Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 13:46:16.768213638 +0000 +++ b2/build.log 2024-05-13 13:51:04.743968372 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 15 08:06:11 -12 2025 -I: pbuilder-time-stamp: 1750017971 +I: Current time: Tue May 14 03:46:23 +14 2024 +I: pbuilder-time-stamp: 1715607983 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,54 +30,86 @@ dpkg-source: info: applying add-runstatedir.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/108458/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/26111/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +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 13 13:46 /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/26111/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/26111/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='9717ed87a23547739c7f4bf0cb587c2a' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='108458' - PS1='# ' - PS2='> ' + INVOCATION_ID=3bfd96a7274145029c601aff8b6f2005 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=26111 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.XkdwlI58/pbuilderrc_uGef --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.XkdwlI58/b1 --logfile b1/build.log smalt_0.7.6-13.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.XkdwlI58/pbuilderrc_0bAf --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.XkdwlI58/b2 --logfile b2/build.log smalt_0.7.6-13.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos6-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 13 17:56 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/108458/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 13 11:26 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/26111/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -191,7 +223,7 @@ Get: 68 http://deb.debian.org/debian trixie/main i386 libhts3t64 i386 1.19+ds-1.1+b1 [491 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.4+20240414-1 [112 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 samtools i386 1.19.2-1+b1 [682 kB] -Fetched 29.8 MB in 1s (48.4 MB/s) +Fetched 29.8 MB in 1s (56.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19684 files and directories currently installed.) @@ -438,8 +470,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jun 15 20:06:30 UTC 2025. -Universal Time is now: Sun Jun 15 20:06:30 UTC 2025. +Local time is now: Mon May 13 13:46:51 UTC 2024. +Universal Time is now: Mon May 13 13:46:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -498,7 +530,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/smalt-0.7.6/ && 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 > ../smalt_0.7.6-13_source.changes +I: user script /srv/workspace/pbuilder/26111/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/26111/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/smalt-0.7.6/ && 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 > ../smalt_0.7.6-13_source.changes dpkg-buildpackage: info: source package smalt dpkg-buildpackage: info: source version 0.7.6-13 dpkg-buildpackage: info: source distribution unstable @@ -614,7 +650,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -a - make -j22 + make -j10 make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' make all-recursive make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6' @@ -630,38 +666,10 @@ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c -gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c diffstr.c: In function 'diffStrGetDiffStats': diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress] 978 | if (diffstrp+1 != NULL) { | ^~ -hashidx.c: In function 'countPerfectKey': -hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter] - 191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) - | ~~~~~~~~~~^~~~~~~~ -hashidx.c: In function 'countCollisionKey': -hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter] - 206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) - | ~~~~~~~~~~^~~~~~~~ -hashidx.c: In function 'collectWords': -hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter] - 223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) - | ~~~~~~~~~~^~~~~~~~ -hashidx.c: In function 'countWords': -hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter] - 265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) - | ~~~~~~~~~~^~~~~~~~ sequence.c: In function 'make3BitMangledCodec': sequence.c:298:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare] 298 | for (i=1; i' [-Wsign-compare] - 1559 | if (maxnhits < HITLST_MINSIZ) maxnhits = HITLST_MINSIZ; - | ^ +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c +score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=] + 49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */ + | ^~~~~~ +alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] + 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) + | ^~~~~~~~~~~~~ sequence.c: In function 'fprintSeqFastqSequence': sequence.c:1700:16: warning: comparison of integer expressions of different signedness: 'short int' and 'enum SEQ_CONSTANTS' [-Wsign-compare] 1700 | if (linewidth>OUTBUFSIZE) linewidth = OUTBUFSIZE; | ^ -hashidx.c: At top level: -hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function] - 446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp) - | ^~~~~~~~~~~~ -hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=] - 63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file"; - | ^~~~~~~~~~~~~~~~~~~~~ -score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=] - 49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */ - | ^~~~~~ sequence.c: In function 'seqFastqGetConstSequence': sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2079 | if (length) @@ -698,33 +699,68 @@ sequence.c:2081:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2081 | return NULL; | ^~~~~~ -segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function] - 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs) - | ^~~~~~~~~~~~~~~~~~~~~~ sequence.c: In function 'seqFastqGetSequence': -segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function] - 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2094 | if (length) | ^~ sequence.c:2096:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2096 | return NULL; | ^~~~~~ -alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] - 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) - | ^~~~~~~~~~~~~ -smalt.c: In function 'cleanupSmaltOutput': -smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] - 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) - | ~~~~~~~~^~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c sequence.c: In function 'seqIOopen': +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=] 489 | strcpy(p->fmode, "r"); | ^~~~~~~~~~~~~~~~~~~~~ sequence.c:491:3: note: here 491 | case SEQIO_WRITE_GZIP_FASTA: | ^~~~ +hashidx.c: In function 'countPerfectKey': +hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter] + 191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) + | ~~~~~~~~~~^~~~~~~~ +hashidx.c: In function 'countCollisionKey': +hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter] + 206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) + | ~~~~~~~~~~^~~~~~~~ +hashidx.c: In function 'collectWords': +hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter] + 223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) + | ~~~~~~~~~~^~~~~~~~ +hashidx.c: In function 'countWords': +hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter] + 265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) + | ~~~~~~~~~~^~~~~~~~ +hashidx.c: At top level: +hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function] + 446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp) + | ^~~~~~~~~~~~ +hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=] + 63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file"; + | ^~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c +hashhit.c: In function 'hashCreateHitList': +hashhit.c:1559:18: warning: comparison of integer expressions of different signedness: 'int' and 'enum ' [-Wsign-compare] + 1559 | if (maxnhits < HITLST_MINSIZ) maxnhits = HITLST_MINSIZ; + | ^ +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c +segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function] + 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs) + | ^~~~~~~~~~~~~~~~~~~~~~ +segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function] + 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c +smalt.c: In function 'cleanupSmaltOutput': +smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] + 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) + | ~~~~~~~~^~~~~~~ +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c +gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c rm -f libseq.a ar cru libseq.a elib.o filio.o sequence.o @@ -756,15 +792,15 @@ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c basqual.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c simqual.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c +gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz +gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz +gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz ../src/diffstr.c: In function 'diffStrGetDiffStats': ../src/diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress] 978 | if (diffstrp+1 != NULL) { | ^~ -gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz -gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz -gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz @@ -781,7 +817,7 @@ make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -Nsmalt - make -j22 + make -j10 make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' make all-recursive make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' @@ -804,7 +840,7 @@ make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_auto_test - make -j22 check "TESTSUITEFLAGS=-j22 --verbose" VERBOSE=1 + make -j10 check "TESTSUITEFLAGS=-j10 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making check in src make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/src' @@ -888,9 +924,9 @@ dh_gencontrol dh_md5sums dh_builddeb +dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_i386.deb'. dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-13_all.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_i386.deb'. -dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_i386.deb'. dpkg-genbuildinfo --build=binary -O../smalt_0.7.6-13_i386.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-13_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -898,12 +934,14 @@ 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/26111/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26111/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/108458 and its subdirectories -I: Current time: Sun Jun 15 08:09:14 -12 2025 -I: pbuilder-time-stamp: 1750018154 +I: removing directory /srv/workspace/pbuilder/26111 and its subdirectories +I: Current time: Tue May 14 03:51:04 +14 2024 +I: pbuilder-time-stamp: 1715608264