@ | int | %ld msa_format.c: In function 'read_pir': -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); - | ^~~~~~ -In file included from ./lpo.h:6, - from numeric_data.c:3: -numeric_data.c: In function 'new_numeric_data': +align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' + 201 | CALLOC (move[i], len_x, DPMove_T); + | ^~~~~~ 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -890,42 +792,69 @@ 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: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: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:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 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); +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 +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: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 +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 -buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' - 330 | CALLOC (score_list, max_nscore, SeqPairScore_T); +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)); \ @@ -938,19 +867,36 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' - 254 | CALLOC (move, len_y, DPMove_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: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); +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: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: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)); \ @@ -958,15 +904,39 @@ | | | int | %ld -In file included from heaviest_bundle.c:3: -heaviest_bundle.c: In function 'heaviest_bundle': +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:250:7: note: in expansion of macro 'REALLOC' - 250 | REALLOC (seq_titles, n_seqs, char *); +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)); \ @@ -974,21 +944,14 @@ | | | int | %ld -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 stringptr.c:2: -stringptr.c: In function 'stringptr_cat_pos': +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 -heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' - 27 | CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ +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)); \ @@ -996,31 +959,15 @@ | | | 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); \ - | ^~~~~~~ -numeric_data.c:18:3: note: in expansion of macro 'REBUFF' - 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); - | ^~~~~~ +buildup_lpo.c: In function 'read_seqpair_scorefile': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -stringptr.c:30:3: note: in expansion of macro 'CALLOC' - 30 | CALLOC(s2_temp,s2_len,char); /* ALLOCATE TEMP STORAGE */ +buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' + 327 | CALLOC (adj_score, nseq, 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:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1032,16 +979,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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: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:73:3: note: in expansion of macro 'CALLOC' - 73 | CALLOC(pos_count,nsource_seq,int); +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)); \ @@ -1049,34 +988,28 @@ | | | 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 +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)); \ | ~^ | | | 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: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:28:3: note: in expansion of macro 'CALLOC' - 28 | CALLOC(score,len,LPOScore_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)); \ | ~^ @@ -1102,37 +1035,37 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); - | ^~~~~~ -./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: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:155:37: note: format string is defined here +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 +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); + | ^~~~~~ 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: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)); \ | ~^ @@ -1144,8 +1077,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' - 29 | CALLOC(contains_pos,nsource_seq,int); +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)); \ @@ -1153,16 +1086,27 @@ | | | 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 -default.h:241:5: note: in expansion of macro 'CALLOC' - 241 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -stringptr.c:40:3: note: in expansion of macro 'GETMEM' - 40 | GETMEM(s1->p,total_len, +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)); \ @@ -1170,21 +1114,14 @@ | | | 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",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' - 262 | CALLOC (score_rows, len_y+1, DPScore_T *); +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)); \ @@ -1192,44 +1129,21 @@ | | | int | %ld -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 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 +msa_format.c:369:3: note: in expansion of macro 'REALLOC' + 369 | REALLOC (lposeq->sequence, len+1, char); + | ^~~~~~~ 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 */ - | ^~~~~~ -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);\ - | ^~~~~~~ -stringptr.c:40:3: note: in expansion of macro 'GETMEM' - 40 | GETMEM(s1->p,total_len, +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:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ @@ -1248,38 +1162,36 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); +msa_format.c:375:5: note: in expansion of macro 'CALLOC' + 375 | CALLOC (curr_seq, 1, LPOSequence_T); + | ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 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) */ | ^~~~~~ -lpo.c: In function 'build_seq_to_po_index': 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: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:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +default.h:155:37: note: format string is defined here 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); - | ^~~~~~ + | ~^ + | | + | 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_format.c:159:3: note: in expansion of macro 'CALLOC' - 159 | CALLOC(seq,1,LPOSequence_T); +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)); \ @@ -1287,12 +1199,14 @@ | | | int | %ld -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: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); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1304,23 +1218,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 -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); - | ^~~~~~~ +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)); \ | ~^ @@ -1332,56 +1232,64 