Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 07:21:19.226872779 +0000 +++ b2/build.log 2024-05-13 07:22:55.970753616 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 15 01:43:11 -12 2025 -I: pbuilder-time-stamp: 1749994991 +I: Current time: Mon May 13 21:21:22 +14 2024 +I: pbuilder-time-stamp: 1715584882 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying typo.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3069414/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/932717/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 13 07:21 /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/932717/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/932717/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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=20 ' + 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='dff8150c5a1a43189388c3af0f671d4f' - 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='3069414' - PS1='# ' - PS2='> ' + INVOCATION_ID=c4de8a95d5b644d28c4a4d116057c5e0 + 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=932717 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.BKmsuqbS/pbuilderrc_g82p --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.BKmsuqbS/b1 --logfile b1/build.log poa_2.0+20060928-9.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.BKmsuqbS/pbuilderrc_RkWb --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.BKmsuqbS/b2 --logfile b2/build.log poa_2.0+20060928-9.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 14 18:01 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3069414/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/932717/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -142,7 +174,7 @@ 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 13.15.3 [901 kB] -Fetched 19.0 MB in 1s (14.0 MB/s) +Fetched 19.0 MB in 1s (24.4 MB/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 ... 19699 files and directories currently installed.) @@ -277,7 +309,11 @@ 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+20060928-9_source.changes +I: user script /srv/workspace/pbuilder/932717/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/932717/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+20060928-9_source.changes dpkg-buildpackage: info: source package poa dpkg-buildpackage: info: source version 2.0+20060928-9 dpkg-buildpackage: info: source distribution unstable @@ -287,7 +323,7 @@ debian/rules clean dh clean dh_auto_clean - make -j42 clean + make -j20 clean make[1]: Entering directory '/build/reproducible-path/poa-2.0+20060928' rm -f align_score.o main.o black_flag.o seq_util.o fasta_format.o msa_format.o align_lpo2.o align_lpo_po2.o buildup_lpo.o lpo.o heaviest_bundle.o lpo_format.o create_seq.o remove_bundle.o numeric_data.o stringptr.o poa liblpo.a poa_doc libbflag.a make[1]: Leaving directory '/build/reproducible-path/poa-2.0+20060928' @@ -300,7 +336,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/poa-2.0+20060928' dh_auto_build -- poa - make -j42 "INSTALL=install --strip-program=true" poa + make -j20 "INSTALL=install --strip-program=true" poa make[2]: Entering directory '/build/reproducible-path/poa-2.0+20060928' gcc -g -O2 -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 align_score.o align_score.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 main.o main.c @@ -318,31 +354,15 @@ 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 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 stringptr.o stringptr.c -In file included from black_flag.c:4: -black_flag.c: In function 'black_flag_init_args': -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 -black_flag.c:109:3: note: in expansion of macro 'CALLOC' - 109 | CALLOC(Program_name,len,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 lpo.c:3: -lpo.c: In function 'lpo_init': +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 -lpo.c:15:3: note: in expansion of macro 'CALLOC' - 15 | CALLOC(seq->letter,seq->length,LPOLetter_T); +buildup_lpo.c:146:3: note: in expansion of macro 'CALLOC' + 146 | CALLOC(temp,seq->length,LPOLetter_T); /* ALLOCATE NEW letter[] COPY */ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -350,34 +370,28 @@ | | | int | %ld -In file included from align_lpo2.c:2: -align_lpo2.c: In function 'get_seq_left_and_final': +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 -align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC (is_final_node_x, len_x, int); +buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' + 327 | CALLOC (adj_score, nseq, 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 align_lpo_po2.c:2: -align_lpo_po2.c: In function 'get_lpo_stats': 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); +buildup_lpo.c:330:3: note: in expansion of macro 'CALLOC' + 330 | CALLOC (score_list, max_nscore, SeqPairScore_T); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -390,22 +404,51 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:169:7: note: in expansion of macro 'REALLOC' - 169 | REALLOC (seq_names, n_seqs, char *); - | ^~~~~~~ +buildup_lpo.c:353:9: note: in expansion of macro 'REALLOC' + 353 | 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:197:22: 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: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 +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 +buildup_lpo.c: In function 'buildup_progressive_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 -align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' - 66 | CALLOC (x_left, len_x, 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)); \ @@ -418,11 +461,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:42:3: note: in expansion of macro 'CALLOC' - 42 | CALLOC (refs_from_right, len, 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 */ | ^~~~~~ -In file included from heaviest_bundle.c:3: -heaviest_bundle.c: In function 'heaviest_bundle': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -434,8 +475,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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 */ +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)); \ @@ -448,8 +489,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' - 