Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 07:17:25.712815420 +0000 +++ b2/build.log 2024-05-13 07:18:17.350616759 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 12 19:16:37 -12 2024 -I: pbuilder-time-stamp: 1715584597 +I: Current time: Mon Jun 16 03:40:29 +14 2025 +I: pbuilder-time-stamp: 1749994829 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/675035/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3033829/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Jun 15 13:40 /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/3033829/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3033829/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=20 ' - 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=42 ' + 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='3efc48e1ceaa4902b53d88cc70a9c8a6' - 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='675035' - PS1='# ' - PS2='> ' + INVOCATION_ID=24040c1b7d154e0398a3d4f758ea7744 + 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=3033829 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.4DKhYrAW/pbuilderrc_UnOG --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.4DKhYrAW/b1 --logfile b1/build.log codonw_1.4.4-8.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://46.16.76.132:3128' + 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.4DKhYrAW/pbuilderrc_Ul9F --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.4DKhYrAW/b2 --logfile b2/build.log codonw_1.4.4-8.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 10 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/675035/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 14 18:01 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3033829/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 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 0s (71.9 MB/s) +Fetched 19.0 MB in 2s (9246 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 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/3033829/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3033829/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 @@ -306,7 +342,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/codonw-1.4.4' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codon_us.c cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/codonw-1.4.4=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 codons.c @@ -350,6 +386,41 @@ 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: 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 +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 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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -361,6 +432,13 @@ /usr/include/x86_64-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) | ^~~~~ +codons.c: In function 'toutput': +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 */ + | ^ 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) ; @@ -371,16 +449,62 @@ 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: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 +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 In file included from tester.c:48: tester.c: In function 'asummary': -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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tester.c:235:5: note: in expansion of macro 'pause' 235 | pause; | ^~~~~ +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 +In file included from commline.c:28: +commline.c: In function 'proc_comm_line': +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 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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -399,73 +523,30 @@ commline.c:142:9: note: in expansion of macro 'pause' 142 | pause; | ^~~~~ -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 -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 menu.c: In function 'printinfo': +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 +codons.c:659:25: note: format string is defined here + 659 | "in sequence %i\n" + | ~^ + | | + | int + | %li 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} -coresp.c: In function 'textbin': codon_us.c: In function 'codon_usage_out': -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: In function 'output': In file included from menu.c:31: menu.c: In function 'main_menu': -codons.c: In function 'toutput': 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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -478,18 +559,13 @@ | | | | int long int | %li -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 */ - | ^ -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: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: In function 'menu_initial': -codon_us.c: In function 'raau_usage_out': menu.c:106:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 106 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -499,41 +575,23 @@ menu.c:122:29: note: in expansion of macro 'pause' 122 | pause; | ^~~~~ -codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] - 479 | fprintf(fblkout, "\n",sp); - | ^~~~ +codon_us.c: In function 'raau_usage_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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:132:17: note: in expansion of macro 'pause' 132 | 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 -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:479:21: warning: too many arguments for format [-Wformat-extra-args] + 479 | fprintf(fblkout, "\n",sp); + | ^~~~ +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_2': -codons.c:648:25: note: format string is defined here - 648 | "in sequence %i\n" - | ~^ - | | - | int - | %li menu.c:233:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 233 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -543,33 +601,6 @@ menu.c:250:17: note: in expansion of macro 'pause' 250 | pause; | ^~~~~ -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 -In function 'fgets', - inlined from 'open_file' at open_fil.c:88:13: -/usr/include/x86_64-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: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 -codon_us.c: In function 'cbi_out': 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); @@ -583,6 +614,7 @@ menu.c:345:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 345 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'cbi_out': menu.c:382:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -603,28 +635,20 @@ | ~~~~~~~~~~~~~~~~ | | | 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:832:38: note: format string is defined here 832 | " an illegal CBI