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); +buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' + 538 | CALLOC (perm, nseq_tot, int); | ^~~~~~ -stringptr.c: In function 'stringptr_cpy': 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:147:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 147 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 148 | __FILE__,__LINE__,STRINGIFY(memptr),(N)); \ - | ~~~ -default.h:147:22: note: in definition of macro 'CALLOC' - 147 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ -heaviest_bundle.c: In function 'assign_sequence_bundle_id': -default.h:147:68: note: format string is defined here - 147 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ~^ - | | - | 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)); \ + | ~^ + | | + | 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 -heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' - 90 | CALLOC(bundle_count,seq->nsource_seq,int); - | ^~~~~~ +msa_format.c:407:5: note: in expansion of macro 'CALLOC' + 407 | CALLOC (al_y, lposeq->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 +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); + | ^~~~~~ +In file included from stringptr.c:2: +stringptr.c: In function 'stringptr_cat_pos': default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1393,9 +1301,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); - | ^~~~~~ +stringptr.c:30:3: note: in expansion of macro 'CALLOC' + 30 | CALLOC(s2_temp,s2_len,char); /* ALLOCATE TEMP STORAGE */ + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1407,15 +1315,53 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); +default.h:241:5: note: in expansion of macro 'CALLOC' + 241 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ | ^~~~~~ +stringptr.c:40:3: note: in expansion of macro 'GETMEM' + 40 | GETMEM(s1->p,total_len, + | ^~~~~~ 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);\ + | ^~~~~~~ +stringptr.c:40:3: note: in expansion of macro 'GETMEM' + 40 | GETMEM(s1->p,total_len, + | ^~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +stringptr.c: In function 'stringptr_cpy': +default.h:147:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 147 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 148 | __FILE__,__LINE__,STRINGIFY(memptr),(N)); \ + | ~~~ +default.h:147:22: note: in definition of macro 'CALLOC' + 147 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +default.h:147:68: note: format string is defined here + 147 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ~^ + | | + | int + | %ld default.h:154:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 154 | fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ @@ -1431,23 +1377,6 @@ | | | 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 -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)); \ - | ~^ - | | - | int - | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ @@ -1463,8 +1392,6 @@ | | | 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1482,13 +1409,15 @@ | | | int | %ld +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=] 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 *); +align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' + 41 | CALLOC (node_type, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1496,13 +1425,45 @@ | | | 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",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +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)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +default.h:245:5: note: in expansion of macro 'REALLOC' + 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,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: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:445:3: note: in expansion of macro 'CALLOC' - 445 | CALLOC(seq_cluster,nseq,int); /* MAPS SEQS (or CLUSTERS) TO CLUSTER THEY'RE IN */ +align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' + 42 | CALLOC (refs_from_right, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1518,8 +1479,8 @@ 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); +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); | ^~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ @@ -1527,24 +1488,13 @@ | | | 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",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:319:3: note: in expansion of macro 'CALLOC' - 319 | CALLOC (res_ids, n_seqs+1, int *); +align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' + 43 | CALLOC (tmp, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1557,165 +1507,110 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 */ +align_lpo_po2.c:44:3: note: in expansion of macro 'CALLOC' + 44 | CALLOC (left_links, len, LPOLetterLink_T *); | ^~~~~~ -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: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 -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:155:20: 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); - | ^~~~~~ +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 +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)); \ | ~^ | | | 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:447:3: note: in expansion of macro 'CALLOC' - 447 | CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ +align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' + 121 | CALLOC (y_al, len_y, LPOLetterRef_T); | ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -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)); \ | ~^ | | | 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 +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)); \ | ~^ | | | 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)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -default.h:245:5: note: in expansion of macro 'REALLOC' - 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,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 -default.h:245:5: note: in expansion of macro 'REALLOC' - 245 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,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:327:5: note: in expansion of macro 'CALLOC' - 327 | CALLOC (res_ids[i], max_aln_length, int); - | ^~~~~~ -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, +heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' + 28 | CALLOC(score,len,LPOScore_T); | ^~~~~~ -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 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:196:39: 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 -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) */ +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 +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 -lpo_format.c:196:3: note: in expansion of macro 