Diff of the two buildlogs: -- --- b1/build.log 2024-05-09 23:35:38.598436038 +0000 +++ b2/build.log 2024-05-09 23:36:07.273213714 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jun 11 17:58:16 -12 2025 -I: pbuilder-time-stamp: 1749707896 +I: Current time: Thu Jun 12 19:58:41 +14 2025 +I: pbuilder-time-stamp: 1749707921 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying remove-gets.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2099862/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3062494/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 12 05:58 /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/3062494/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3062494/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='508254b3a6b442a99b1b8ac5981ee277' - 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='2099862' - PS1='# ' - PS2='> ' + INVOCATION_ID=a71002beeac7482f939dc493134fe7ae + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3062494 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.Jz5KSqFd/pbuilderrc_WLpu --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.Jz5KSqFd/b1 --logfile b1/build.log codonw_1.4.4-8.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.Jz5KSqFd/pbuilderrc_VCb4 --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.Jz5KSqFd/b2 --logfile b2/build.log codonw_1.4.4-8.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 10 17:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2099862/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 9 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3062494/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] -Fetched 18.7 MB in 0s (144 MB/s) +Fetched 18.7 MB in 0s (136 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 ... 19744 files and directories currently installed.) @@ -282,7 +314,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/codonw-1.4.4/ && 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 > ../codonw_1.4.4-8_source.changes +I: user script /srv/workspace/pbuilder/3062494/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3062494/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/codonw-1.4.4/ && 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 > ../codonw_1.4.4-8_source.changes dpkg-buildpackage: info: source package codonw dpkg-buildpackage: info: source version 1.4.4-8 dpkg-buildpackage: info: source distribution unstable @@ -338,9 +374,41 @@ | ~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} +codon_us.c: In function 'codon_usage_out': +codons.c: In function 'main': +codons.c:190:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n", + | ~^ + | | + | int + | %li + 191 | num_sequence); + | ~~~~~~~~~~~~ + | | + | long int +codon_us.c:373:24: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 373 | fprintf(fblkout, "%i%c",nncod[x],sp); + | ~^ ~~~~~~~~ + | | | + | int long int + | %li open_fil.c:88:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:196:32: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in your" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 197 | " input file has\ninternal stop codons (found %i" + 198 | " internal stops) \tWARNING\n",num_seq_int_stop); + | ~~~~~~~~~~~~~~~~ + | | + | long int +codons.c:197:68: note: format string is defined here + 197 | " input file has\ninternal stop codons (found %i" + | ~^ + | | + | int + | %li open_fil.c:133:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 133 | fgets(answer, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -350,40 +418,84 @@ open_fil.c:186:21: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 186 | fgets(answer, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:200:46: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal " + | ~^ + | | + | int + | %li + 201 | "stop codons \tWARNING\n",num_seq_int_stop); + | ~~~~~~~~~~~~~~~~ + | | + | long int +codon_us.c: In function 'raau_usage_out': +codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] + 479 | fprintf(fblkout, "\n",sp); + | ^~~~ open_fil.c:88:13: warning: 'fgets' writing 8192 bytes into a region of size 90 overflows the destination [-Wstringop-overflow=] 88 | fgets(infile_name, BUFSIZ, stdin); /* get filename */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c: In function 'toutput': +codon_us.c: In function 'cbi_out': +codon_us.c:831:32: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] + 831 | sprintf(pm->messages, " Serious error in CBI information found" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 836 | pcbi->fop_cod[x], x); + | ~~~~~~~~~~~~~~~~ + | | + | int +codon_us.c:832:38: note: format string is defined here + 832 | " an illegal CBI value of %f for codon %i" + | ~^ + | | + | double + | %d +codon_us.c: In function 'fop_out': +codon_us.c:988:28: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] + 988 | sprintf(pm->messages, " Serious error