Diff of the two buildlogs: -- --- b1/build.log 2024-05-23 16:51:54.752488034 +0000 +++ b2/build.log 2024-05-23 16:55:55.258240736 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 23 04:44:46 -12 2024 -I: pbuilder-time-stamp: 1716482686 +I: Current time: Fri May 24 06:52:04 +14 2024 +I: pbuilder-time-stamp: 1716483124 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/481/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15455/tmp/hooks/D01_modify_environment starting +debug: Running on virt64a. +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 May 23 16:52 /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/15455/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15455/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='unstable' - 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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='bfa6aa5980a74bc59a55384ca72d3935' - 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='481' - PS1='# ' - PS2='> ' + INVOCATION_ID=57cc9786c46e4a7db4bc086b5a7069d8 + 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=15455 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.k9DSCzTv/pbuilderrc_dsyy --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k9DSCzTv/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.k9DSCzTv/pbuilderrc_PC8J --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.k9DSCzTv/b2 --logfile b2/build.log codonw_1.4.4-8.dsc' + SUDO_GID=114 + SUDO_UID=108 + 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 wbq0 6.1.0-21-armmp #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 21 07:47 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/481/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 23 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/15455/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -152,7 +184,7 @@ Get: 33 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf debhelper all 13.15.3 [901 kB] -Fetched 18.5 MB in 4s (4971 kB/s) +Fetched 18.5 MB in 1s (14.1 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 ... 19463 files and directories currently installed.) @@ -307,7 +339,11 @@ 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/15455/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/15455/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 @@ -331,11 +367,12 @@ 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 */ @@ -399,16 +436,9 @@ codons.c:640:25: warning: unknown conversion type character '=' in format [-Wformat=] 640 | fprintf(pm->my_err, "%3li>\t%6li %-40.40s\tDNA\tGC%" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -codon_us.c: In function 'codon_usage_out': 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: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 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 " | ~^ @@ -420,6 +450,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~ | | | long int +In file included from commline.c:28: +commline.c: In function 'proc_comm_line': 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 " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -428,16 +460,12 @@ | ~~~~~~~~~~~~ | | | long int -codon_us.c: In function 'raau_usage_out': codons.c:648:25: note: format string is defined here 648 | "in sequence %i\n" | ~^ | | | int | %li -codon_us.c:479:21: warning: too many arguments for format [-Wformat-extra-args] - 479 | fprintf(fblkout, "\n",sp); - | ^~~~ 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" | ~~^ @@ -448,6 +476,24 @@ | ~~~~~~~~~~~~ | | | long int +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:103:9: note: in expansion of macro 'pause' + 103 | pause; + | ^~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:127:9: note: in expansion of macro 'pause' + 127 | pause; + | ^~~~~ +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +commline.c:142:9: note: in expansion of macro 'pause' + 142 | pause; + | ^~~~~ codons.c: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 " | ~^ @@ -480,13 +526,29 @@ | | | | char * int | %d -codon_us.c: In function 'cbi_out': +In function 'fgets', + inlined from 'open_file' at open_fil.c:88:13: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 201 | return __fgets_chk_warn (__s, sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codons.c: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 '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" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -501,6 +563,14 @@ | | | double | %d +In file included from codons.c:90: +codons.c: In function 'main': +codonW.h:38:74: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | #define pause {fprintf(stderr,"\nPress return or enter to continue -> ");fgets(pm->junk, BUFSIZ, stdin);} + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +codons.c:204:35: note: in expansion of macro 'pause' + 204 | if ( pm->codonW && pm->menu ) pause; + | ^~~~~ codon_us.c: In function '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" @@ -528,20 +598,12 @@ 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 codons.c:90: -codons.c: In function 'main': 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); | ^~ -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:994:18: warning: too many arguments for format [-Wformat-extra-args] 994 | printf ("opt %l, std %l, nonopt %l\n",opt,std,nonopt); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -553,42 +615,6 @@ codon_us.c:1476:39: warning: precision used with '%c' gnu_printf format [-Wformat=] 1476 | fprintf(fblkout,"%c%c%4.4c",bases[x],bases[i],sp); | ^ -codons.c: In function 'chelp': -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; - | ^~~~~ -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; - | ^~~~~ -In function 'fgets', - inlined from 'open_file' at open_fil.c:88:13: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:201:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 201 | return __fgets_chk_warn (__s, sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ codon_us.c: 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); @@ -609,6 +635,13 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 */ + | ^~~~~ 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); @@ -620,7 +653,31 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 'gen_cusort_fop': +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: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 */ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -633,30 +690,6 @@ 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 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 ); - | ^~ 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 In file included from menu.c:31: menu.c: In function 'main_menu': @@ -802,6 +835,9 @@ 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] @@ -886,24 +922,24 @@ mkdir -p /build/reproducible-path/codonw-1.4.4/debian/man /build/reproducible-path/codonw-1.4.4/debian/make_man.pl /build/reproducible-path/codonw-1.4.4/debian/template.man \ /build/reproducible-path/codonw-1.4.4/debian/man -calculate Frequency of OPtimal codons index (FOP) -calculate codon usage -calculate Codon Adaptation Index (CAI) -calculate Relative Amino Acid Usage (RAAU) -calculate Relative Synonymous Codon Usage (RSCU) -clean up sequence in FASTA format -calculate Amino Acid Usage (AAU) -GC of synonymous codons 3rd positions -silent base G+C+A+T calculating program -tabulation of datasets codon usage -output sequence in reader format -conceptual translation of DNA to amino acid G+C content of gene (all 3 codon positions) -dinucleotide usage of the three codon positions calculate Codon Bias Index (CBI) tabulation of codon usage +calculate Relative Synonymous Codon Usage (RSCU) +GC of synonymous codons 3rd positions calculate Effective Number of Codons (ENc) +dinucleotide usage of the three codon positions +tabulation of datasets codon usage +conceptual translation of DNA to amino acid +silent base G+C+A+T calculating program +output sequence in reader format detailed report of base composition +calculate codon usage +calculate Frequency of OPtimal codons index (FOP) +calculate Relative Amino Acid Usage (RAAU) +calculate Codon Adaptation Index (CAI) +calculate Amino Acid Usage (AAU) +clean up sequence in FASTA format dh_installman -- make[1]: Leaving directory '/build/reproducible-path/codonw-1.4.4' dh_perl @@ -924,8 +960,8 @@ dh_gencontrol dh_md5sums dh_builddeb -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-deb: building package 'codonw' in '../codonw_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) @@ -933,12 +969,14 @@ 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/15455/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15455/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/481 and its subdirectories -I: Current time: Thu May 23 04:51:50 -12 2024 -I: pbuilder-time-stamp: 1716483110 +I: removing directory /srv/workspace/pbuilder/15455 and its subdirectories +I: Current time: Fri May 24 06:55:51 +14 2024 +I: pbuilder-time-stamp: 1716483351