Diff of the two buildlogs: -- --- b1/build.log 2023-04-16 18:17:01.899802428 +0000 +++ b2/build.log 2023-04-16 18:18:08.912829101 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat May 18 12:39:05 -12 2024 -I: pbuilder-time-stamp: 1716079145 +I: Current time: Mon Apr 17 08:17:06 +14 2023 +I: pbuilder-time-stamp: 1681669026 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./poa_2.0+20060928.orig.tar.gz] I: copying [./poa_2.0+20060928-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Fri May 1 08:11:31 2020 -12 +gpgv: Signature made Sat May 2 10:11:31 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,52 +29,84 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30251/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29834/tmp/hooks/D01_modify_environment starting +debug: Running on codethink10-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 17 08:17 /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/29834/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29834/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges: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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='30251' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=29834 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.zrG6SqbP/pbuilderrc_Y3D2 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zrG6SqbP/b1 --logfile b1/build.log poa_2.0+20060928-8.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.zrG6SqbP/pbuilderrc_f47o --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zrG6SqbP/b2 --logfile b2/build.log --extrapackages usrmerge poa_2.0+20060928-8.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink11-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 18 04:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/30251/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 15 02:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/29834/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 0s (42.2 MB/s) +Fetched 18.3 MB in 3s (6324 kB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19616 files and directories currently installed.) @@ -274,8 +306,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/poa-2.0+20060928/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../poa_2.0+20060928-8_source.changes +I: user script /srv/workspace/pbuilder/29834/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/29834/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/poa-2.0+20060928/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../poa_2.0+20060928-8_source.changes dpkg-buildpackage: info: source package poa dpkg-buildpackage: info: source version 2.0+20060928-8 dpkg-buildpackage: info: source distribution unstable @@ -308,6 +349,36 @@ gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o msa_format.o msa_format.c gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align_lpo2.o align_lpo2.c gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align_lpo_po2.o align_lpo_po2.c +In file included from seq_util.c:2: +seq_util.c: In function 'read_score_matrix': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +seq_util.c:170:3: note: in expansion of macro 'CALLOC' + 170 | CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_T); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +seq_util.c:171:3: note: in expansion of macro 'CALLOC' + 171 | CALLOC (m->gap_penalty_y, m->max_gap_length+2, LPOScore_T); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld In file included from lpo.h:6, from main.c:3: main.c: In function 'main': @@ -385,16 +456,15 @@ | | | int | %ld -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o buildup_lpo.o buildup_lpo.c -In file included from align_lpo2.c:2: -align_lpo2.c: In function 'get_seq_left_and_final': +In file included from align_lpo_po2.c:2: +align_lpo_po2.c: In function 'get_lpo_stats': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC (is_final_node_x, len_x, int); +align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' + 41 | CALLOC (node_type, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -407,8 +477,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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:42:3: note: in expansion of macro 'CALLOC' + 42 | CALLOC (refs_from_right, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -416,15 +486,13 @@ | | | int | %ld -In file included from align_lpo_po2.c:2: -align_lpo_po2.c: In function 'get_lpo_stats': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:41:3: note: in expansion of macro 'CALLOC' - 41 | CALLOC (node_type, len, int); +align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' + 43 | CALLOC (tmp, len, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -437,36 +505,37 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' - 42 | CALLOC (refs_from_right, len, int); +align_lpo_po2.c:44:3: note: in expansion of macro 'CALLOC' + 44 | CALLOC (left_links, len, LPOLetterLink_T *); | ^~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' - 70 | CALLOC (x_left[i], 1, LPOLetterLink_T); - | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' + 71 | CALLOC (left_links[i], 1, LPOLetterLink_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +align_lpo_po2.c: In function 'trace_back_lpo_alignment': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' - 43 | CALLOC (tmp, len, int); +align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' + 120 | CALLOC (x_al, len_x, LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -474,22 +543,28 @@ | | | int | %ld -align_lpo2.c: In function 'trace_back_lpo_alignment': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' - 96 | CALLOC (x_al, len_x, LPOLetterRef_T); +align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' + 121 | CALLOC (y_al, len_y, LPOLetterRef_T); | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +align_lpo_po2.c: In function 'align_lpo_po': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:44:3: note: in expansion of macro 'CALLOC' - 44 | CALLOC (left_links, len, LPOLetterLink_T *); +align_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' + 227 | CALLOC (next_gap_array, max_gap_length + 2, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -497,6 +572,19 @@ | | | int | %ld +fasta_format.c: In function 'read_fasta': +fasta_format.c:48:9: warning: implicit declaration of function 'stringptr_cat_pos'; did you mean 'stringptr_cat'? [-Wimplicit-function-declaration] + 48 | stringptr_cat_pos(&tmp_seq,line,&length); + | ^~~~~~~~~~~~~~~~~ + | stringptr_cat +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' + 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -508,8 +596,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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:254:3: note: in expansion of macro 'CALLOC' + 254 | CALLOC (move, len_y, DPMove_T *); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -522,9 +610,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:71:7: note: in expansion of macro 'CALLOC' - 71 | CALLOC (left_links[i], 1, LPOLetterLink_T); - | ^~~~~~ +align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' + 256 | CALLOC (move[i], len_x, DPMove_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -548,6 +636,20 @@ | | | int | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' + 259 | CALLOC (init_col_score, len_y+1, DPScore_T); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -562,6 +664,20 @@ | | | int | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' + 262 | CALLOC (score_rows, len_y+1, DPScore_T *); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -576,28 +692,13 @@ | | | int | %ld -align_lpo_po2.c: In function 'trace_back_lpo_alignment': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' - 120 | CALLOC (x_al, len_x, LPOLetterRef_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' - 121 | CALLOC (y_al, len_y, LPOLetterRef_T); +align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' + 264 | CALLOC (score_rows[-1], len_x+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -619,7 +720,6 @@ | | | int | %ld -align_lpo2.c: In function 'align_lpo': default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -630,26 +730,12 @@ default.h:184:22: note: in definition of macro 'REALLOC' 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' - 185 | CALLOC (next_gap_array, max_gap_length + 2, int); - | ^~~~~~ default.h:184:68: note: format string is defined here 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ | ~^ | | | int | %ld -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ @@ -662,14 +748,6 @@ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' - 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); - | ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -678,49 +756,29 @@ 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:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -In file included from seq_util.c:2: -seq_util.c: In function 'read_score_matrix': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -seq_util.c:170:3: note: in expansion of macro 'CALLOC' - 170 | CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -seq_util.c:171:3: note: in expansion of macro 'CALLOC' - 171 | CALLOC (m->gap_penalty_y, m->max_gap_length+2, LPOScore_T); - | ^~~~~~ +align_lpo_po2.c:312:5: note: in expansion of macro 'CALLOC' + 312 | CALLOC (score_rows[i], len_x+1, DPScore_T); + | ^~~~~~ +In file included from align_lpo2.c:2: +align_lpo2.c: In function 'get_seq_left_and_final': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' - 199 | CALLOC (move, len_y, DPMove_T *); +align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC (is_final_node_x, len_x, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -728,62 +786,77 @@ | | | int | %ld -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' - 201 | CALLOC (move[i], len_x, DPMove_T); - | ^~~~~~ +align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' + 66 | CALLOC (x_left, len_x, LPOLetterLink_T *); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -align_lpo_po2.c: In function 'align_lpo_po': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' - 227 | CALLOC (next_gap_array, max_gap_length + 2, int); - | ^~~~~~ +align_lpo2.c:70:7: note: in expansion of macro 'CALLOC' + 70 | CALLOC (x_left[i], 1, LPOLetterLink_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' - 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); - | ^~~~~~ +msa_format.c: In function 'read_pir': +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:248:7: note: in expansion of macro 'REALLOC' + 248 | REALLOC (seq_names, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +msa_format.c:250:7: note: in expansion of macro 'REALLOC' + 250 | REALLOC (seq_titles, n_seqs, char *); + | ^~~~~~~ +default.h:196:39: note: format string is defined here + 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +align_lpo2.c: In function 'trace_back_lpo_alignment': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' - 204 | CALLOC (init_col_score, len_y+1, DPScore_T); +align_lpo2.c:96:3: note: in expansion of macro 'CALLOC' + 96 | CALLOC (x_al, len_x, LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -791,14 +864,13 @@ | | | int | %ld -msa_format.c: In function 'read_pir': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' - 207 | CALLOC (curr_score, len_x+1, DPScore_T); +align_lpo2.c:97:3: note: in expansion of macro 'CALLOC' + 97 | CALLOC (y_al, len_y, LPOLetterRef_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -811,8 +883,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:248:7: note: in expansion of macro 'REALLOC' - 248 | REALLOC (seq_names, n_seqs, char *); +msa_format.c:252:7: note: in expansion of macro 'REALLOC' + 252 | REALLOC (aln_mat, n_seqs, char *); | ^~~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ @@ -820,55 +892,80 @@ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' - 209 | CALLOC (prev_score, len_x+1, DPScore_T); - | ^~~~~~ default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:250:7: note: in expansion of macro 'REALLOC' - 250 | REALLOC (seq_titles, n_seqs, char *); +msa_format.c:254:7: note: in expansion of macro 'REALLOC' + 254 | REALLOC (aln_lengths, n_seqs, int); | ^~~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +align_lpo2.c: In function 'align_lpo': +align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] + 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + | ~~^ ~~~~~~~~~ + | | | + | long int int + | %d +default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 185 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ + | ~~~~~ +default.h:184:22: note: in definition of macro 'REALLOC' + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +default.h:184:68: note: format string is defined here + 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ~^ + | | + | int + | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' + 185 | CALLOC (next_gap_array, max_gap_length + 2, int); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] + 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + | ~~^ ~~~~~~~~~ + | | | + | long int int + | %d +default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:252:7: note: in expansion of macro 'REALLOC' - 252 | REALLOC (aln_mat, n_seqs, char *); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +msa_format.c:268:7: note: in expansion of macro 'REALLOC' + 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); | ^~~~~~~ -default.h:196:39: note: format string is defined here +default.h:196:34: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld + | ~^ + | | + | int + | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:254:7: note: in expansion of macro 'REALLOC' - 254 | REALLOC (aln_lengths, n_seqs, int); +msa_format.c:268:7: note: in expansion of macro 'REALLOC' + 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); | ^~~~~~~ default.h:196:39: note: format string is defined here 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ @@ -876,13 +973,14 @@ | | | int | %ld +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o buildup_lpo.o buildup_lpo.c default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | 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 *); +align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' + 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -895,23 +993,24 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' - 256 | CALLOC (move[i], len_x, DPMove_T); - | ^~~~~~ +align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' + 199 | CALLOC (move, len_y, DPMove_T *); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +msa_format.c: In function 'lpo_from_aln_mat': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' - 259 | CALLOC (init_col_score, len_y+1, DPScore_T); - | ^~~~~~ +align_lpo2.c:201:5: note: in expansion of macro 'CALLOC' + 201 | CALLOC (move[i], len_x, DPMove_T); + | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -923,8 +1022,16 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' - 262 | CALLOC (score_rows, len_y+1, DPScore_T *); +msa_format.c:318:3: note: in expansion of macro 'CALLOC' + 318 | CALLOC (column_ids, n_seqs+1, int *); + | ^~~~~~ +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' + 204 | CALLOC (init_col_score, len_y+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -937,8 +1044,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); +align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' + 207 | CALLOC (curr_score, len_x+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -946,54 +1053,13 @@ | | | int | %ld -default.h:184:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 185 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ - | ~~~~~ -default.h:184:22: note: in definition of macro 'REALLOC' - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -default.h:184:68: note: format string is defined here - 184 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -msa_format.c:268:7: note: in expansion of macro 'REALLOC' - 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ -default.h:196:34: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -msa_format.c:268:7: note: in expansion of macro 'REALLOC' - 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ -default.h:196:39: note: format string is defined here - 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -msa_format.c: In function 'lpo_from_aln_mat': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:318:3: note: in expansion of macro 'CALLOC' - 318 | CALLOC (column_ids, n_seqs+1, int *); +align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' + 209 | CALLOC (prev_score, len_x+1, DPScore_T); | ^~~~~~ default.h:155:37: note: format string is defined here 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1001,6 +1067,12 @@ | | | int | %ld +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1043,37 +1115,6 @@ | | | int | %ld -fasta_format.c: In function 'read_fasta': -fasta_format.c:48:9: warning: implicit declaration of function 'stringptr_cat_pos'; did you mean 'stringptr_cat'? [-Wimplicit-function-declaration] - 48 | stringptr_cat_pos(&tmp_seq,line,&length); - | ^~~~~~~~~~~~~~~~~ - | stringptr_cat -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -align_lpo_po2.c:312:5: note: in expansion of macro 'CALLOC' - 312 | CALLOC (score_rows[i], len_x+1, DPScore_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] - 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); - | ~~^ ~~~~~~~~~ - | | | - | long int int - | %d -align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] - 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); - | ~~^ ~~~~~~~~~ - | | | - | long int int - | %d default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1221,6 +1262,7 @@ | | | int | %ld +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo.o lpo.c In file included from buildup_lpo.c:3: buildup_lpo.c: In function 'clip_unaligned_ends': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -1294,7 +1336,6 @@ | | | int | %ld -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo.o lpo.c default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1352,6 +1393,15 @@ | | | int | %ld +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", + | ^~ default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1381,15 +1431,6 @@ | int | %ld gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o heaviest_bundle.o heaviest_bundle.c -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 lpo.c:3: lpo.c: In function 'lpo_init': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -1467,36 +1508,6 @@ | | | int | %ld -In file included from heaviest_bundle.c:3: -heaviest_bundle.c: In function 'heaviest_bundle': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' - 27 | CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' - 28 | CALLOC(score,len,LPOScore_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld default.h:196:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 196 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1529,49 +1540,6 @@ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' - 29 | CALLOC(contains_pos,nsource_seq,int); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' - 67 | CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -heaviest_bundle.c: In function 'assign_sequence_bundle_id': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' - 90 | CALLOC(bundle_count,seq->nsource_seq,int); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld lpo.c: In function 'add_lpo_link': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1762,7 +1730,79 @@ | int | %ld gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lpo_format.o lpo_format.c -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o create_seq.o create_seq.c +In file included from heaviest_bundle.c:3: +heaviest_bundle.c: In function 'heaviest_bundle': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:27:3: note: in expansion of macro 'CALLOC' + 27 | CALLOC(path,len,LPOLetterRef_T); /* GET MEMORY FOR DYNAMIC PROGRAMMING */ + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:28:3: note: in expansion of macro 'CALLOC' + 28 | CALLOC(score,len,LPOScore_T); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' + 29 | CALLOC(contains_pos,nsource_seq,int); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:67:3: note: in expansion of macro 'CALLOC' + 67 | CALLOC(best_path,len,LPOLetterRef_T); /* MEMORY FOR STORING BEST PATH */ + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +heaviest_bundle.c: In function 'assign_sequence_bundle_id': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' + 90 | CALLOC(bundle_count,seq->nsource_seq,int); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld In file included from lpo_format.c:3: lpo_format.c: In function 'read_lpo': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -2071,8 +2111,8 @@ 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 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o create_seq.o create_seq.c gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o remove_bundle.o remove_bundle.c -gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o numeric_data.o numeric_data.c In file included from create_seq.c:3: create_seq.c: In function 'create_seq': default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] @@ -2109,6 +2149,53 @@ | | | int | %ld +In file included from remove_bundle.c:4: +remove_bundle.c: In function 'compact_links': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' + 16 | CALLOC(link,1,LPOLetterLink_T); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +remove_bundle.c: In function 'compact_sources': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' + 59 | CALLOC(source,1,LPOLetterSource_T); + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +remove_bundle.c: In function 'remove_bundle': +default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | long unsigned int +remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' + 128 | CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ + | ^~~~~~ +default.h:155:37: note: format string is defined here + 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o numeric_data.o numeric_data.c In file included from ./lpo.h:6, from numeric_data.c:3: numeric_data.c: In function 'new_numeric_data': @@ -2164,52 +2251,6 @@ numeric_data.c:139:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 139 | fscanf(ifile," %lf",data->data+j); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from remove_bundle.c:4: -remove_bundle.c: In function 'compact_links': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' - 16 | CALLOC(link,1,LPOLetterLink_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -remove_bundle.c: In function 'compact_sources': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' - 59 | CALLOC(source,1,LPOLetterSource_T); - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -remove_bundle.c: In function 'remove_bundle': -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' - 128 | CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ - | ^~~~~~ -default.h:155:37: note: format string is defined here - 155 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld gcc -g -O2 -ffile-prefix-map=/build/poa-2.0+20060928=. -fstack-protector-strong -Wformat -Werror=format-security -g -DUSE_WEIGHTED_LINKS -DUSE_PROJECT_HEADER -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stringptr.o stringptr.c In file included from stringptr.c:2: stringptr.c: In function 'stringptr_cat_pos': @@ -2401,7 +2442,7 @@ 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.ZFViJXpcW5... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.cYB7oPOvJw... 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 @@ -2442,12 +2483,14 @@ 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/29834/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29834/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/30251 and its subdirectories -I: Current time: Sat May 18 12:39:59 -12 2024 -I: pbuilder-time-stamp: 1716079199 +I: removing directory /srv/workspace/pbuilder/29834 and its subdirectories +I: Current time: Mon Apr 17 08:18:07 +14 2023 +I: pbuilder-time-stamp: 1681669087