43 | CALLOC (tmp, len, int); +buildup_lpo.c:448:3: note: in expansion of macro 'CALLOC' + 448 | CALLOC(initial_nseq,nseq,int); /* COUNTS SEQS INITIALLY IN EACH CLUSTER (not updated w/ merges) */ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -457,41 +498,29 @@ | | | 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:171:7: note: in expansion of macro 'REALLOC' - 171 | 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: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); - | ^~~~~~ +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)); \ | ~^ | | | int | %ld +In file included from align_lpo_po2.c:2: +align_lpo_po2.c: In function 'get_lpo_stats': 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); +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)); \ @@ -499,43 +528,34 @@ | | | 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 -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: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:174:7: note: in expansion of macro 'REALLOC' - 174 | REALLOC (aln_mat, n_seqs, char *); - | ^~~~~~~ +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)); \ | ~^ | | | 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 -heaviest_bundle.c:29:3: note: in expansion of macro 'CALLOC' - 29 | CALLOC(contains_pos,nsource_seq,int); +align_lpo_po2.c:43:3: note: in expansion of macro 'CALLOC' + 43 | CALLOC (tmp, 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 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -550,20 +570,28 @@ | | | 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: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_lpo2.c: In function 'trace_back_lpo_alignment': +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_lpo2.c:96:3: note: in expansion of macro 'CALLOC' - 96 | CALLOC (x_al, len_x, LPOLetterRef_T); +align_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' + 120 | 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)); \ @@ -571,66 +599,43 @@ | | | int | %ld -In file included from lpo.h:6, - from main.c:3: -main.c: In function 'main': -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:156:20: 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:158:5: note: in expansion of macro 'CALLOC' - 158 | CALLOC(seq->source_seq[i].po_to_seq,seq->length,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 -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=] +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 -main.c:183:3: note: in expansion of macro 'CALLOC' - 183 | CALLOC (input_seqs, max_input_seqs, LPOSequence_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:156:37: note: format string is defined here +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 numeric_data.c:3: -numeric_data.c: In function 'new_numeric_data': 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:228:3: note: in expansion of macro 'CALLOC' + 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); | ^~~~~~ -In file included from buildup_lpo.c:3: -buildup_lpo.c: In function 'clip_unaligned_ends': -In file included from stringptr.c:2: -stringptr.c: In function 'stringptr_cat_pos': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -642,8 +647,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -stringptr.c:30:3: note: in expansion of macro 'CALLOC' - 30 | CALLOC(s2_temp,s2_len,char); /* ALLOCATE TEMP STORAGE */ +align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' + 254 | 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)); \ @@ -651,50 +656,41 @@ | | | int | %ld -./default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +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) } \ +align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' + 256 | CALLOC (move[i], len_x, DPMove_T); | ^~~~~~ -numeric_data.c:18:3: note: in expansion of macro 'REBUFF' - 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); - | ^~~~~~ -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +default.h:156:37: note: format string is defined here 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: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",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} - 186 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ - | ~~~~~ -msa_format.c:185:5: note: in expansion of macro 'REALLOC' - 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ + | ~^ + | | + | 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:159:5: note: in expansion of macro 'CALLOC' - 159 | CALLOC(seq->source_seq[i].sequence,seq->source_seq[i].length+1,char); - | ^~~~~~ +align_lpo_po2.c: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)); \ + | ~^ + | | + | 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 */ +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)); \ @@ -702,37 +698,58 @@ | | | 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)); \ | ~^ | | | 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:156:37: note: format string is defined here +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 + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ + | | + | 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld +align_lpo_po2.c:438:44: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'int' [-Wformat=] + 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + | ~~^ ~~~~~~~~~ + | | | + | long int int + | %d +align_lpo_po2.c:438:69: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'int' [-Wformat=] + 438 | fprintf (stderr, "aligned (%d nodes, %ld edges) to (%d nodes, %ld edges): ", len_x, n_edges_x, len_y, n_edges_y); + | ~~^ ~~~~~~~~~ + | | | + | long int int + | %d +In file included from 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=] 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:213:5: note: in expansion of macro 'CALLOC' + 213 | CALLOC(memptr,BUF,ATYPE) } \ + | ^~~~~~ +create_seq.c:29:3: note: in expansion of macro 'REBUFF' + 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -740,116 +757,62 @@ | | | 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:197:34: 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:185:5: note: in expansion of macro 'REALLOC' - 185 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), 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 -./default.h:216:5: note: in expansion of macro 'REALLOC' +default.h:216:5: note: in expansion of macro 'REALLOC' 216 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ | ^~~~~~~ -numeric_data.c:18:3: note: in expansion of macro 'REBUFF' - 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); +create_seq.c:29:3: note: in expansion of macro 'REBUFF' + 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ | ^~~~~~ -./default.h:197:39: note: format string is defined here +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 lpo_format.c:3: +lpo_format.c: In function 'read_lpo': +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 -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -stringptr.c:40:3: note: in expansion of macro 'GETMEM' - 40 | GETMEM(s1->p,total_len, +lpo_format.