value of %f for codon %i" | ~^ | | | double | %d -codons.c:659:25: note: format string is defined here - 659 | "in sequence %i\n" - | ~^ - | | - | int - | %li -codons.c: In function 'output': -codon_us.c: In function 'fop_out': +In file included from codons.c:90: +codons.c: In function 'main': +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_4': menu.c:580:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 580 | fgets(pm->junk, BUFSIZ, stdin); @@ -647,13 +671,7 @@ menu.c:660:17: note: in expansion of macro 'pause' 660 | pause; | ^~~~~ -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': 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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -662,12 +680,6 @@ | ~~~~~~~~~~~~~~~~ | | | int -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 codon_us.c:989:37: note: format string is defined here 989 | " an illegal fop value of %f for codon %l" | ~^ @@ -678,18 +690,12 @@ menu.c:764:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 764 | 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 -codon_us.c:988:28: warning: unknown conversion type character ' ' in format [-Wformat=] - 988 | sprintf(pm->messages, " Serious error in fop information found" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: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" | ^ @@ -706,14 +712,7 @@ codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] 988 | sprintf(pm->messages, " Serious error in fop information found" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_7': -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); - | ^ menu.c:893:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 893 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -723,25 +722,50 @@ menu.c:912:17: note: in expansion of macro 'pause' 912 | pause; | ^~~~~ +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); + | ^ +coresp.c: In function 'textbin': 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); | ^ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_8': -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); - | ^~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:975:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 975 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1007:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1007 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1024:11: note: in expansion of macro 'pause' 1024 | pause; | ^~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~ +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:994:18: warning: too many arguments for format [-Wformat-extra-args] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -761,68 +785,80 @@ menu.c:1117:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1117 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c: In function 'chelp': menu.c:1130:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1130 | fgets ( pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'gc_out': -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:1181:10: warning: too many arguments for format [-Wformat-extra-args] - 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from codons.c:90: -codons.c: In function 'main': -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: 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); - | ^ -codons.c: In function 'chelp': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 */ | ^~~~~ +codon_us.c: In function 'gc_out': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:1181:10: warning: too many arguments for format [-Wformat-extra-args] + 1181 | "Gene_description%cLen_aa%cLen_sym%cGC%cGC3s%cGCn3s%cGC1%cGC2" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: In function 'hydro_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:1124:4: note: in expansion of macro 'pause' 1124 | pause; | ^~~~~ -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:1128:5: note: in expansion of macro 'pause' 1128 | pause; | ^~~~~ +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); + | ^ +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 '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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +coresp.c: In function 'suprow': codon_us.c: In function 'aromo_out': +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: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 function 'fgets', + inlined from 'open_file' at open_fil.c:88:13: +/usr/include/x86_64-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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] @@ -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 +G+C content of gene (all 3 codon positions) calculate Effective Number of Codons (ENc) -calculate Codon Bias Index (CBI) -calculate codon usage -clean up sequence in FASTA format -calculate Relative Synonymous Codon Usage (RSCU) calculate Amino Acid Usage (AAU) -G+C content of gene (all 3 codon positions) tabulation of datasets codon usage -dinucleotide usage of the three codon positions +calculate Relative Amino Acid Usage (RAAU) +silent base G+C+A+T calculating program +detailed report of base composition +clean up sequence in FASTA format tabulation of codon usage +calculate codon usage +calculate Relative Synonymous Codon Usage (RSCU) output sequence in reader format -conceptual translation of DNA to amino acid +GC of synonymous codons 3rd positions +dinucleotide usage of the three codon positions +calculate Codon Bias Index (CBI) calculate Codon Adaptation Index (CAI) calculate Frequency of OPtimal codons index (FOP) -GC of synonymous codons 3rd positions -detailed report of base composition -calculate Relative Amino Acid Usage (RAAU) -silent base G+C+A+T calculating program +conceptual translation of DNA to amino acid dh_installman -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_perl @@ -927,8 +963,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_amd64.deb'. dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_amd64.deb'. +dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_amd64.buildinfo dpkg-genchanges --build=binary -O../codonw_1.4.4-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -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/3033829/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3033829/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/675035 and its subdirectories -I: Current time: Sun May 12 19:17:24 -12 2024 -I: pbuilder-time-stamp: 1715584644 +I: removing directory /srv/workspace/pbuilder/3033829 and its subdirectories +I: Current time: Mon Jun 16 03:41:16 +14 2025 +I: pbuilder-time-stamp: 1749994876