'CALLOC' - 196 | CALLOC(iseq_compact,nsource_seq,int); +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)); \ @@ -1723,29 +1618,27 @@ | | | 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 +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)); \ | ~^ | | | int | %ld -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 -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); +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)); \ @@ -1753,13 +1646,14 @@ | | | 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 -lpo_format.c:197:3: note: in expansion of macro 'CALLOC' - 197 | CALLOC(last_pos,nsource_seq,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)); \ @@ -1767,16 +1661,13 @@ | | | int | %ld -In file included from remove_bundle.c:4: -remove_bundle.c: In function 'compact_links': -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 -lpo.c:213:3: note: in expansion of macro 'CALLOC' - 213 | CALLOC(list,nsource_seq,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)); \ @@ -1789,16 +1680,27 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' - 16 | CALLOC(link,1,LPOLetterLink_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 +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 -msa_format.c:347:3: note: in expansion of macro 'CALLOC' - 347 | CALLOC (lposeq, 1, LPOSequence_T); +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)); \ @@ -1806,19 +1708,44 @@ | | | 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: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)); \ | ~^ | | | 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 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:198:3: note: in expansion of macro 'CALLOC' - 198 | CALLOC(match_pos,nsource_seq,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)); \ @@ -1826,14 +1753,13 @@ | | | 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 -msa_format.c:351:3: note: in expansion of macro 'CALLOC' - 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); +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)); \ @@ -1846,31 +1772,56 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 */ - | ^~~~~~ +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)); \ | ~^ | | | int | %ld -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=] +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 +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 -buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' - 538 | CALLOC (perm, nseq_tot, 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 +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 -remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' - 59 | CALLOC(source,1,LPOLetterSource_T); +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)); \ @@ -1878,49 +1829,79 @@ | | | 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 +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)); \ | ~^ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +./default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 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 */ +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 +./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 '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_format.c:230:3: note: in expansion of macro 'CALLOC' - 230 | CALLOC(pos_compact,seq->length,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: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: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: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)); \ | ~^ @@ -1932,39 +1913,41 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:252:7: note: in expansion of macro 'CALLOC' - 252 | CALLOC(new_s->more,1,LPOLetterSource_T); - | ^~~~~~ +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)); \ | ~^ | | | int | %ld -remove_bundle.c: In function 'remove_bundle': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -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:159:3: note: in expansion of macro 'CALLOC' + 159 | CALLOC(seq,1,LPOSequence_T); | ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +default.h:155:37: note: format string is defined here 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); - | ^~~~~~ + | ~^ + | | + | 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_format.c:231:3: note: in expansion of macro 'CALLOC' - 231 | CALLOC(ring_old,seq->length,int); +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)); \ @@ -1972,26 +1955,47 @@ | | | int | %ld -default.h:155:37: note: format string is defined here +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)); \ - | ~^ - | | - | int - | %ld + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | 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: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 -lpo.c: In function 'reindex_lpo_source_seqs': +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:270:3: note: in expansion of macro 'CALLOC' - 270 | CALLOC (map, len, int); +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)); \ @@ -2004,9 +2008,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:380:5: note: in expansion of macro 'CALLOC' - 380 | CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); - | ^~~~~~ +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)); \ | ~^ @@ -2018,8 +2022,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:271:3: note: in expansion of macro 'CALLOC' - 271 | CALLOC (invmap, len, int); +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)); \ @@ -2027,14 +2031,13 @@ | | | int | %ld -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*/ +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)); \ @@ -2042,14 +2045,13 @@ | | | 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_format.c:354:3: note: in expansion of macro 'CALLOC' - 354 | CALLOC(p,seq->nsource_seq*nring,char); +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)); \ @@ -2062,8 +2064,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 */ +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)); \ @@ -2071,28 +2073,13 @@ | | | 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 -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 -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 -lpo.c:500:3: note: in expansion of macro 'CALLOC' - 500 | CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ +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)); \ @@ -2100,16 +2087,14 @@ | | | 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); - | ^~~~~~~~~~~~~~~~~~~~~ +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.c:501:3: note: in expansion of macro 'CALLOC' - 501 | CALLOC(new_x,len_x,LPOLetterRef_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)); \ @@ -2117,22 +2102,30 @@ | | | int | %ld -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 -msa_format.c:406:5: note: in expansion of macro 'CALLOC' - 406 | CALLOC (al_x, len, int); - | ^~~~~~ +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)); \ | ~^ | | | 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 +lpo.c:15:3: note: in expansion of macro 'CALLOC' + 15 | CALLOC(seq->letter,seq->length,LPOLetter_T); + | ^~~~~~ 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -2147,13 +2140,20 @@ | | | int | %ld +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 '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:407:5: note: in expansion of macro 'CALLOC' - 407 | CALLOC (al_y, lposeq->length, 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)); \ @@ -2166,12 +2166,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:502:3: note: in expansion of macro 'CALLOC' - 502 | CALLOC(new_y,len_y,LPOLetterRef_T); - | ^~~~~~ -msa_format.c:428:5: warning: implicit declaration of function 'fuse_ring_identities' [-Wimplicit-function-declaration] - 428 | fuse_ring_identities (lposeq->length, lposeq->letter, - | ^~~~~~~~~~~~~~~~~~~~ +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)); \ | ~^ @@ -2183,25 +2180,24 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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.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)); \ | ~^ | | | int | %ld -In file included from msa_format.h:17, - from msa_format.c:17: -msa_format.c: In function 'filter_sequence_set': +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 -msa_format.c:485:3: note: in expansion of macro 'CALLOC' - 485 | CALLOC (keep_seq, n_seqs, int); +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)); \ @@ -2209,14 +2205,14 @@ | | | 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)); \ @@ -2224,27 +2220,17 @@ | | | 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.c: In function 'fuse_lpo_remap': +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 -lpo.c:618:3: note: in expansion of macro 'CALLOC' - 618 | CALLOC(new_x,len_x,LPOLetterRef_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)); \ @@ -2252,13 +2238,14 @@ | | | 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 -lpo.c:619:3: note: in expansion of macro 'CALLOC' - 619 | CALLOC(new_y,len_y,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)); \ @@ -2271,37 +2258,54 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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: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_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.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 +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)); \ + | ~^ + | | + | 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: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: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: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: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:185:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 185 | fscanf(ifile,"%*[ \t]"); +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 align_lpo2.c:2: -align_lpo2.c: In function 'get_seq_left_and_final': +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_lpo2.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC (is_final_node_x, len_x, int); +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)); \ @@ -2309,42 +2313,43 @@ | | | 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_lpo2.c:66:3: note: in expansion of macro 'CALLOC' - 66 | CALLOC (x_left, len_x, LPOLetterLink_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 -align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' - 70 | CALLOC (x_left[i], 1, LPOLetterLink_T); - | ^~~~~~ +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 -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); +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)); \ @@ -2352,13 +2357,14 @@ | | | 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 -align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' - 97 | CALLOC (y_al, len_y, LPOLetterRef_T); +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)); \ @@ -2366,14 +2372,27 @@ | | | int | %ld -align_lpo2.c: In function 'align_lpo': +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]"); + | ^~~~~~~~~~~~~~~~~~~~~~~ +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_lpo2.c:185:3: note: in expansion of macro 'CALLOC' - 185 | CALLOC (next_gap_array, max_gap_length + 2, int); +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)); \ @@ -2386,8 +2405,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); +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)); \ @@ -2400,8 +2419,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' - 199 | CALLOC (move, len_y, DPMove_T *); +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)); \ @@ -2414,22 +2433,23 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' - 201 | CALLOC (move[i], len_x, DPMove_T); - | ^~~~~~ +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 +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 -align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' - 204 | CALLOC (init_col_score, len_y+1, DPScore_T); +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)); \ @@ -2437,13 +2457,14 @@ | | | 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 -align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' - 207 | CALLOC (curr_score, len_x+1, DPScore_T); +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)); \ @@ -2456,8 +2477,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' - 209 | CALLOC (prev_score, len_x+1, DPScore_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)); \ @@ -2465,6 +2486,20 @@ | | | 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 rm -f liblpo.a ar rc liblpo.a black_flag.o seq_util.o fasta_format.o msa_format.o align_lpo2.o align_lpo_po2.o buildup_lpo.o lpo.o heaviest_bundle.o lpo_format.o create_seq.o remove_bundle.o numeric_data.o stringptr.o ranlib liblpo.a @@ -2491,7 +2526,7 @@ 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.x2kdx6VxMd... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.UmpxDYhj0j... 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 @@ -2532,12 +2567,14 @@ 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/2314433/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2314433/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/671806 and its subdirectories -I: Current time: Sat Aug 16 10:14:05 -12 2025 -I: pbuilder-time-stamp: 1755382445 +I: removing directory /srv/workspace/pbuilder/2314433 and its subdirectories +I: Current time: Mon Jul 15 05:52:24 +14 2024 +I: pbuilder-time-stamp: 1720972344