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC(seq,1,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 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': -lpo.c: In function 'save_lpo_source': -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 -heaviest_bundle.c:90:3: note: in expansion of macro 'CALLOC' - 90 | CALLOC(bundle_count,seq->nsource_seq,int); +align_lpo2.c:60:3: note: in expansion of macro 'CALLOC' + 60 | CALLOC (is_final_node_x, len_x, int); | ^~~~~~ -./default.h: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:221:9: note: in expansion of macro 'REALLOC' - 221 | REALLOC (input_seqs, max_input_seqs, LPOSequence_T *); - | ^~~~~~~ -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 -./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_lpo_po2.c:120:3: note: in expansion of macro 'CALLOC' - 120 | CALLOC (x_al, len_x, LPOLetterRef_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 -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, +align_lpo2.c:66:3: note: in expansion of macro 'CALLOC' + 66 | CALLOC (x_left, len_x, LPOLetterLink_T *); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -857,15 +820,13 @@ | | | int | %ld -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=] 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' - 185 | CALLOC (next_gap_array, max_gap_length + 2, int); +lpo_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)); \ @@ -873,6 +834,14 @@ | | | 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: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)); \ | ~^ @@ -884,8 +853,11 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' - 16 | CALLOC(link,1,LPOLetterLink_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)); \ @@ -893,27 +865,7 @@ | | | int | %ld -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)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ - | | - | long unsigned int -numeric_data.c:25:3: note: in expansion of macro 'CALLOC' - 25 | CALLOC(data->data,source_seq->length,double); /* ALLOCATE THE ARRAY */ - | ^~~~~~ -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,\ - | ^~~~~~~ +align_lpo2.c: In function 'trace_back_lpo_alignment': 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -922,41 +874,22 @@ default.h:246:5: note: in expansion of macro 'REALLOC' 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ | ^~~~~~~ -stringptr.c:40:3: note: in expansion of macro 'GETMEM' - 40 | GETMEM(s1->p,total_len, +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)); \ - | ~^ - | | - | 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 -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_lpo_po2.c:121:3: note: in expansion of macro 'CALLOC' - 121 | CALLOC (y_al, len_y, LPOLetterRef_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_format.c:60:3: note: in expansion of macro 'CALLOC' - 60 | CALLOC(seq,1,LPOSequence_T); +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)); \ @@ -964,6 +897,14 @@ | | | 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:73:3: note: in expansion of macro 'CALLOC' + 73 | CALLOC(pos_count,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)); \ | ~^ @@ -975,8 +916,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:186:3: note: in expansion of macro 'CALLOC' - 186 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); +align_lpo2.c: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)); \ @@ -984,91 +925,43 @@ | | | 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 -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:197:39: note: format string is defined here - 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ - | ~^ - | | - | int - | %ld -remove_bundle.c: In function 'compact_sources': +align_lpo2.c: In function 'align_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 -remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' - 59 | CALLOC(source,1,LPOLetterSource_T); +align_lpo2.c:185:3: note: in expansion of macro 'CALLOC' + 185 | CALLOC (next_gap_array, max_gap_length + 2, int); | ^~~~~~ -stringptr.c: In function 'stringptr_cpy': 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:148:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 148 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 149 | __FILE__,__LINE__,STRINGIFY(memptr),(N)); \ - | ~~~ -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ +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:71:3: note: in expansion of macro 'CALLOC' - 71 | CALLOC(seq->letter,length,LPOLetter_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:148:68: note: format string is defined here - 148 | 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 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: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 -align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' - 199 | CALLOC (move, len_y, DPMove_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)); \ @@ -1076,78 +969,28 @@ | | | int | %ld -default.h:155:20: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 155 | fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ -default.h:155:49: note: format string is defined here - 155 | fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ - | ~^ - | | - | int - | %ld -align_lpo_po2.c: In function 'align_lpo_po': -msa_format.c: In function 