Diff of the two buildlogs: -- --- b1/build.log 2024-12-24 03:39:28.886994060 +0000 +++ b2/build.log 2024-12-24 04:35:47.345170593 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 23 14:58:28 -12 2024 -I: pbuilder-time-stamp: 1735009108 +I: Current time: Tue Dec 24 17:39:45 +14 2024 +I: pbuilder-time-stamp: 1735011585 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying reenable-simde.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/15357/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/26343/tmp/hooks/D01_modify_environment starting +debug: Running on ff64a. +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 Dec 24 03:40 /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/26343/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/26343/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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' + 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='6acdb88147c14f35a62225b39c355bac' - 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='15357' - PS1='# ' - PS2='> ' + INVOCATION_ID=18127d9695a3473e87df671f6a9d82f3 + 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=26343 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.TK3qLXG5/pbuilderrc_rgw3 --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.TK3qLXG5/b1 --logfile b1/build.log minimap2_2.27+dfsg-1.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.TK3qLXG5/pbuilderrc_92KZ --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.TK3qLXG5/b2 --logfile b2/build.log minimap2_2.27+dfsg-1.dsc' + SUDO_GID=114 + SUDO_UID=109 + 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 cbxi4a 6.1.0-23-armmp #1 SMP Debian 6.1.99-1 (2024-07-15) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/15357/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/26343/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -344,7 +376,7 @@ Get: 203 http://deb.debian.org/debian unstable/main armhf texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 204 http://deb.debian.org/debian unstable/main armhf texlive-latex-extra all 2024.20241115-1 [24.6 MB] Get: 205 http://deb.debian.org/debian unstable/main armhf texlive-science all 2024.20241115-1 [3876 kB] -Fetched 271 MB in 14s (20.0 MB/s) +Fetched 271 MB in 11s (24.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package poppler-data. (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 ... 19694 files and directories currently installed.) @@ -1019,8 +1051,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 24 03:02:17 UTC 2024. -Universal Time is now: Tue Dec 24 03:02:17 UTC 2024. +Local time is now: Tue Dec 24 03:44:51 UTC 2024. +Universal Time is now: Tue Dec 24 03:44:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:armhf (3.13.1-2) ... @@ -1212,7 +1244,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/minimap2-2.27+dfsg/ && 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 > ../minimap2_2.27+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/26343/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/26343/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/minimap2-2.27+dfsg/ && 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 > ../minimap2_2.27+dfsg-1_source.changes dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.27+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1224,7 +1260,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_clean - make -j3 clean + make -j6 clean make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' rm -fr gmon.out *.o a.out minimap2 sdust minimap2-lite *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' @@ -1273,11 +1309,14 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' dh_auto_build -- -f Makefile.simde - make -j3 "INSTALL=install --strip-program=true" -f Makefile.simde + make -j6 "INSTALL=install --strip-program=true" -f Makefile.simde make[2]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 main.c -o main.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kthread.c -o kthread.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 kalloc.c -o kalloc.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 misc.c -o misc.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bseq.c -o bseq.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 sketch.c -o sketch.o kalloc.c: In function 'km_stat_print': kalloc.c:222:42: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 222 | fprintf(stderr, "[km_stat] cap=%ld, avail=%ld, largest=%ld, n_core=%ld, n_block=%ld\n", @@ -1329,12 +1368,10 @@ | ~~~~~~~~~~ | | | size_t {aka unsigned int} -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 misc.c -o misc.o -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 bseq.c -o bseq.o -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 sketch.c -o sketch.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 sdust.c -o sdust.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 options.c -o options.