Diff of the two buildlogs: -- --- b1/build.log 2025-02-11 09:26:46.460757563 +0000 +++ b2/build.log 2025-02-11 09:27:32.322694210 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Feb 10 21:26:22 -12 2025 -I: pbuilder-time-stamp: 1739265982 +I: Current time: Tue Mar 17 05:49:49 +14 2026 +I: pbuilder-time-stamp: 1773676189 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ 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/2594876/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2762068/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 Mar 16 15:49 /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/2762068/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2762068/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=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='252e7bd3ff054763bf19243c1947eb35' - 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='2594876' - PS1='# ' - PS2='> ' + INVOCATION_ID=3aca9795af694657b82de6b2bd0c2331 + 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=2762068 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.6HRUcWck/pbuilderrc_5wVC --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.6HRUcWck/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.6HRUcWck/pbuilderrc_5Go3 --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.6HRUcWck/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 codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2594876/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2762068/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -90,7 +122,7 @@ Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19954 files and directories currently installed.) +(Reading database ... 19920 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -143,10 +175,10 @@ 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 13.24.1 [920 kB] -Fetched 20.1 MB in 0s (142 MB/s) +Fetched 20.1 MB in 0s (79.7 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19954 files and directories currently installed.) +(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 ... 19920 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. @@ -278,7 +310,11 @@ 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/2762068/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2762068/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 @@ -311,70 +347,6 @@ 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 -mbranch-protection=standard -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 menu.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 -mbranch-protection=standard -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 tester.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 -mbranch-protection=standard -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -open_fil.c: In function 'open_file': -open_fil.c:128:28: warning: field precision specifier '.*' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 128 | fprintf(stderr,"\nThese are the files in the current directory " - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); - | ~~~~~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -open_fil.c:129:34: note: format string is defined here - 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); - | ~~^~ - | | - | int -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] - 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; - | ^~~~~ -open_fil.c:162:52: warning: field precision specifier '.*' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] - 162 | fprintf(stderr, "\nWarning :File %.*s " - | ~~^~ - | | - | int -...... - 165 | strlen(infile_name), infile_name); - | ~~~~~~~~~~~~~~~~~~~ - | | - | size_t {aka long unsigned int} -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 */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -open_fil.c:133:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 133 | fgets(answer, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 166 | fgets(temp, 3, stdin); - | ^~~~~~~~~~~~~~~~~~~~~ -open_fil.c:186:21: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 186 | fgets(answer, BUFSIZ, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -open_fil.c:71:12: note: destination object 'infile_name' of size 90 - 71 | char infile_name[MAX_FILENAME_LEN]=""; - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from open_fil.c:47: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' - 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, - | ^~~~~ 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", @@ -386,7 +358,6 @@ | ~~~~~~~~~~~~ | | | long int -coresp.c: In function 'textbin': 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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -395,33 +366,12 @@ | ~~~~~~~~~~~~~~~~ | | | long int -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:197:68: note: format string is defined here 197 | " input file has\ninternal stop codons (found %i" | ~^ | | | int | %li -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: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 " | ~^ @@ -432,10 +382,41 @@ | ~~~~~~~~~~~~~~~~ | | | long int -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +open_fil.c: In function 'open_file': +open_fil.c:128:28: warning: field precision specifier '.*' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 128 | fprintf(stderr,"\nThese are the files in the current directory " + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); + | ~~~~~~~~~~~~~~~~~~~ + | | + | size_t {aka long unsigned int} +open_fil.c:129:34: note: format string is defined here + 129 | "I cannot find %.*s \n\n",strlen(infile_name),infile_name); + | ~~^~ + | | + | int +open_fil.c:162:52: warning: field precision specifier '.*' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] + 162 | fprintf(stderr, "\nWarning :File %.*s " + | ~~^~ + | | + | int +...... + 165 | strlen(infile_name), infile_name); + | ~~~~~~~~~~~~~~~~~~~ + | | + | size_t {aka long unsigned int} +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 */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +open_fil.c:133:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 133 | fgets(answer, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 166 | fgets(temp, 3, stdin); + | ^~~~~~~~~~~~~~~~~~~~~ +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 '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%" @@ -462,19 +443,43 @@ | ~~~~~~~~~~~~ | | | long int +codon_us.c: In function 'codon_usage_out': +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 +In file included from commline.c:28: +commline.c: In function 'proc_comm_line': +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);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~ +codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] + 479 | fprintf(fblkout, "\n",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);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:142:9: note: in expansion of macro 'pause' + 142 | pause; + | ^~~~~ codons.c:648:25: note: format string is defined here 648 | "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: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" | ~~^ @@ -496,11 +501,6 @@ | ~~~~~~~~~~~~ | | | long int -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 '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 " | ^~~~~~~~~~~~~~~~~~~~~~ @@ -515,12 +515,134 @@ | | | int | %li +codons.c: In