'read_pir': -default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ default.h: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); +align_lpo2.c:199:3: note: in expansion of macro 'CALLOC' + 199 | 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: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:197:39: 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_lpo_po2.c:227:3: note: in expansion of macro 'CALLOC' - 227 | CALLOC (next_gap_array, max_gap_length + 2, int); +lpo_format.c:170:3: note: in expansion of macro 'CALLOC' + 170 | CALLOC(seq->letter,length,LPOLetter_T); | ^~~~~~ -default.h:156:32: 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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1173,20 +1016,19 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:242:5: note: in expansion of macro 'CALLOC' - 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); +align_lpo2.c:204:3: note: in expansion of macro 'CALLOC' + 204 | CALLOC (init_col_score, len_y+1, DPScore_T); | ^~~~~~ -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 -lpo.c:213:3: note: in expansion of macro 'CALLOC' - 213 | CALLOC(list,nsource_seq,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); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1205,25 +1047,40 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:327:3: note: in expansion of macro 'CALLOC' - 327 | CALLOC (adj_score, nseq, int); +align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' + 207 | CALLOC (curr_score, len_x+1, DPScore_T); | ^~~~~~ -In file included from seq_util.c:2: -seq_util.c: In function 'read_score_matrix': +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:250:7: note: in expansion of macro 'REALLOC' - 250 | REALLOC (seq_titles, n_seqs, char *); - | ^~~~~~~ +default.h:246:5: note: in expansion of macro 'REALLOC' + 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +lpo_format.c:171:3: note: in expansion of macro 'GETMEM' + 171 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); + | ^~~~~~ default.h: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: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)); \ | ~^ @@ -1235,8 +1092,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:228:3: note: in expansion of macro 'CALLOC' - 228 | CALLOC (next_perp_gap_array, max_gap_length + 2, int); +lpo_format.c:172:3: note: in expansion of macro 'CALLOC' + 172 | CALLOC(pos_count,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)); \ @@ -1249,41 +1106,23 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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_format.c:196:3: note: in expansion of macro 'CALLOC' + 196 | CALLOC(iseq_compact,nsource_seq,int); | ^~~~~~ -remove_bundle.c: In function 'remove_bundle': 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 -default.h:246:5: note: in expansion of macro 'REALLOC' - 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -lpo_format.c:72:3: note: in expansion of macro 'GETMEM' - 72 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); - | ^~~~~~ default.h: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); +lpo_format.c:197:3: note: in expansion of macro 'CALLOC' + 197 | CALLOC(last_pos,nsource_seq,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:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1295,8 +1134,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' - 128 | CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ +lpo_format.c:198:3: note: in expansion of macro 'CALLOC' + 198 | CALLOC(match_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)); \ @@ -1304,53 +1143,27 @@ | | | int | %ld -lpo.c: In function 'add_lpo_link': -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)); \ - | ~~~~~ -default.h:246:5: note: in expansion of macro 'REALLOC' - 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ -default.h: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 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: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 */ +lpo_format.c:229:3: note: in expansion of macro 'CALLOC' + 229 | CALLOC(link_list,seq->length,int); /*TEMPORARY DATA FOR COMPACTION MAPPING */ | ^~~~~~ +default.h: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:73:3: note: in expansion of macro 'CALLOC' - 73 | CALLOC(pos_count,nsource_seq,int); +lpo_format.c:230:3: note: in expansion of macro 'CALLOC' + 230 | CALLOC(pos_compact,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)); \ @@ -1358,19 +1171,28 @@ | | | 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 +lpo_format.c:231:3: note: in expansion of macro 'CALLOC' + 231 | CALLOC(ring_old,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 +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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:207:3: note: in expansion of macro 'CALLOC' - 207 | CALLOC (curr_score, len_x+1, DPScore_T); +lpo_format.c:353:3: note: in expansion of macro 'CALLOC' + 353 | CALLOC(seq_pos,seq->nsource_seq,char *); /* ALLOCATE MAP ARRAY*/ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1378,83 +1200,131 @@ | | | 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)); \ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ -default.h:246:5: note: in expansion of macro 'REALLOC' - 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ default.h: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); +lpo_format.c:354:3: note: in expansion of macro 'CALLOC' + 354 | CALLOC(p,seq->nsource_seq*nring,char); | ^~~~~~ -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: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); - | ^~~~~~ +lpo_format.c:374:5: note: in expansion of macro 'CALLOC' + 374 | CALLOC(include_in_save,nring,char); /* BLANK FLAGS: WHAT RINGS TO SHOW*/ + | ^~~~~~ default.h: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:254:7: note: in expansion of macro 'REALLOC' - 254 | REALLOC (aln_lengths, n_seqs, int); - | ^~~~~~~ -default.h:156:37: note: format string is defined here +lpo_format.c: In function 'read_lpo': +lpo_format.c:61:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 61 | fscanf(ifile,"VERSION=%s",version); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:62:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 