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 index.c -o index.o +cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 lchain.c -o lchain.o index.c: In function 'mm_idx_load': index.c:520:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 520 | fread(&l, 1, 1, fp); @@ -1360,7 +1397,6 @@ index.c:554:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 lchain.c -o lchain.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 align.c -o align.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 hit.c -o hit.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/minimap2-2.27+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 seed.c -o seed.o @@ -1892,7 +1928,7 @@ c/uhvr8a.pfb> -Output written on minimap2.pdf (5 pages, 255400 bytes). +Output written on minimap2.pdf (5 pages, 255407 bytes). Transcript written on minimap2.log. This is BibTeX, Version 0.99d (TeX Live 2025/dev/Debian) The top-level auxiliary file: minimap2.aux @@ -2321,7 +2357,7 @@ c/uhvr8a.pfb> -Output written on minimap2.pdf (6 pages, 266723 bytes). +Output written on minimap2.pdf (6 pages, 266729 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. @@ -2553,7 +2589,7 @@ c/uhvr8a.pfb> -Output written on minimap2.pdf (6 pages, 270238 bytes). +Output written on minimap2.pdf (6 pages, 270247 bytes). Transcript written on minimap2.log. make[2]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg/tex' dh_auto_build --buildsystem=pybuild @@ -3101,32 +3137,32 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/minimap2-2.27+dfsg' debian/test_script -[M::mm_idx_gen::0.013*1.46] collected minimizers -[M::mm_idx_gen::0.018*1.78] sorted minimizers -[M::main::0.019*1.75] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.021*1.67] mid_occ = 10 +[M::mm_idx_gen::0.016*1.32] collected minimizers +[M::mm_idx_gen::0.048*0.75] sorted minimizers +[M::main::0.049*0.74] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.053*0.74] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.023*1.60] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 -[M::worker_pipeline::0.842*1.01] mapped 1 sequences +[M::mm_idx_stat::0.056*0.74] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::worker_pipeline::1.491*0.99] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa -[M::main] Real time: 0.850 sec; CPU: 0.859 sec; Peak RSS: 0.003 GB -[M::mm_idx_gen::0.013*1.60] collected minimizers -[M::mm_idx_gen::0.017*1.85] sorted minimizers -[M::main::0.029*1.50] loaded/built the index for 1 target sequence(s) +[M::main] Real time: 1.504 sec; CPU: 1.479 sec; Peak RSS: 0.003 GB +[M::mm_idx_gen::0.016*1.32] collected minimizers +[M::mm_idx_gen::0.033*1.12] sorted minimizers +[M::main::0.050*1.07] loaded/built the index for 1 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.031*1.46] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::mm_idx_stat::0.054*1.04] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa -[M::main] Real time: 0.036 sec; CPU: 0.050 sec; Peak RSS: 0.002 GB -[M::main::0.017*1.19] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.021*1.13] mid_occ = 10 +[M::main] Real time: 0.067 sec; CPU: 0.065 sec; Peak RSS: 0.002 GB +[M::main::0.028*1.21] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.031*1.17] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.022*1.11] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 -[M::worker_pipeline::0.842*1.00] mapped 1 sequences +[M::mm_idx_stat::0.034*1.12] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 +[M::worker_pipeline::1.470*1.00] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa -[M::main] Real time: 0.852 sec; CPU: 0.853 sec; Peak RSS: 0.004 GB +[M::main] Real time: 1.487 sec; CPU: 1.481 sec; Peak RSS: 0.004 GB rm test.sam make[1]: Leaving directory '/build/reproducible-path/minimap2-2.27+dfsg' create-stamp debian/debhelper-build-stamp @@ -3272,9 +3308,9 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_armhf.deb'. +dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_armhf.deb'. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_armhf.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.27+dfsg-1_armhf.deb'. -dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_armhf.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.27+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../minimap2_2.27+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../minimap2_2.27+dfsg-1_armhf.changes @@ -3283,12 +3319,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/26343/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26343/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/15357 and its subdirectories -I: Current time: Mon Dec 23 15:39:24 -12 2024 -I: pbuilder-time-stamp: 1735011564 +I: removing directory /srv/workspace/pbuilder/26343 and its subdirectories +I: Current time: Tue Dec 24 18:35:42 +14 2024 +I: pbuilder-time-stamp: 1735014942