Diff of the two buildlogs: -- --- b1/build.log 2025-03-05 22:38:10.377580248 +0000 +++ b2/build.log 2025-03-05 22:38:45.100009533 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 7 16:59:45 -12 2026 -I: pbuilder-time-stamp: 1775624385 +I: Current time: Thu Mar 6 12:38:12 +14 2025 +I: pbuilder-time-stamp: 1741214292 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,51 +28,83 @@ dpkg-source: info: applying gcc-15.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1854045/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4042010/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-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 Mar 5 22:38 /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/4042010/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4042010/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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 parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6d0fb29792354297b3d0a9db61350436' - 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='1854045' - PS1='# ' - PS2='> ' + INVOCATION_ID=edff7d2d083c440aaac5958fab8c1945 + 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=4042010 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.JELidJCF/pbuilderrc_zGnb --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JELidJCF/b1 --logfile b1/build.log poa_2.0+20060928-10.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.JELidJCF/pbuilderrc_lu67 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.JELidJCF/b2 --logfile b2/build.log poa_2.0+20060928-10.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1854045/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4042010/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -138,7 +170,7 @@ Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] -Fetched 20.6 MB in 1s (18.0 MB/s) +Fetched 20.6 MB in 0s (113 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19800 files and directories currently installed.) @@ -273,7 +305,11 @@ 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+20060928-10_source.changes +I: user script /srv/workspace/pbuilder/4042010/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4042010/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+20060928-10_source.changes dpkg-buildpackage: info: source package poa dpkg-buildpackage: info: source version 2.0+20060928-10 dpkg-buildpackage: info: source distribution unstable @@ -312,30 +348,6 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo_format.o lpo_format.c In file included from black_flag.c:4: black_flag.c: In function 'black_flag_init_args': -In file included from seq_util.c:2: -seq_util.c: In function 'read_score_matrix': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -350,12 +362,6 @@ | | | int | %ld -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld In file included from lpo.h:6, from main.c:3: main.c: In function 'main': @@ -381,65 +387,21 @@ main.c:221:9: note: in expansion of macro 'REALLOC' 221 | REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); | ^~~~~~~ +In file included from align_lpo_po2.c:2: +align_lpo_po2.c: In function 'get_lpo_stats': ./default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -In file included from ./default.h:16: -main.c:225:30: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'FILE *' [-Wformat=] - 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 226 | po_list_file),"$Revision: 1.2.2.9 $"); - | ~~~~~~~~~~~~ - | | - | FILE * -./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' - 212 | (sprintf MESSAGE,\ - | ^~~~~~~ -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:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -main.c:254:9: note: in expansion of macro 'REALLOC' - 254 | REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); - | ^~~~~~~ -./default.h:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -In file included from align_lpo2.c:2: -align_lpo2.c: In function 'get_seq_left_and_final': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); - | ^~~~~~ -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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 *); +align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' + 41 | CALLOC (node_type, len, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -447,28 +409,24 @@ | | | int | %ld +In file included from ./default.h:16: +main.c:225:30: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'FILE *' [-Wformat=] + 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 226 | po_list_file),"$Revision: 1.2.2.9 $"); + | ~~~~~~~~~~~~ + | | + | FILE * +./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' + 212 | (sprintf MESSAGE,\ + | ^~~~~~~ default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); - | ^~~~~~ -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -align_lpo2.c: In function 'trace_back_lpo_alignment': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); +align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' + 42 | CALLOC (refs_from_right, len, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -476,23 +434,28 @@ | | | int | %ld +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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' + 43 | CALLOC (tmp, len, int); | ^~~~~~ +In file included from msa_format.h:17, + from msa_format.c:17: +msa_format.c: In function 'read_clustal': default.h:156:37: note: format string is defined here 156 | 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': default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -501,13 +464,28 @@ msa_format.c:169:7: note: in expansion of macro 'REALLOC' 169 | REALLOC (seq_names, n_seqs, char *); | ^~~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -align_lpo2.c: In function 'align_lpo': +default.h:156:37: note: format string is defined here + 156 | 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:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -527,9 +505,11 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' - 185 | CALLOC (next_gap_array, max_gap_length + 2, int); - | ^~~~~~ +align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' + 71 | CALLOC (left_links[i], 1, LPOLetterLink_T); + | ^~~~~~ +In file included from align_lpo2.c:2: +align_lpo2.c: In function 'get_seq_left_and_final': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -544,35 +524,72 @@ msa_format.c:174:7: note: in expansion of macro 'REALLOC' 174 | REALLOC (aln_mat, n_seqs, char *); | ^~~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' + 146 | CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ + | ^~~~~~ default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' - 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); +align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC (is_final_node_x, len_x, int); | ^~~~~~ +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:176:7: note: in expansion of macro 'REALLOC' + 176 | REALLOC (aln_lengths, n_seqs, int); + | ^~~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +./default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:176:7: note: in expansion of macro 'REALLOC' - 176 | REALLOC (aln_lengths, n_seqs, int); - | ^~~~~~~ -default.h:197:39: note: format string is defined here +main.c:254:9: note: in expansion of macro 'REALLOC' + 254 | REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); + | ^~~~~~~ +align_lpo_po2.c: In function 'trace_back_lpo_alignment': +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | @@ -583,9 +600,11 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' - 199 | CALLOC (move, len_y, DPMove_T *); +align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' + 66 | CALLOC (x_left, len_x, LPOLetterLink_T *); | ^~~~~~ +In file included from lpo.c:3: +lpo.c: In function 'lpo_init': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -608,53 +627,13 @@ | | | int | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -msa_format.c:185:5: note: in expansion of macro 'REALLOC' - 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' - 201 | CALLOC (move[i], len_x, DPMove_T); - | ^~~~~~ -default.h:197:34: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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:15:3: note: in expansion of macro 'CALLOC' + 15 | CALLOC(seq->letter,seq->length,LPOLetter_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -662,14 +641,6 @@ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); - | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -681,92 +652,21 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' - 209 | CALLOC (prev_score, len_x+1, DPScore_T); +align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' + 121 | CALLOC (y_al, len_y, LPOLetterRef_T); | ^~~~~~ +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +msa_format.c:185:5: note: in expansion of macro 'REALLOC' + 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); + | ^~~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -msa_format.c: In function 'read_pir': -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:248:7: note: in expansion of macro 'REALLOC' - 248 | REALLOC (seq_names, n_seqs, char *); - | ^~~~~~~ -default.h:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:185:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 185 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 186 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ - | ~~~~~ -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:185:68: note: format string is defined here - 185 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ~^ - | | - | int - | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 197 | 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:197:34: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ @@ -778,24 +678,25 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); - | ^~~~~~~ +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 heaviest_bundle.c:3: +heaviest_bundle.c: In function 'heaviest_bundle': default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -msa_format.c: In function 'lpo_from_aln_mat': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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_lpo2.c:70:7: note: in expansion of macro 'CALLOC' + 70 | CALLOC (x_left[i], 1, LPOLetterLink_T); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -807,8 +708,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:319:3: note: in expansion of macro 'CALLOC' - 319 | CALLOC (res_ids, n_seqs+1, 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -816,28 +717,31 @@ | | | int | %ld +align_lpo2.c: In function 'trace_back_lpo_alignment': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); - | ^~~~~~ +heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' + 28 | CALLOC(score,len,LPOScore_T); + | ^~~~~~ +align_lpo_po2.c: In function 'align_lpo_po': +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); - | ^~~~~~ +buildup_lpo.c: In function 'read_seqpair_scorefile': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -849,8 +753,16 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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:227:3: note: in expansion of macro 'CALLOC' + 227 | CALLOC (next_gap_array, max_gap_length + 2, int); + | ^~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' + 327 | CALLOC (adj_score, nseq, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -863,8 +775,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:347:3: note: in expansion of macro 'CALLOC' - 347 | CALLOC (lposeq, 1, LPOSequence_T); +align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' + 97 | CALLOC (y_al, len_y, LPOLetterRef_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -877,8 +789,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:351:3: note: in expansion of macro 'CALLOC' - 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); +heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' + 29 | CALLOC(contains_pos,nsource_seq,int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -886,56 +798,36 @@ | | | int | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); - | ^~~~~~ +msa_format.c: In function 'read_pir': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +lpo.c: In function 'build_seq_to_po_index': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); - | ^~~~~~ +buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' + 330 | CALLOC (score_list, max_nscore, SeqPairScore_T); + | ^~~~~~ +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:248:7: note: in expansion of macro 'REALLOC' + 248 | REALLOC (seq_names, n_seqs, char *); + | ^~~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ @@ -947,8 +839,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:406:5: note: in expansion of macro 'CALLOC' - 406 | CALLOC (al_x, len, int); +lpo.c:157:5: note: in expansion of macro 'CALLOC' + 157 | CALLOC(seq->source_seq[i].seq_to_po,seq->source_seq[i].length,int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -961,18 +853,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:407:5: note: in expansion of macro 'CALLOC' - 407 | CALLOC (al_y, lposeq->length, int); - | ^~~~~~ -In file included from buildup_lpo.c:3: -buildup_lpo.c: In function 'clip_unaligned_ends': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' - 146 | CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ +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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -980,50 +862,57 @@ | | | int | %ld -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -buildup_lpo.c: In function 'read_seqpair_scorefile': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' - 327 | CALLOC (adj_score, nseq, int); +heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' + 67 | CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ | ^~~~~~ +align_lpo2.c: In function 'align_lpo': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -msa_format.c: In function 'filter_sequence_set': +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | 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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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:185:3: note: in expansion of macro 'CALLOC' + 185 | CALLOC (next_gap_array, max_gap_length + 2, int); | ^~~~~~ default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:485:3: note: in expansion of macro 'CALLOC' - 485 | CALLOC (keep_seq, n_seqs, int); - | ^~~~~~ +lpo.c:158:5: note: in expansion of macro 'CALLOC' + 158 | CALLOC(seq->source_seq[i].po_to_seq,seq->length,int); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1044,24 +933,30 @@ | | | int | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -buildup_lpo.c:374:9: note: in expansion of macro 'REALLOC' - 374 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ -In file included from heaviest_bundle.c:3: -heaviest_bundle.c: In function 'heaviest_bundle': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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 */ +align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' + 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); | ^~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' + 254 | CALLOC (move, len_y, DPMove_T *); + | ^~~~~~ +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1074,27 +969,28 @@ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); - | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +heaviest_bundle.c: In function 'assign_sequence_bundle_id': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' - 29 | CALLOC(contains_pos,nsource_seq,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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' + 90 | CALLOC(bundle_count,seq->nsource_seq,int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1107,51 +1003,56 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:394:9: note: in expansion of macro 'REALLOC' - 394 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ +msa_format.c:254:7: note: in expansion of macro 'REALLOC' + 254 | REALLOC (aln_lengths, n_seqs, int); + | ^~~~~~~ default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -buildup_lpo.c: In function 'buildup_progressive_lpo': +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +buildup_lpo.c:374:9: note: in expansion of macro 'REALLOC' + 374 | REALLOC (score_list, max_nscore, SeqPairScore_T); + | ^~~~~~~ default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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:256:5: note: in expansion of macro 'CALLOC' + 256 | CALLOC (move[i], len_x, DPMove_T); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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_lpo2.c:199:3: note: in expansion of macro 'CALLOC' + 199 | CALLOC (move, len_y, DPMove_T *); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1159,13 +1060,21 @@ | | | int | %ld +default.h:185:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 185 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 186 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ + | ~~~~~ +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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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:259:3: note: in expansion of macro 'CALLOC' + 259 | CALLOC (init_col_score, len_y+1, DPScore_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1173,13 +1082,27 @@ | | | int | %ld +default.h:185:68: note: format string is defined here + 185 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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) */ +align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' + 201 | CALLOC (move[i], len_x, DPMove_T); + | ^~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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 *); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1187,30 +1110,61 @@ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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:197:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 197 | 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:156:37: note: format string is defined here 156 | 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:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +buildup_lpo.c:394:9: note: in expansion of macro 'REALLOC' + 394 | REALLOC (score_list, max_nscore, SeqPairScore_T); + | ^~~~~~~ +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:197:34: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +lpo.c: In function 'save_lpo_source': +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:268:7: note: in expansion of macro 'REALLOC' + 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); + | ^~~~~~~ default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' + 264 | CALLOC (score_rows[-1], len_x+1, DPScore_T); | ^~~~~~ +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1222,8 +1176,11 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' - 42 | CALLOC (refs_from_right, len, int); +default.h:213:5: note: in expansion of macro 'CALLOC' + 213 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1236,8 +1193,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' - 43 | CALLOC (tmp, len, int); +align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' + 204 | CALLOC (init_col_score, len_y+1, DPScore_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1245,29 +1202,48 @@ | | | int | %ld -heaviest_bundle.c: In function 'assign_sequence_bundle_id': +buildup_lpo.c: In function 'buildup_progressive_lpo': +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +default.h:216:5: note: in expansion of macro 'REALLOC' + 216 | 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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' + 207 | CALLOC (curr_score, len_x+1, DPScore_T); | ^~~~~~ -default.h:156:37: note: format string is defined here +msa_format.c: In function 'lpo_from_aln_mat': +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o create_seq.o create_seq.c + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | 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); + | ^~~~~~ default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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 *); +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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1275,28 +1251,19 @@ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' - 71 | CALLOC (left_links[i], 1, LPOLetterLink_T); - | ^~~~~~ default.h:156:37: note: format string is defined here 156 | 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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +msa_format.c:318:3: note: in expansion of macro 'CALLOC' + 318 | CALLOC (column_ids, n_seqs+1, int *); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1304,43 +1271,27 @@ | | | int | %ld -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o remove_bundle.o remove_bundle.c -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -align_lpo_po2.c: In function 'align_lpo_po': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +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:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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:209:3: note: in expansion of macro 'CALLOC' + 209 | CALLOC (prev_score, len_x+1, DPScore_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1353,8 +1304,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' - 254 | CALLOC (move, len_y, DPMove_T *); +msa_format.c:319:3: note: in expansion of macro 'CALLOC' + 319 | CALLOC (res_ids, n_seqs+1, int *); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1362,41 +1313,28 @@ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' - 256 | CALLOC (move[i], len_x, DPMove_T); - | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +lpo.c: In function 'save_lpo_source_list': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +buildup_lpo.c:447:3: note: in expansion of macro 'CALLOC' + 447 | CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ | ^~~~~~ -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' - 262 | CALLOC (score_rows, len_y+1, DPScore_T *); +lpo.c:213:3: note: in expansion of macro 'CALLOC' + 213 | CALLOC(list,nsource_seq,int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1404,14 +1342,6 @@ | | | int | %ld -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' - 264 | CALLOC (score_rows[-1], len_x+1, DPScore_T); - | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1423,8 +1353,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); +msa_format.c:326:5: note: in expansion of macro 'CALLOC' + 326 | CALLOC (column_ids[i], max_aln_length, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1432,16 +1362,29 @@ | | | int | %ld -In file included from lpo.c:3: -lpo.c: In function 'lpo_init': +lpo.c: In function 'add_lpo_link': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1454,21 +1397,63 @@ | | | | long int int | %d +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | 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 */ + | ^~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:156:37: note: format string is defined here + 156 | 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 -lpo.c: In function 'build_seq_to_po_index': +lpo.c: In function 'add_lpo_sources': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); - | ^~~~~~ +msa_format.c:347:3: note: in expansion of macro 'CALLOC' + 347 | CALLOC (lposeq, 1, LPOSequence_T); + | ^~~~~~ +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +lpo.c:252:7: note: in expansion of macro 'CALLOC' + 252 | CALLOC(new_s->more,1,LPOLetterSource_T); + | ^~~~~~ +default.h:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1480,8 +1465,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1494,26 +1479,23 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); - | ^~~~~~ +msa_format.c:351:3: note: in expansion of macro 'CALLOC' + 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); + | ^~~~~~ +lpo.c: In function 'reindex_lpo_source_seqs': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'save_lpo_source': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:213:5: note: in expansion of macro 'CALLOC' - 213 | CALLOC(memptr,BUF,ATYPE) } \ - | ^~~~~~ -lpo.c:189:3: note: in expansion of macro 'REBUFF' - 189 | REBUFF(seq->source_seq,seq->nsource_seq,SOURCE_SEQ_BUFFER_CHUNK, +lpo.c:270:3: note: in expansion of macro 'CALLOC' + 270 | CALLOC (map, len, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1521,76 +1503,78 @@ | | | int | %ld +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +lpo.c:271:3: note: in expansion of macro 'CALLOC' + 271 | CALLOC (invmap, len, int); + | ^~~~~~ default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:216:5: note: in expansion of macro 'REALLOC' - 216 | 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, - | ^~~~~~ +msa_format.c:369:3: note: in expansion of macro 'REALLOC' + 369 | REALLOC (lposeq->sequence, len+1, char); + | ^~~~~~~ default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'save_lpo_source_list': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'add_lpo_link': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 */ - | ^~~~~~ +msa_format.c:375:5: note: in expansion of macro 'CALLOC' + 375 | CALLOC (curr_seq, 1, LPOSequence_T); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'add_lpo_sources': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:252:7: note: in expansion of macro 'CALLOC' - 252 | CALLOC(new_s->more,1,LPOLetterSource_T); - | ^~~~~~ +msa_format.c:380:5: note: in expansion of macro 'CALLOC' + 380 | CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'reindex_lpo_source_seqs': +lpo.c: In function 'reindex_lpo_fusion': +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | 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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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.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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1598,38 +1582,43 @@ | | | int | %ld +default.h:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:271:3: note: in expansion of macro 'CALLOC' - 271 | CALLOC (invmap, len, int); - | ^~~~~~ +msa_format.c:406:5: note: in expansion of macro 'CALLOC' + 406 | CALLOC (al_x, len, int); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'reindex_lpo_fusion': -In file included from lpo_format.c:3: -lpo_format.c: In function 'read_lpo': +lpo.c: In function 'copy_fuse_lpo_remap': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:427:3: note: in expansion of macro 'CALLOC' - 427 | CALLOC(do_fuse,len_y,char); /* MARK POSITIONS TO FUSE seq_y TO seq_x */ - | ^~~~~~ +msa_format.c:407:5: note: in expansion of macro 'CALLOC' + 407 | CALLOC (al_y, lposeq->length, int); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'copy_fuse_lpo_remap': +In file included from lpo_format.c:3: +lpo_format.c: In function 'read_lpo': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1649,8 +1638,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:501:3: note: in expansion of macro 'CALLOC' - 501 | CALLOC(new_x,len_x,LPOLetterRef_T); +lpo_format.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC(seq,1,LPOSequence_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1663,22 +1652,16 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:502:3: note: in expansion of macro 'CALLOC' - 502 | CALLOC(new_y,len_y,LPOLetterRef_T); +lpo_format.c:71:3: note: in expansion of macro 'CALLOC' + 71 | CALLOC(seq->letter,length,LPOLetter_T); | ^~~~~~ -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:505:3: note: in expansion of macro 'CALLOC' - 505 | CALLOC(new_lpo,new_len,LPOLetter_T); /* ALLOCATE NEW LINEARIZED PO */ +lpo.c:501:3: note: in expansion of macro 'CALLOC' + 501 | CALLOC(new_x,len_x,LPOLetterRef_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1686,43 +1669,31 @@ | | | int | %ld -lpo.c: In function 'copy_lpo': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 156 | 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); - | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo.c: In function 'fuse_lpo_remap': +msa_format.c: In function 'filter_sequence_set': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +lpo.c:502:3: note: in expansion of macro 'CALLOC' + 502 | CALLOC(new_y,len_y,LPOLetterRef_T); | ^~~~~~ -default.h:156:37: note: format