Diff of the two buildlogs: -- --- b1/build.log 2023-04-14 23:19:57.975596132 +0000 +++ b2/build.log 2023-04-14 23:20:39.809738461 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 16 17:42:05 -12 2024 -I: pbuilder-time-stamp: 1715924525 +I: Current time: Sat Apr 15 13:20:01 +14 2023 +I: pbuilder-time-stamp: 1681514401 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./codonw_1.4.4.orig.tar.gz] I: copying [./codonw_1.4.4-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Feb 28 09:11:44 2023 -12 +gpgv: Signature made Wed Mar 1 11:11:44 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,11 +35,20 @@ dpkg-source: info: applying remove_nondeterminism I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/8425/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28054/tmp/hooks/D01_modify_environment starting +debug: Running on codethink14-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 +lrwxrwxrwx 1 root root 4 Jan 6 03:20 /bin/sh -> dash +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/28054/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28054/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME='pbuilder2' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' @@ -49,38 +58,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='8425' + PPID='28054' PS1='# ' PS2='> ' 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.zacPbnoY/pbuilderrc_UE57 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zacPbnoY/b1 --logfile b1/build.log codonw_1.4.4-7.dsc' + 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.zacPbnoY/pbuilderrc_NKg9 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.zacPbnoY/b2 --logfile b2/build.log --extrapackages usrmerge codonw_1.4.4-7.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink15-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 15 05:12 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/8425/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 14 00:50 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/28054/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -146,7 +155,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] -Fetched 18.3 MB in 0s (41.8 MB/s) +Fetched 18.3 MB in 0s (48.0 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 ... 19616 files and directories currently installed.) @@ -280,8 +289,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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_1.4.4-7_source.changes +I: user script /srv/workspace/pbuilder/28054/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/28054/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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_1.4.4-7_source.changes dpkg-buildpackage: info: source package codonw dpkg-buildpackage: info: source version 1.4.4-7 dpkg-buildpackage: info: source distribution unstable @@ -314,114 +332,6 @@ cc -c -g -O2 -ffile-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 menu.c cc -c -g -O2 -ffile-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 tester.c cc -c -g -O2 -ffile-prefix-map=/build/codonw-1.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -DLINUX -Wdate-time -D_FORTIFY_SOURCE=2 coresp.c -In file included from commline.c:28: -commline.c: In function 'proc_comm_line': -codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} - | ^~~~ -commline.c:103:9: note: in expansion of macro 'pause' - 103 | pause; - | ^~~~~ -open_fil.c: In function 'open_file': -open_fil.c:88:13: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] - 88 | gets(infile_name); /* get filename */ - | ^~~~ - | fgets -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:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 166 | fgets(temp, 3, stdin); - | ^~~~~~~~~~~~~~~~~~~~~ -In file included from codon_us.c:77: -codon_us.c: In function 'codon_error': -codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} - | ^~~~ -codon_us.c:347:6: note: in expansion of macro 'pause' - 347 | 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 -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); - | ^~~~ -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 -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from menu.c:31: menu.c: In function 'main_menu': codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] @@ -430,14 +340,6 @@ menu.c:69:9: note: in expansion of macro 'pause' 69 | pause; | ^~~~~ -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" - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ^ tester.c: In function 'tester': tester.c:88:17: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] 88 | gets( pm->junk ) ; @@ -485,14 +387,14 @@ codons.c:204:35: note: in expansion of macro 'pause' 204 | if ( pm->codonW && pm->menu ) 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 commline.c:28: +commline.c: In function 'proc_comm_line': +codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} + | ^~~~ +commline.c:103:9: note: in expansion of macro 'pause' + 103 | pause; + | ^~~~~ 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%" @@ -567,31 +469,126 @@ | | | | char * int | %d +open_fil.c: In function 'open_file': +open_fil.c:88:13: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] + 88 | gets(infile_name); /* get filename */ + | ^~~~ + | fgets 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 '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 */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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} 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} -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 */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +open_fil.c:166:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 166 | fgets(temp, 3, stdin); + | ^~~~~~~~~~~~~~~~~~~~~ +In file included from codon_us.c:77: +codon_us.c: In function 'codon_error': +codonW.h:38:74: warning: implicit declaration of function 'gets'; did you mean 'fgets'? [-Wimplicit-function-declaration] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");gets(pm->junk);} + | ^~~~ +codon_us.c:347:6: note: in expansion of macro 'pause' + 347 | 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 +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); + | ^~~~ +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 +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" + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 '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); @@ -618,6 +615,14 @@ coresp.c:277:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | 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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -629,6 +634,19 @@ 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: 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 */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~ commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] 620 | printf("Could not open input file - %s\n", p ); | ^~ @@ -661,24 +679,24 @@ mkdir -p /build/codonw-1.4.4/debian/man /build/codonw-1.4.4/debian/make_man.pl /build/codonw-1.4.4/debian/template.man \ /build/codonw-1.4.4/debian/man -calculate Relative Amino Acid Usage (RAAU) -calculate Relative Synonymous Codon Usage (RSCU) conceptual translation of DNA to amino acid calculate Frequency of OPtimal codons index (FOP) -tabulation of codon usage -calculate Amino Acid Usage (AAU) -calculate Effective Number of Codons (ENc) -detailed report of base composition -tabulation of datasets codon usage -calculate Codon Bias Index (CBI) silent base G+C+A+T calculating program G+C content of gene (all 3 codon positions) -calculate Codon Adaptation Index (CAI) +calculate Relative Synonymous Codon Usage (RSCU) +tabulation of codon usage +calculate Effective Number of Codons (ENc) clean up sequence in FASTA format -calculate codon usage output sequence in reader format -GC of synonymous codons 3rd positions +calculate codon usage +calculate Codon Bias Index (CBI) +calculate Codon Adaptation Index (CAI) +tabulation of datasets codon usage dinucleotide usage of the three codon positions +calculate Relative Amino Acid Usage (RAAU) +calculate Amino Acid Usage (AAU) +GC of synonymous codons 3rd positions +detailed report of base composition dh_installman -- make[1]: Leaving directory '/build/codonw-1.4.4' dh_perl @@ -708,12 +726,14 @@ 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/28054/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28054/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/8425 and its subdirectories -I: Current time: Thu May 16 17:42:56 -12 2024 -I: pbuilder-time-stamp: 1715924576 +I: removing directory /srv/workspace/pbuilder/28054 and its subdirectories +I: Current time: Sat Apr 15 13:20:38 +14 2023 +I: pbuilder-time-stamp: 1681514438