62 | fscanf(ifile," NAME=%[^\n]",name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:63:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 63 | fscanf(ifile," TITLE=%[^\n]",title); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:86:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 86 | fscanf(ifile,"%*[ \t]"); + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from lpo.h:6, + from main.c:3: +main.c: In function 'main': +./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 +main.c:183:3: note: in expansion of macro 'CALLOC' + 183 | CALLOC (input_seqs, max_input_seqs, 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:197:39: note: format string is defined here +./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:221:9: note: in expansion of macro 'REALLOC' + 221 | 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 -default.h:197:22: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=] +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 -default.h:246:5: note: in expansion of macro 'REALLOC' - 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -stringptr.c:67:3: note: in expansion of macro 'GETMEM' - 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); - | ^~~~~~ +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 +lpo_format.c: In function 'read_lpo_select': +lpo_format.c:160:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 160 | fscanf(ifile,"VERSION=%s",version); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:161:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 161 | fscanf(ifile," NAME=%[^\n]",name); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:162:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 162 | fscanf(ifile," TITLE=%[^\n]",title); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +lpo_format.c:185:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 185 | fscanf(ifile,"%*[ \t]"); + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from 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 -align_lpo_po2.c:254:3: note: in expansion of macro 'CALLOC' - 254 | CALLOC (move, len_y, DPMove_T *); +seq_util.c:170:3: note: in expansion of macro 'CALLOC' + 170 | CALLOC (m->gap_penalty_x, m->max_gap_length+2, LPOScore_T); | ^~~~~~ -lpo.c: In function 'add_lpo_sources': default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ @@ -1466,42 +1336,39 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo2.c:209:3: note: in expansion of macro 'CALLOC' - 209 | CALLOC (prev_score, len_x+1, DPScore_T); +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: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 +In file included from lpo.c:3: +lpo.c: In function 'lpo_init': 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); - | ^~~~~~ +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)); \ | ~^ | | | 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 -align_lpo_po2.c:256:5: note: in expansion of macro 'CALLOC' - 256 | CALLOC (move[i], len_x, DPMove_T); +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)); \ @@ -1509,43 +1376,31 @@ | | | 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); - | ^~~~~~~ -lpo.c: In function 'reindex_lpo_source_seqs': -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 -lpo.c:270:3: note: in expansion of macro 'CALLOC' - 270 | CALLOC (map, 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 -buildup_lpo.c:353:9: note: in expansion of macro 'REALLOC' - 353 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ +lpo.c:158:5: note: in expansion of macro 'CALLOC' + 158 | CALLOC(seq->source_seq[i].po_to_seq,seq->length,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 +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:169:7: note: in expansion of macro 'REALLOC' + 169 | 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)); \ | ~^ @@ -1557,63 +1412,58 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -align_lpo_po2.c:259:3: note: in expansion of macro 'CALLOC' - 259 | CALLOC (init_col_score, len_y+1, DPScore_T); - | ^~~~~~ +lpo.c:159:5: note: in expansion of macro 'CALLOC' + 159 | CALLOC(seq->source_seq[i].sequence,seq->source_seq[i].length+1,char); + | ^~~~~~ default.h:156:37: 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 'read_lpo_select': -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)); \ - | ~^ - | | - | 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 -lpo_format.c:159:3: note: in expansion of macro 'CALLOC' - 159 | CALLOC(seq,1,LPOSequence_T); +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)); \ + | ~^ + | | + | 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:268:7: note: in expansion of macro 'REALLOC' - 268 | REALLOC (aln_mat[curr_seq], aln_lengths[curr_seq] + strlen(aln), char); - | ^~~~~~~ +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: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 +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:271:3: note: in expansion of macro 'CALLOC' - 271 | CALLOC (invmap, len, 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)); \ @@ -1621,13 +1471,28 @@ | | | 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:171:7: note: in expansion of macro 'REALLOC' + 171 | REALLOC (seq_titles, n_seqs, char *); + | ^~~~~~~ +lpo.c: In function 'add_lpo_link': +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_lpo_po2.c:262:3: note: in expansion of macro 'CALLOC' - 262 | CALLOC (score_rows, len_y+1, DPScore_T *); +lpo.c:238:3: note: in expansion of macro 'CALLOC' + 238 | CALLOC(list->more,1,LPOLetterLink_T); /* ADD ENTRY TO LINKED LIST */ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1640,40 +1505,63 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:374:9: note: in expansion of macro 'REALLOC' - 374 | REALLOC (score_list, max_nscore, SeqPairScore_T); - | ^~~~~~~ +msa_format.c:174:7: note: in expansion of macro 'REALLOC' + 174 | 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 -numeric_data.c: In function 'read_numeric_data': +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 + 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),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 -align_lpo_po2.c:264:3: note: in expansion of macro 