string is defined here - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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:242:5: note: in expansion of macro 'CALLOC' + 242 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1730,16 +1701,19 @@ | | | int | %ld +default.h:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -lpo_format.c:72:3: note: in expansion of macro 'GETMEM' - 72 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); +msa_format.c:485:3: note: in expansion of macro 'CALLOC' + 485 | CALLOC (keep_seq, n_seqs, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1778,14 +1752,13 @@ | | | int | %ld -lpo_format.c: In function 'read_lpo_select': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +lpo.c:505:3: note: in expansion of macro 'CALLOC' + 505 | CALLOC(new_lpo,new_len,LPOLetter_T); /* ALLOCATE NEW LINEARIZED PO */ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1793,13 +1766,14 @@ | | | int | %ld +lpo.c: In function 'copy_lpo': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +lpo.c:564:3: note: in expansion of macro 'CALLOC' + 564 | CALLOC(x_to_y,holder_x->length,LPOLetterRef_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1807,25 +1781,30 @@ | | | int | %ld +lpo_format.c: In function 'read_lpo_select': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | 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); +lpo_format.c:159:3: note: in expansion of macro 'CALLOC' + 159 | CALLOC(seq,1,LPOSequence_T); | ^~~~~~ +default.h:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | 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); +lpo_format.c:170:3: note: in expansion of macro 'CALLOC' + 170 | CALLOC(seq->letter,length,LPOLetter_T); | ^~~~~~ +lpo.c: In function 'fuse_lpo_remap': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1837,8 +1816,19 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:619:3: note: in expansion of macro 'CALLOC' - 619 | CALLOC(new_y,len_y,LPOLetterRef_T); +default.h:242:5: note: in expansion of macro 'CALLOC' + 242 | 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:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1846,20 +1836,6 @@ | | | int | %ld -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 197 | 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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1888,6 +1864,20 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int +lpo.c:619:3: note: in expansion of macro 'CALLOC' + 619 | CALLOC(new_y,len_y,LPOLetterRef_T); + | ^~~~~~ +default.h:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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); | ^~~~~~ @@ -1897,6 +1887,20 @@ | | | int | %ld +default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 197 | 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:197:39: note: format string is defined here + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1967,6 +1971,8 @@ | | | int | %ld +In file included from seq_util.c:2: +seq_util.c: In function 'read_score_matrix': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1981,6 +1987,34 @@ | | | int | %ld +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 156 | 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:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld lpo_format.c: In function 'xlate_lpo_to_al': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2025,15 +2059,6 @@ | int | %ld lpo_format.c: In function 'read_lpo': -main.c:225:30: warning: '%s' directive argument is null [-Wformat-overflow=] - 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' - 212 | (sprintf MESSAGE,\ - | ^~~~~~~ -main.c:225:58: note: format string is defined here - 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", - | ^~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2059,7 +2084,8 @@ lpo_format.c:185:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 185 | fscanf(ifile,"%*[ \t]"); | ^~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o numeric_data.o numeric_data.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o create_seq.o create_seq.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o remove_bundle.o remove_bundle.c In file included from create_seq.c:3: create_seq.c: In function 'create_seq': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -2096,6 +2122,16 @@ | | | int | %ld +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/poa-2.0+20060928=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o numeric_data.o numeric_data.c +main.c:225:30: warning: '%s' directive argument is null [-Wformat-overflow=] + 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +./black_flag.h:212:10: note: in definition of macro 'WARN_MSG' + 212 | (sprintf MESSAGE,\ + | ^~~~~~~ +main.c:225:58: note: format string is defined here + 225 | WARN_MSG(USERR,(ERRTXT,"Error reading PO list file %s.\nExiting", + | ^~ In file included from remove_bundle.c:4: remove_bundle.c: In function 'compact_links': default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -2388,7 +2424,7 @@ 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.cXITygzvb3... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.xmI4S019Nq... 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 @@ -2429,12 +2465,14 @@ 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/4042010/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4042010/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/1854045 and its subdirectories -I: Current time: Tue Apr 7 17:01:09 -12 2026 -I: pbuilder-time-stamp: 1775624469 +I: removing directory /srv/workspace/pbuilder/4042010 and its subdirectories +I: Current time: Thu Mar 6 12:38:44 +14 2025 +I: pbuilder-time-stamp: 1741214324