function 'output': +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 +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 +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 */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +open_fil.c:71:12: note: destination object 'infile_name' of size 90 + 71 | char infile_name[MAX_FILENAME_LEN]=""; + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from open_fil.c:47: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' + 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, + | ^~~~~ +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 +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: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); + | ^ +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; + | ^~~~~ +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; + | ^~~~~ +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: 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:1128:5: note: in expansion of macro 'pause' + 1128 | 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); + | ^ +menu.c: In function 'printinfo': 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} -codons.c: In function 'output': 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] @@ -529,12 +651,6 @@ menu.c:69:9: note: in expansion of macro 'pause' 69 | 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 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); @@ -551,12 +667,40 @@ menu.c:132:17: note: in expansion of macro 'pause' 132 | pause; | ^~~~~ -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: In function 'hydro_out': +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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': +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] + 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; + | ^~~~~ +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; + | ^~~~~ menu.c: In function 'menu_2': menu.c:233:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 233 | fgets(pm->junk, BUFSIZ, stdin); @@ -567,13 +711,6 @@ menu.c:250:17: note: in expansion of macro 'pause' 250 | pause; | ^~~~~ -codon_us.c: In function 'codon_usage_out': -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 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); @@ -599,18 +736,6 @@ menu.c:450:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 450 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^~~~ -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); @@ -633,21 +758,18 @@ menu.c:660:17: note: in expansion of macro 'pause' 660 | 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: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: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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c: In function 'menu_5': menu.c:764:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 764 | fgets(pm->junk, BUFSIZ, stdin); @@ -665,7 +787,6 @@ menu.c:861:17: note: in expansion of macro 'pause' 861 | pause; | ^~~~~ -codon_us.c: In function 'fop_out': menu.c: In function 'menu_7': menu.c:893:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 893 | fgets(pm->junk, BUFSIZ, stdin); @@ -676,20 +797,6 @@ menu.c:912:17: note: in expansion of macro 'pause' 912 | pause; | ^~~~~ -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 -codon_us.c:989:37: note: format string is defined here - 989 | " an illegal fop value of %f for codon %l" - | ~^ - | | - | double - | %d menu.c: In function 'menu_8': menu.c:975:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 975 | fgets(pm->junk, BUFSIZ, stdin); @@ -703,16 +810,7 @@ menu.c:1024:11: note: in expansion of macro 'pause' 1024 | pause; | ^~~~~ -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" - | ^ menu.c: In function 'menu_coa': -codon_us.c:988:28: warning: too many arguments for format [-Wformat-extra-args] - 988 | sprintf(pm->messages, " Serious error in fop information found" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ menu.c:1067:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1067 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -731,114 +829,10 @@ 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: In function 'chelp': -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 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; - | ^~~~~ -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); - | ^ -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; - | ^~~~~ -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: 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:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^~ -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:994:18: warning: too many arguments for format [-Wformat-extra-args] - 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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; - | ^~~~~ -In function 'fgets', - inlined from 'open_file' at open_fil.c:88:13: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: In function 'gc_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:1128:5: note: in expansion of macro 'pause' - 1128 | 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" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^ -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -855,6 +849,48 @@ 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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'open_file' at open_fil.c:88:13: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:316:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] 620 | printf("Could not open input file - %s\n", p ); | ^~ @@ -885,24 +921,24 @@ 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 +detailed report of base composition calculate Relative Synonymous Codon Usage (RSCU) -calculate Relative Amino Acid Usage (RAAU) -clean up sequence in FASTA format -tabulation of datasets codon usage +calculate Frequency of OPtimal codons index (FOP) +calculate Amino Acid Usage (AAU) +G+C content of gene (all 3 codon positions) calculate Codon Bias Index (CBI) +tabulation of datasets codon usage +clean up sequence in FASTA format +output sequence in reader format tabulation of codon usage -calculate codon usage -conceptual translation of DNA to amino acid +calculate Relative Amino Acid Usage (RAAU) calculate Codon Adaptation Index (CAI) +calculate codon usage silent base G+C+A+T calculating program -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 -G+C content of gene (all 3 codon positions) -calculate Amino Acid Usage (AAU) -detailed report of base composition calculate Effective Number of Codons (ENc) -calculate Frequency of OPtimal codons index (FOP) 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' in '../codonw_1.4.4-8_arm64.deb'. dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_arm64.deb'. +dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_arm64.buildinfo dpkg-genchanges --build=binary -O../codonw_1.4.4-8_arm64.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/2762068/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2762068/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/2594876 and its subdirectories -I: Current time: Mon Feb 10 21:26:45 -12 2025 -I: pbuilder-time-stamp: 1739266005 +I: removing directory /srv/workspace/pbuilder/2762068 and its subdirectories +I: Current time: Tue Mar 17 05:50:31 +14 2026 +I: pbuilder-time-stamp: 1773676231