'CALLOC' - 264 | CALLOC (score_rows[-1], len_x+1, DPScore_T); - | ^~~~~~ +lpo.c:252:7: note: in expansion of macro 'CALLOC' + 252 | CALLOC(new_s->more,1,LPOLetterSource_T); + | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ | ~^ | | | int | %ld -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: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",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + | | + | size_t {aka long unsigned int} + 186 | __FILE__,__LINE__,STRINGIFY(memptr),(NUM)); \ + | ~~~~~ +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 -lpo_format.c:170:3: note: in expansion of macro 'CALLOC' - 170 | CALLOC(seq->letter,length,LPOLetter_T); +remove_bundle.c:16:3: note: in expansion of macro 'CALLOC' + 16 | CALLOC(link,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)); \ @@ -1681,45 +1569,47 @@ | | | int | %ld -msa_format.c: In function 'lpo_from_aln_mat': +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:185:5: note: in expansion of macro 'REALLOC' + 185 | 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)); \ + | ~^ + | | + | 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:394:9: note: in expansion of macro 'REALLOC' - 394 | 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 -msa_format.c:318:3: note: in expansion of macro 'CALLOC' - 318 | CALLOC (column_ids, n_seqs+1, 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); + | ^~~~~~~ +lpo.c: In function 'reindex_lpo_source_seqs': 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 +remove_bundle.c: In function 'compact_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 -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); +remove_bundle.c:59:3: note: in expansion of macro 'CALLOC' + 59 | CALLOC(source,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)); \ @@ -1732,16 +1622,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | 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); - | ^~~~~~ -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:319:3: note: in expansion of macro 'CALLOC' - 319 | CALLOC (res_ids, n_seqs+1, int *); +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)); \ @@ -1749,34 +1631,14 @@ | | | 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 create_seq.c:3: -create_seq.c: In function 'create_seq': -lpo.c: In function 'reindex_lpo_fusion': +remove_bundle.c: In function 'remove_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 -msa_format.c:326:5: note: in expansion of macro 'CALLOC' - 326 | CALLOC (column_ids[i], max_aln_length, int); - | ^~~~~~ -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:246:5: note: in expansion of macro 'REALLOC' - 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ - | ^~~~~~~ -lpo_format.c:171:3: note: in expansion of macro 'GETMEM' - 171 | GETMEM(seq->source_seq,nsource_seq,last_alloc,SOURCE_SEQ_BUFFER_CHUNK,LPOSourceInfo_T); +lpo.c:271:3: note: in expansion of macro 'CALLOC' + 271 | CALLOC (invmap, len, int); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1784,22 +1646,13 @@ | | | 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 -default.h:213:5: note: in expansion of macro 'CALLOC' - 213 | CALLOC(memptr,BUF,ATYPE) } \ - | ^~~~~~ -create_seq.c:29:3: note: in expansion of macro 'REBUFF' - 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ +remove_bundle.c:128:3: note: in expansion of macro 'CALLOC' + 128 | CALLOC(old_to_new,seq->length,int); /* CREATE MAPPING ARRAY */ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -1807,14 +1660,7 @@ | | | 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:445:3: note: in expansion of macro 'CALLOC' - 445 | CALLOC(seq_cluster,nseq,int); /* MAPS SEQS (or CLUSTERS) TO CLUSTER THEY'RE IN */ - | ^~~~~~ +lpo.c: In function 'reindex_lpo_fusion': 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)); \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ @@ -1829,33 +1675,57 @@ | | | 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 +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 -msa_format.c:327:5: note: in expansion of macro 'CALLOC' - 327 | CALLOC (res_ids[i], max_aln_length, int); - | ^~~~~~ +lpo.c:500:3: note: in expansion of macro 'CALLOC' + 500 | CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ + | ^~~~~~ 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: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); +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)); \ @@ -1868,27 +1738,30 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -default.h:216:5: note: in expansion of macro 'REALLOC' - 216 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ - | ^~~~~~~ -create_seq.c:29:3: note: in expansion of macro 'REBUFF' - 29 | REBUFF(*p_seq,nseq,SEQUENCE_BUFFER_CHUNK,Sequence_T); /* ALLOCATE MEMORY*/ - | ^~~~~~ -default.h: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 */ - | ^~~~~~ +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: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); +lpo.c:502:3: note: in expansion of macro 'CALLOC' + 502 | CALLOC(new_y,len_y,LPOLetterRef_T); | ^~~~~~ default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ @@ -1902,20 +1775,68 @@ | | | 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: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 */ + | ^~~~~~ 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': +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)); \ + | ~^ + | | + | 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:268:7: note: in expansion of macro 'REALLOC' + 268 | 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 +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 -buildup_lpo.c:447:3: note: in expansion of macro 'CALLOC' - 447 | CALLOC(cluster_size,nseq,int); /* COUNTS SEQS IN SAME CLUSTER (updated w/ merges) */ +lpo.c: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)); \ @@ -1923,13 +1844,14 @@ | | | int | %ld +lpo.c: In function '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 -msa_format.c:347:3: note: in expansion of macro 'CALLOC' - 347 | CALLOC (lposeq, 1, LPOSequence_T); +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)); \ @@ -1937,19 +1859,13 @@ | | | 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 