Diff of the two buildlogs: -- --- b1/build.log 2024-04-30 07:22:01.049051940 +0000 +++ b2/build.log 2024-04-30 07:23:25.753447376 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 29 19:20:32 -12 2024 -I: pbuilder-time-stamp: 1714461632 +I: Current time: Tue Apr 30 21:22:14 +14 2024 +I: pbuilder-time-stamp: 1714461734 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/21661/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1830/tmp/hooks/D01_modify_environment starting +debug: Running on virt32c. +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 Apr 30 07:22 /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/1830/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1830/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='06b18e179a174c07966cf214e71642e4' - 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='21661' - PS1='# ' - PS2='> ' + INVOCATION_ID=df06f6c3ea7c41d4be2553539c8bfeca + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=1830 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.kGfB7pkR/pbuilderrc_T9V8 --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.kGfB7pkR/b1 --logfile b1/build.log codonw_1.4.4-8.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.kGfB7pkR/pbuilderrc_2V5y --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.kGfB7pkR/b2 --logfile b2/build.log codonw_1.4.4-8.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 28 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/21661/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 27 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1830/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 armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] -Fetched 18.4 MB in 1s (28.8 MB/s) +Fetched 18.4 MB in 0s (42.5 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 ... 19470 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/1830/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1830/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 @@ -306,11 +342,12 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 codons.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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 open_fil.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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 commline.c open_fil.c: In function 'open_file': 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 */ @@ -335,6 +372,26 @@ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ +In file included from commline.c:28: +commline.c: In function 'proc_comm_line': +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:103:9: note: in expansion of macro 'pause' + 103 | pause; + | ^~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:127:9: note: in expansion of macro 'pause' + 127 | pause; + | ^~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:142:9: note: in expansion of macro 'pause' + 142 | pause; + | ^~~~~ codon_us.c: In function '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); @@ -346,7 +403,42 @@ codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] 479 | fprintf(fblkout, "\n",sp); | ^~~~ +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 codon_us.c: In function 'cbi_out': +codons.c:200:46: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] + 200 | fprintf(pm->my_err, "\tWARNING\t %i sequences had internal " + | ~^ + | | + | int + | %li + 201 | "stop codons \tWARNING\n",num_seq_int_stop); + | ~~~~~~~~~~~~~~~~ + | | + | long int codon_us.c: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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -388,70 +480,16 @@ 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); - | ^ -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 codons.c: In function 'toutput': -codon_us.c: In function 'hydro_out': codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=] 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:641:11: note: format string is defined here 641 | " =%5.3f\n" /* with G+C content and length of gene */ | ^ -codon_us.c: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:994:33: warning: unknown conversion type character ',' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^ 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 " | ~^ @@ -463,6 +501,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long int +codon_us.c:994:44: warning: unknown conversion type character '\x0a' in format [-Wformat=] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^~ +codon_us.c:994:18: warning: too many arguments for format [-Wformat-extra-args] + 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c: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 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -477,9 +521,6 @@ | | | int | %li -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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" | ~~^ @@ -490,14 +531,10 @@ | ~~~~~~~~~~~~ | | | long int -In file included from codon_us.c:77: -codon_us.c: In function 'codon_error': -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c:347:6: note: in expansion of macro 'pause' - 347 | pause; - | ^~~~~ +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: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 " | ~^ @@ -523,39 +560,29 @@ | | | int | %li -In function 'fgets', - inlined from 'open_file' at open_fil.c:88:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 215 | return __fgets_chk_warn (__s, sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'dinuc_out': codons.c: In function 'output': +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: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: 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': 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: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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'fgets', + inlined