in fop information found" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 993 | pfop->fop_cod[x], x); + | ~~~~~~~~~~~~~~~~ + | | + | int open_fil.c:71:12: note: destination object 'infile_name' of size 90 71 | char infile_name[MAX_FILENAME_LEN]=""; | ^~~~~~~~~~~ +tester.c: In function 'tester': +tester.c:88:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 88 | fgets( pm->junk , BUFSIZ, stdin) ; + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:964, from open_fil.c:47: /usr/include/aarch64-linux-gnu/bits/stdio2.h:195:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 195 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ -tester.c: In function 'tester': -tester.c:88:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 88 | fgets( pm->junk , BUFSIZ, stdin) ; - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 125 | fgets( pm->junk , BUFSIZ, stdin) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:170:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 170 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c: In function 'main': -codons.c:190:55: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 190 | fprintf(pm->my_err,"\n\n\t\tNumber of sequences: %i\n", - | ~^ - | | - | int - | %li - 191 | num_sequence); - | ~~~~~~~~~~~~ - | | - | long int -In file included from commline.c:28: -commline.c: In function 'proc_comm_line': +codon_us.c:989:37: note: format string is defined here + 989 | " an illegal fop value of %f for codon %l" + | ~^ + | | + | double + | %d +codon_us.c:988:28: warning: unknown conversion type character ' ' in format [-Wformat=] + 988 | sprintf(pm->messages, " Serious error in fop information found" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:990:11: note: format string is defined here + 990 | " permissible values are \n 1 for non-optimal" + | ^ +codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] + 988 | sprintf(pm->messages, " Serious error in fop information found" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:994:25: warning: unknown conversion type character ',' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^ In file included from tester.c:48: tester.c: In function 'asummary': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -392,54 +504,96 @@ tester.c:235:5: note: in expansion of macro 'pause' 235 | pause; | ^~~~~ -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -commline.c:103:9: note: in expansion of macro 'pause' - 103 | pause; - | ^~~~~ -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -commline.c:127:9: note: in expansion of macro 'pause' - 127 | pause; - | ^~~~~ -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -commline.c:142:9: note: in expansion of macro 'pause' - 142 | pause; - | ^~~~~ -codons.c:196:32: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 196 | fprintf(pm->my_err, "\tWARNING\t At least one sequence in your" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 197 | " input file has\ninternal stop codons (found %i" - 198 | " internal stops) \tWARNING\n",num_seq_int_stop); - | ~~~~~~~~~~~~~~~~ - | | - | long int -codons.c:197:68: note: format string is defined here - 197 | " input file has\ninternal stop codons (found %i" - | ~^ - | | - | int - | %li -codons.c:200:46: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal " - | ~^ - | | - | int - | %li - 201 | "stop codons \tWARNING\n",num_seq_int_stop); - | ~~~~~~~~~~~~~~~~ - | | - | long int +codon_us.c:994:33: warning: unknown conversion type character ',' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^ +codon_us.c:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^~ +codon_us.c:994:18: warning: too many arguments for format [-Wformat-extra-args] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=] + 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:641:11: note: format string is defined here + 641 | " =%5.3f\n" /* with G+C content and length of gene */ + | ^ +codon_us.c: In function 'gc_out': +codons.c:647:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " + | ~^ + | | + | int + | %ld + 648 | "in sequence %i\n" + 649 | ,non_std_char - IUBC_TOT + | ~~~~~~~~~~~~~~~~~~~~~~~ + | | + | long int +codon_us.c:1181:10: warning: too many arguments for format [-Wformat-extra-args] + 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c: In function 'textbin': +coresp.c:98:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 98 | fscanf(pm->fcoa_in,"%s",pm->junk); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:104:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 104 | fscanf(pm->fcoa_in,"%i",&v2); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:108:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 108 | fscanf(pm->fcoa_in,"%i\n",&v2); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:115:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 115 | fscanf(pm->fcoa_in,"%i",&v2); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:119:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 119 | fscanf(pm->fcoa_in,"%i\n",&v2); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:127:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 127 | fscanf(pm->fcoa_in,"%i",&v2); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:131:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last codon */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:647:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] + 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 650 | ,num_sequence); + | ~~~~~~~~~~~~ + | | + | long int +codons.c:648:25: note: format string is defined here + 648 | "in sequence %i\n" + | ~^ + | | + | int + | %li menu.c: In function 'printinfo': +coresp.c: In function 'rowout': +coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 277 | fgets(pm->junk,BUFSIZ,fnam); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:652:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n" + | ~~^ + | | + | int + | %3li + 653 | ,num_sequence + | ~~~~~~~~~~~~ + | | + | long int menu.c:1285:26: warning: field precision specifier '.*' expects argument of type 'int', but argument 2 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 1285 | printf("\tVersion : %.*s\n", strlen(Revision) , Revision ); | ~~^~ ~~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} +codon_us.c: In function 'dinuc_out': +codon_us.c:1476:39: warning: precision used with '%c' gnu_printf format [-Wformat=] + 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); + | ^ In file included from menu.c:31: menu.c: In function 'main_menu': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -448,7 +602,6 @@ menu.c:69:9: note: in expansion of macro 'pause' 69 | pause; | ^~~~~ -codons.c: In function 'toutput': menu.c: In function 'menu_initial': menu.c:106:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fgets(pm->junk, BUFSIZ, stdin); @@ -465,13 +618,71 @@ menu.c:132:17: note: in expansion of macro 'pause' 132 | pause; | ^~~~~ -codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=] - 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:641:11: note: format string is defined here - 641 | " =%5.3f\n" /* with G+C content and length of gene */ - | ^ menu.c: In function 'menu_2': +codons.c:657:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 657 | fprintf(pm->my_err, "\t\t WARNING %d non " + | ~^ + | | + | int + | %ld +...... + 660 | ,non_std_char + | ~~~~~~~~~~~~ + | | + | long int +codons.c:657:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] + 657 | fprintf(pm->my_err, "\t\t WARNING %d non " + | ^~~~~~~~~~~~~~~~~~~~~~ +...... + 661 | ,num_sequence); + | ~~~~~~~~~~~~ + | | + | long int +codon_us.c: In function 'hydro_out': +codons.c:659:25: note: format string is defined here + 659 | "in sequence %i\n" + | ~^ + | | + | int + | %li +coresp.c: In function 'inertialig': +coresp.c:1271:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1271 | fgets(pm->junk,BUFSIZ,fnam); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c:1315:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1315 | fgets(pm->junk,BUFSIZ,fnam); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c: In function 'output': +codon_us.c:2115:27: warning: too many arguments for format [-Wformat-extra-args] + 2115 | fprintf(pm->my_err, "No output was written to file \n", title); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from commline.c:28: +commline.c: In function 'proc_comm_line': +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:103:9: note: in expansion of macro 'pause' + 103 | pause; + | ^~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:127:9: note: in expansion of macro 'pause' + 127 | pause; + | ^~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:142:9: note: in expansion of macro 'pause' + 142 | pause; + | ^~~~~ +codon_us.c: In function 'aromo_out': +codons.c:800:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] + 800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog); + | ~^ ~~~~~~~~ + | | | + | char * int + | %d menu.c:233:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 233 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -481,40 +692,23 @@ menu.c:250:17: note: in expansion of macro 'pause' 250 | pause; | ^~~~~ -codons.c:647:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " - | ~^ - | | - | int - | %ld - 648 | "in sequence %i\n" - 649 | ,non_std_char - IUBC_TOT - | ~~~~~~~~~~~~~~~~~~~~~~~ - | | - | long int -In function 'fgets', - inlined from 'open_file' at open_fil.c:88:13: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 201 | return __fgets_chk_warn (__s, sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:647:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] - 647 | fprintf(pm->my_err, "\t\t WARNING %d non IUBC standard characters " - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 650 | ,num_sequence); - | ~~~~~~~~~~~~ - | | - | long int +codon_us.c:2148:27: warning: too many arguments for format [-Wformat-extra-args] + 2148 | fprintf(pm->my_err, "No output was written to file \n", title); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c: In function 'suprow': +coresp.c:1619:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1619 | fgets(pm->junk,BUFSIZ,fnam); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:805:32: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] + 805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog); + | ~^ ~~~~~~~~ + | | | + | char * int + | %d menu.c: In function 'menu_3': menu.c:305:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:648:25: note: format string is defined here - 648 | "in sequence %i\n" - | ~^ - | | - | int - | %li codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -536,28 +730,25 @@ menu.c:450:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:652:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 652 | fprintf(pm->my_err, "\t%3i>\t%6li %-40.40s\tPROTEIN\n" - | ~~^ - | | - | int - | %3li - 653 | ,num_sequence - | ~~~~~~~~~~~~ - | | - | long int -codons.c:657:42: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 657 | fprintf(pm->my_err, "\t\t WARNING %d non " - | ~^ - | | - | int - | %ld -...... - 660 | ,non_std_char - | ~~~~~~~~~~~~ - | | - | long int +In file included from codon_us.c:77: +codon_us.c: In function 'codon_error': +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:347:6: note: in expansion of macro 'pause' + 347 | pause; + | ^~~~~ menu.c: In function 'menu_4': +In file included from codons.c:90: +codons.c: In function 'main': +codon_us.c: In function 'cai_out': +codon_us.c:652:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 652 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'cbi_out': +codon_us.c:759:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 759 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:580:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 580 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -579,61 +770,27 @@ menu.c:660:17: note: in expansion of macro 'pause' 660 | pause; | ^~~~~ -codons.c:657:27: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] - 657 | fprintf(pm->my_err, "\t\t WARNING %d non " - | ^~~~~~~~~~~~~~~~~~~~~~ -...... - 661 | ,num_sequence); - | ~~~~~~~~~~~~ - | | - | long int -coresp.c: In function 'textbin': -coresp.c:98:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 98 | fscanf(pm->fcoa_in,"%s",pm->junk); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:104:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 104 | fscanf(pm->fcoa_in,"%i",&v2); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:108:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 108 | fscanf(pm->fcoa_in,"%i\n",&v2); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:115:10: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 115 | fscanf(pm->fcoa_in,"%i",&v2); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:119:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 119 | fscanf(pm->fcoa_in,"%i\n",&v2); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:127:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 127 | fscanf(pm->fcoa_in,"%i",&v2); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:131:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 131 | fscanf(pm->fcoa_in,"%i\n",&v2); /* read last codon */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'codon_usage_out': +codon_us.c: In function 'fop_out': +codon_us.c:899:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 899 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:957:14: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 957 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_5': -codons.c:659:25: note: format string is defined here - 659 | "in sequence %i\n" - | ~^ - | | - | int - | %li menu.c:764:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 764 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:814:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 814 | fgets( pm->junk , BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:373:24: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] - 373 | fprintf(fblkout, "%i%c",nncod[x],sp); - | ~^ ~~~~~~~~ - | | | - | int long int - | %li +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:204:35: note: in expansion of macro 'pause' + 204 | if ( pm->codonW && pm->menu ) pause; + | ^~~~~ menu.c: In function 'menu_6': -coresp.c: In function 'rowout': -coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 277 | fgets(pm->junk,BUFSIZ,fnam); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:844:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 844 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -643,9 +800,7 @@ menu.c:861:17: note: in expansion of macro 'pause' 861 | pause; | ^~~~~ -codons.c: In function 'output': menu.c: In function 'menu_7': -codon_us.c: In function 'raau_usage_out': menu.c:893:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 893 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -655,10 +810,29 @@ menu.c:912:17: note: in expansion of macro 'pause' 912 | pause; | ^~~~~ -codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] - 479 | fprintf(fblkout, "\n",sp); - | ^~~~ menu.c: In function 'menu_8': +codon_us.c: In function 'gen_cusort_fop': +codon_us.c:1699:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:1700:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c: In function 'chelp': +In function 'fgets', + inlined from 'open_file' at open_fil.c:88:13: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 201 | return __fgets_chk_warn (__s, sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:1703:8: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */ + | ^~~~~~~~~~~~~~~~~~~~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:1078:20: note: in expansion of macro 'pause' + 1078 | pause; /* make sure they Ack. the error mesg */ + | ^~~~~ menu.c:975:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 975 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -671,12 +845,21 @@ menu.c:1024:11: note: in expansion of macro 'pause' 1024 | pause; | ^~~~~ -codons.c:800:34: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] - 800 | fprintf(stderr, "ERROR-23 %s bulk undefined\n", pm->prog); - | ~^ ~~~~~~~~ - | | | - | char * int - | %d +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:1097:35: note: in expansion of macro 'pause' + 1097 | if ( line_counter )pause; + | ^~~~~ +codon_us.c:1711:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:1115:5: note: in expansion of macro 'pause' + 1115 | pause; + | ^~~~~ menu.c: In function 'menu_coa': menu.c:1067:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1067 | fgets(pm->junk, BUFSIZ, stdin); @@ -696,113 +879,6 @@ menu.c:1130:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1130 | fgets ( pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:805:32: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=] - 805 | fprintf(stderr, "ERROR-24 %s -prog undefined\n", pm->prog); - | ~^ ~~~~~~~~ - | | | - | char * int - | %d -menu.c: In function 'select_coa': -menu.c:1224:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1224 | fgets(pm->junk, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'cbi_out': -codon_us.c:831:32: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] - 831 | sprintf(pm->messages, " Serious error in CBI information found" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 836 | pcbi->fop_cod[x], x); - | ~~~~~~~~~~~~~~~~ - | | - | int -codon_us.c:832:38: note: format string is defined here - 832 | " an illegal CBI value of %f for codon %i" - | ~^ - | | - | double - | %d -coresp.c: In function 'inertialig': -coresp.c:1271:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1271 | fgets(pm->junk,BUFSIZ,fnam); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -coresp.c:1315:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1315 | fgets(pm->junk,BUFSIZ,fnam); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'fop_out': -In file included from codons.c:90: -codons.c: In function 'main': -codon_us.c:988:28: warning: format '%f' expects argument of type 'double', but argument 3 has type 'int' [-Wformat=] - 988 | sprintf(pm->messages, " Serious error in fop information found" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 993 | pfop->fop_cod[x], x); - | ~~~~~~~~~~~~~~~~ - | | - | int -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:204:35: note: in expansion of macro 'pause' - 204 | if ( pm->codonW && pm->menu ) pause; - | ^~~~~ -codon_us.c:989:37: note: format string is defined here - 989 | " an illegal fop value of %f for codon %l" - | ~^ - | | - | double - | %d -coresp.c: In function 'suprow': -coresp.c:1619:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1619 | fgets(pm->junk,BUFSIZ,fnam); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:988:28: warning: unknown conversion type character ' ' in format [-Wformat=] - 988 | sprintf(pm->messages, " Serious error in fop information found" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:990:11: note: format string is defined here - 990 | " permissible values are \n 1 for non-optimal" - | ^ -codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] - 988 | sprintf(pm->messages, " Serious error in fop information found" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:994:25: warning: unknown conversion type character ',' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^ -codon_us.c:994:33: warning: unknown conversion type character ',' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^ -codon_us.c:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^~ -codon_us.c:994:18: warning: too many arguments for format [-Wformat-extra-args] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'gc_out': -codon_us.c:1181:10: warning: too many arguments for format [-Wformat-extra-args] - 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c: In function 'chelp': -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:1078:20: note: in expansion of macro 'pause' - 1078 | pause; /* make sure they Ack. the error mesg */ - | ^~~~~ -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:1097:35: note: in expansion of macro 'pause' - 1097 | if ( line_counter )pause; - | ^~~~~ -codon_us.c: In function 'dinuc_out': -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codons.c:1115:5: note: in expansion of macro 'pause' - 1115 | pause; - | ^~~~~ -codon_us.c:1476:39: warning: precision used with '%c' gnu_printf format [-Wformat=] - 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); - | ^ codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -815,50 +891,10 @@ codons.c:1128:5: note: in expansion of macro 'pause' 1128 | pause; | ^~~~~ -codon_us.c: In function 'hydro_out': -codon_us.c:2115:27: warning: too many arguments for format [-Wformat-extra-args] - 2115 | fprintf(pm->my_err, "No output was written to file \n", title); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'aromo_out': -codon_us.c:2148:27: warning: too many arguments for format [-Wformat-extra-args] - 2148 | fprintf(pm->my_err, "No output was written to file \n", title); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from codon_us.c:77: -codon_us.c: In function 'codon_error': -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:347:6: note: in expansion of macro 'pause' - 347 | pause; - | ^~~~~ -codon_us.c: In function 'cai_out': -codon_us.c:652:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 652 | fgets(pm->junk, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'cbi_out': -codon_us.c:759:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 759 | fgets(pm->junk, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'fop_out': -codon_us.c:899:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 899 | fgets(pm->junk, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:957:14: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 957 | fgets(pm->junk, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'gen_cusort_fop': -codon_us.c:1699:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:1700:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:1703:8: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */ - | ^~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:1711:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +menu.c: In function 'select_coa': +menu.c:1224:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1224 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] 620 | printf("Could not open input file - %s\n", p ); | ^~ @@ -889,24 +925,24 @@ mkdir -p /build/reproducible-path/codonw-1.4.4/debian/man /build/reproducible-path/codonw-1.4.4/debian/make_man.pl /build/reproducible-path/codonw-1.4.4/debian/template.man \ /build/reproducible-path/codonw-1.4.4/debian/man -calculate Relative Synonymous Codon Usage (RSCU) -silent base G+C+A+T calculating program conceptual translation of DNA to amino acid -calculate Codon Bias Index (CBI) -calculate codon usage -calculate Codon Adaptation Index (CAI) -calculate Relative Amino Acid Usage (RAAU) -output sequence in reader format -calculate Effective Number of Codons (ENc) -GC of synonymous codons 3rd positions -clean up sequence in FASTA format detailed report of base composition +GC of synonymous codons 3rd positions +dinucleotide usage of the three codon positions G+C content of gene (all 3 codon positions) +output sequence in reader format +calculate Relative Synonymous Codon Usage (RSCU) calculate Amino Acid Usage (AAU) -dinucleotide usage of the three codon positions +calculate Relative Amino Acid Usage (RAAU) +calculate Effective Number of Codons (ENc) +calculate codon usage +clean up sequence in FASTA format tabulation of codon usage calculate Frequency of OPtimal codons index (FOP) +calculate Codon Bias Index (CBI) +calculate Codon Adaptation Index (CAI) tabulation of datasets codon usage +silent base G+C+A+T calculating program dh_installman -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_perl @@ -936,12 +972,14 @@ 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/3062494/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3062494/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/2099862 and its subdirectories -I: Current time: Wed Jun 11 17:58:37 -12 2025 -I: pbuilder-time-stamp: 1749707917 +I: removing directory /srv/workspace/pbuilder/3062494 and its subdirectories +I: Current time: Thu Jun 12 19:59:05 +14 2025 +I: pbuilder-time-stamp: 1749707945