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:196:3: note: in expansion of macro 'CALLOC' - 196 | CALLOC(iseq_compact,nsource_seq,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)); \ @@ -1957,21 +1873,42 @@ | | | 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 +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 -lpo.c:500:3: note: in expansion of macro 'CALLOC' - 500 | CALLOC(new_seq,1,LPOSequence_T); /* CREATE A NEW HOLDER */ +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)); \ + | ~^ + | | + | 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) */ +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)); \ @@ -1979,6 +1916,14 @@ | | | 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: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)); \ | ~^ @@ -1990,28 +1935,22 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:351:3: note: in expansion of macro 'CALLOC' - 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); - | ^~~~~~ +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 -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: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:197:3: note: in expansion of macro 'CALLOC' - 197 | CALLOC(last_pos,nsource_seq,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)); \ @@ -2024,8 +1963,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:501:3: note: in expansion of macro 'CALLOC' - 501 | CALLOC(new_x,len_x,LPOLetterRef_T); +msa_format.c:347:3: note: in expansion of macro 'CALLOC' + 347 | CALLOC (lposeq, 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)); \ @@ -2038,8 +1977,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:198:3: note: in expansion of macro 'CALLOC' - 198 | CALLOC(match_pos,nsource_seq,int); +msa_format.c:351:3: note: in expansion of macro 'CALLOC' + 351 | CALLOC (lposeq->sequence, max_aln_length+1, char); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2066,9 +2005,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:502:3: note: in expansion of macro 'CALLOC' - 502 | CALLOC(new_y,len_y,LPOLetterRef_T); - | ^~~~~~ +msa_format.c: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)); \ | ~^ @@ -2080,16 +2019,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -buildup_lpo.c:538:5: note: in expansion of macro 'CALLOC' - 538 | CALLOC (perm, nseq_tot, 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:375:5: note: in expansion of macro 'CALLOC' - 375 | CALLOC (curr_seq, 1, LPOSequence_T); +msa_format.c:380:5: note: in expansion of macro 'CALLOC' + 380 | CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2097,19 +2028,45 @@ | | | 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)); \ + | ~^ + | | + | int + | %ld +In file included from black_flag.c:4: +black_flag.c: In function 'black_flag_init_args': +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 +black_flag.c:109:3: note: in expansion of macro 'CALLOC' + 109 | CALLOC(Program_name,len,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 stringptr.c:2: +stringptr.c: In function 'stringptr_cat_pos': 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:229:3: note: in expansion of macro 'CALLOC' - 229 | CALLOC(link_list,seq->length,int); /*TEMPORARY DATA FOR COMPACTION MAPPING */ +stringptr.c:30:3: note: in expansion of macro 'CALLOC' + 30 | CALLOC(s2_temp,s2_len,char); /* ALLOCATE TEMP STORAGE */ | ^~~~~~ default.h:156:37: note: format string is defined here 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ @@ -2122,23 +2079,37 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -msa_format.c:380:5: note: in expansion of macro 'CALLOC' - 380 | CALLOC (curr_seq->sequence, aln_lengths[i]+1, char); +default.h:242:5: note: in expansion of macro 'CALLOC' + 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ | ^~~~~~ +stringptr.c:40:3: note: in expansion of macro 'GETMEM' + 40 | GETMEM(s1->p,total_len, + | ^~~~~~ default.h: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 +default.h:246:5: note: in expansion of macro 'REALLOC' + 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +stringptr.c:40:3: note: in expansion of macro 'GETMEM' + 40 | GETMEM(s1->p,total_len, + | ^~~~~~ default.h: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 */ - | ^~~~~~ +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)); \ | ~^ @@ -2150,22 +2121,23 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:230:3: note: in expansion of macro 'CALLOC' - 230 | CALLOC(pos_compact,seq->length,int); - | ^~~~~~ +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 +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:231:3: note: in expansion of macro 'CALLOC' - 231 | CALLOC(ring_old,seq->length,int); +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)); \ @@ -2173,72 +2145,149 @@ | | | 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)); \ | ~^ | | | 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=] +stringptr.c: In function 'stringptr_cpy': +default.h:148:22: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 148 | fprintf(stderr,"%s, line %d: *** invalid memory request: %s[%d].\n",\ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 149 | __FILE__,__LINE__,STRINGIFY(memptr),(N)); \ + | ~~~ +default.h:242:5: note: in expansion of macro 'CALLOC' + 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +default.h:148:68: note: format string is defined here + 148 | 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 'size_t' {aka 'long unsigned int'} [-Wformat=] + 155 | fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ +default.h:242:5: note: in expansion of macro 'CALLOC' + 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +default.h:155:49: note: format string is defined here + 155 | fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N)); \ + | ~^ + | | + | int + | %ld +default.h:156:20: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka '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:242:5: note: in expansion of macro 'CALLOC' + 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); | ^~~~~~ +default.h:156:32: 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:406:5: note: in expansion of macro 'CALLOC' - 406 | CALLOC (al_x, len, int); +default.h:242:5: note: in