from 'open_file' at open_fil.c:88:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 215 | return __fgets_chk_warn (__s, sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'hydro_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] @@ -564,19 +591,21 @@ codons.c:204:35: note: in expansion of macro 'pause' 204 | if ( pm->codonW && pm->menu ) pause; | ^~~~~ -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 */ - | ^~~~~~~~~~~~~~~~~~~~~~~~~ +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; + | ^~~~~ 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);} @@ -590,12 +619,16 @@ codons.c:1097:35: note: in expansion of macro 'pause' 1097 | if ( line_counter )pause; | ^~~~~ +codon_us.c: In function 'cai_out': codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c:1115:5: note: in expansion of macro 'pause' 1115 | pause; | ^~~~~ +codon_us.c:652:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 652 | 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);} | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -608,32 +641,31 @@ codons.c:1128:5: note: in expansion of macro 'pause' 1128 | pause; | ^~~~~ -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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 commline.c -In file included from commline.c:28: -commline.c: In function 'proc_comm_line': -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -commline.c:103:9: note: in expansion of macro 'pause' - 103 | pause; - | ^~~~~ -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -commline.c:127:9: note: in expansion of macro 'pause' - 127 | pause; - | ^~~~~ -codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -commline.c:142:9: note: in expansion of macro 'pause' - 142 | pause; - | ^~~~~ -commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] - 620 | printf("Could not open input file - %s\n", p ); - | ^~ +codon_us.c: In function 'cbi_out': +codon_us.c:759:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 759 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'fop_out': +codon_us.c:899:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 899 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:957:14: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 957 | fgets(pm->junk, BUFSIZ, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c: In function 'gen_cusort_fop': +codon_us.c:1699:8: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1699 | fgets(pm->junk, BUFSIZ,fnam);/* by scanning for lines of CU in */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:1700:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1700 | fscanf(fnam, "%s", pm->junk); /* now we know the name of seq i */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:1703:8: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1703 | fscanf(fnam, "%f", &v2); /* assign it initially to v2 */ + | ^~~~~~~~~~~~~~~~~~~~~~~ +codon_us.c:1711:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1711 | fscanf(fnam, "%f\n", &v2); /* now read the last codon in */ + | ^~~~~~~~~~~~~~~~~~~~~~~~~ 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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 tester.c 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] @@ -778,6 +810,10 @@ menu.c:1224:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1224 | fgets(pm->junk, BUFSIZ, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:620:48: warning: '%s' directive argument is null [-Wformat-overflow=] + 620 | printf("Could not open input file - %s\n", p ); + | ^~ +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 -DLINUX -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 tester.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) ; @@ -861,24 +897,24 @@ 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 -conceptual translation of DNA to amino acid -calculate codon usage -G+C content of gene (all 3 codon positions) -GC of synonymous codons 3rd positions +tabulation of codon usage calculate Codon Bias Index (CBI) -calculate Relative Synonymous Codon Usage (RSCU) -calculate Codon Adaptation Index (CAI) +G+C content of gene (all 3 codon positions) +clean up sequence in FASTA format +calculate Amino Acid Usage (AAU) calculate Effective Number of Codons (ENc) calculate Frequency of OPtimal codons index (FOP) +calculate Relative Amino Acid Usage (RAAU) +output sequence in reader format +calculate Relative Synonymous Codon Usage (RSCU) +conceptual translation of DNA to amino acid dinucleotide usage of the three codon positions -tabulation of datasets codon usage +calculate codon usage silent base G+C+A+T calculating program -output sequence in reader format -calculate Relative Amino Acid Usage (RAAU) +calculate Codon Adaptation Index (CAI) detailed report of base composition -tabulation of codon usage -clean up sequence in FASTA format -calculate Amino Acid Usage (AAU) +GC of synonymous codons 3rd positions +tabulation of datasets codon usage dh_installman -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_perl @@ -899,8 +935,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_armhf.deb'. dpkg-deb: building package 'codonw' in '../codonw_1.4.4-8_armhf.deb'. +dpkg-deb: building package 'codonw-dbgsym' in '../codonw-dbgsym_1.4.4-8_armhf.deb'. dpkg-genbuildinfo --build=binary -O../codonw_1.4.4-8_armhf.buildinfo dpkg-genchanges --build=binary -O../codonw_1.4.4-8_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -908,12 +944,14 @@ 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/1830/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1830/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/21661 and its subdirectories -I: Current time: Mon Apr 29 19:21:56 -12 2024 -I: pbuilder-time-stamp: 1714461716 +I: removing directory /srv/workspace/pbuilder/1830 and its subdirectories +I: Current time: Tue Apr 30 21:23:19 +14 2024 +I: pbuilder-time-stamp: 1714461799