expansion of macro 'CALLOC' + 242 | CALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ | ^~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ default.h: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 +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)); \ + | ~~~~~ +default.h:246:5: note: in expansion of macro 'REALLOC' + 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +default.h: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)); \ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ +default.h:246:5: note: in expansion of macro 'REALLOC' + 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +default.h:197:34: 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 +default.h:246:5: note: in expansion of macro 'REALLOC' + 246 | REALLOC(memptr,((NUM)+1)-((NUM)+1)%(BUF)+(BUF),TYPE);\ + | ^~~~~~~ +stringptr.c:67:3: note: in expansion of macro 'GETMEM' + 67 | GETMEM(s1->p,strlen(s2)+1,s1->last_alloc,STRINGPTR_BUFFER_CHUNK,char); + | ^~~~~~ +default.h: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 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 -msa_format.c:407:5: note: in expansion of macro 'CALLOC' - 407 | CALLOC (al_y, lposeq->length, 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)); \ | ~^ | | | int | %ld -lpo_format.c: In function 'xlate_lpo_to_al': -lpo.c: In function '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_format.c:353:3: note: in expansion of macro 'CALLOC' - 353 | CALLOC(seq_pos,seq->nsource_seq,char *); /* ALLOCATE MAP ARRAY*/ +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)); \ @@ -2251,8 +2300,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo.c:618:3: note: in expansion of macro 'CALLOC' - 618 | CALLOC(new_x,len_x,LPOLetterRef_T); +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)); \ @@ -2265,8 +2314,8 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | long unsigned int -lpo_format.c:354:3: note: in expansion of macro 'CALLOC' - 354 | CALLOC(p,seq->nsource_seq*nring,char); +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)); \ @@ -2274,22 +2323,14 @@ | | | int | %ld -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 -msa_format.c:485:3: note: in expansion of macro 'CALLOC' - 485 | CALLOC (keep_seq, n_seqs, int); - | ^~~~~~ +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 -lpo.c:619:3: note: in expansion of macro 'CALLOC' - 619 | CALLOC(new_y,len_y,LPOLetterRef_T); +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)); \ @@ -2297,66 +2338,61 @@ | | | 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=] +In file included from ./lpo.h:6, + from numeric_data.c:3: +numeric_data.c: In function 'new_numeric_data': +./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:374:5: note: in expansion of macro 'CALLOC' - 374 | CALLOC(include_in_save,nring,char); /* BLANK FLAGS: WHAT RINGS TO SHOW*/ +./default.h:213:5: note: in expansion of macro 'CALLOC' + 213 | CALLOC(memptr,BUF,ATYPE) } \ | ^~~~~~ -default.h:156:37: note: format string is defined here +numeric_data.c:18:3: note: in expansion of macro 'REBUFF' + 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); + | ^~~~~~ +./default.h: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:197:22: 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 +./default.h:216:5: note: in expansion of macro 'REALLOC' + 216 | REALLOC(memptr,(NUM)+(BUF),ATYPE); \ + | ^~~~~~~ +numeric_data.c:18:3: note: in expansion of macro 'REBUFF' + 18 | REBUFF(source_seq->data,source_seq->ndata,NUMDATA_BUFFER_CHUNK,LPONumericData_T); + | ^~~~~~ +./default.h:197:39: note: format string is defined here 197 | fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE)); \ | ~^ | | | int | %ld -lpo_format.c: In function 'read_lpo': -lpo_format.c:61:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 61 | fscanf(ifile,"VERSION=%s",version); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:62:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 62 | fscanf(ifile," NAME=%[^\n]",name); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:63:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 63 | fscanf(ifile," TITLE=%[^\n]",title); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:86:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 86 | fscanf(ifile,"%*[ \t]"); - | ^~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c: In function 'read_lpo_select': -lpo_format.c:160:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 160 | fscanf(ifile,"VERSION=%s",version); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:161:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 161 | fscanf(ifile," NAME=%[^\n]",name); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:162:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 162 | fscanf(ifile," TITLE=%[^\n]",title); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -lpo_format.c:185:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 185 | fscanf(ifile,"%*[ \t]"); - | ^~~~~~~~~~~~~~~~~~~~~~~ +./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 +numeric_data.c:25:3: note: in expansion of macro 'CALLOC' + 25 | CALLOC(data->data,source_seq->length,double); /* ALLOCATE THE ARRAY */ + | ^~~~~~ +./default.h:156:37: note: format string is defined here + 156 | fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE)); \ + | ~^ + | | + | int + | %ld +numeric_data.c: In function 'read_numeric_data': +numeric_data.c:139:11: 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 /usr/include/string.h:548, from default.h:12: In function 'memset', @@ -2393,7 +2429,7 @@ 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.Av78gMsJb7... +...Wrote 4 sequences to CLUSTAL file /tmp/tmp.GG1eViZYWt... 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 @@ -2434,12 +2470,14 @@ 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/932717/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/932717/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/3069414 and its subdirectories -I: Current time: Sun Jun 15 01:44:18 -12 2025 -I: pbuilder-time-stamp: 1749995058 +I: removing directory /srv/workspace/pbuilder/932717 and its subdirectories +I: Current time: Mon May 13 21:22:55 +14 2024 +I: pbuilder-time-stamp: 1715584975