Diff of the two buildlogs: -- --- b1/build.log 2024-01-08 10:18:01.819670272 +0000 +++ b2/build.log 2024-01-08 11:02:51.255611540 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 7 22:12:36 -12 2024 -I: pbuilder-time-stamp: 1704708756 +I: Current time: Tue Jan 9 00:18:16 +14 2024 +I: pbuilder-time-stamp: 1704709096 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./minimap2_2.17+dfsg-12.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.EH4X4Vck/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.asQEB6j9/trustedkeys.kbx': General error gpgv: Signature made Tue Sep 15 08:57:53 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -35,49 +35,80 @@ dpkg-source: info: applying python-sse4-arch.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2083/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4567/tmp/hooks/D01_modify_environment starting +debug: Running on cbxi4b. +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 Jan 8 10:19 /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/4567/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4567/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,-fixfilepath parallel=3 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(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,-fixfilepath parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='e6c2dbf8b4d04faa9b4d44f810360a42' - 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='2083' - PS1='# ' - PS2='> ' + INVOCATION_ID=d424a85ee73149d5a2ba640e5366ad08 + 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=4567 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.QqEp1FSI/pbuilderrc_qK6D --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QqEp1FSI/b1 --logfile b1/build.log minimap2_2.17+dfsg-12.dsc' - SUDO_GID='114' - SUDO_UID='108' - 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.QqEp1FSI/pbuilderrc_FwTQ --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QqEp1FSI/b2 --logfile b2/build.log minimap2_2.17+dfsg-12.dsc' + SUDO_GID=116 + SUDO_UID=112 + 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 jtx1a 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-armmp #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Mar 27 2022 bash @@ -137,7 +168,7 @@ -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 7 09:27 sh -> dash + lrwxrwxrwx 1 root root 9 Jan 8 10:19 sh -> /bin/bash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jan 20 2022 su @@ -163,7 +194,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2083/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/4567/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -498,7 +529,7 @@ Get: 275 http://deb.debian.org/debian bullseye/main armhf texlive-pictures all 2020.20210202-3 [6743 kB] Get: 276 http://deb.debian.org/debian bullseye/main armhf texlive-latex-extra all 2020.20210202-3 [13.7 MB] Get: 277 http://deb.debian.org/debian bullseye/main armhf texlive-science all 2020.20210202-3 [3367 kB] -Fetched 291 MB in 9s (31.0 MB/s) +Fetched 291 MB in 1min 6s (4404 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:armhf. (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 ... 17486 files and directories currently installed.) @@ -1401,8 +1432,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 8 10:15:00 UTC 2024. -Universal Time is now: Mon Jan 8 10:15:00 UTC 2024. +Local time is now: Mon Jan 8 10:32:13 UTC 2024. +Universal Time is now: Mon Jan 8 10:32:13 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libdconf1:armhf (0.38.0-2) ... @@ -1659,7 +1690,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/minimap2-2.17+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_2.17+dfsg-12_source.changes +I: user script /srv/workspace/pbuilder/4567/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/4567/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/minimap2-2.17+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_2.17+dfsg-12_source.changes dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.17+dfsg-12 dpkg-buildpackage: info: source distribution unstable @@ -1675,7 +1710,7 @@ debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/minimap2-2.17+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/minimap2-2.17+dfsg' @@ -1696,7 +1731,7 @@ debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' dh_auto_build -- - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/minimap2-2.17+dfsg' cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC main.c -o main.o cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC kthread.c -o kthread.o @@ -1707,6 +1742,9 @@ cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC sdust.c -o sdust.o cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC options.c -o options.o cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC index.c -o index.o +cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC chain.c -o chain.o +cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC align.c -o align.o +cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC hit.c -o hit.o index.c: In function 'mm_idx_load': index.c:495:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 495 | fread(&l, 1, 1, fp); @@ -1732,9 +1770,6 @@ index.c:528:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 528 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC chain.c -o chain.o -cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC align.c -o align.o -cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC hit.c -o hit.o hit.c: In function 'mm_gen_regs': hit.c:74:18: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 74 | r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t)); @@ -1744,7 +1779,6 @@ 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC map.c -o map.o -cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC format.c -o format.o map.c: In function 'mm_map_frag': map.c:380:39: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=] 380 | fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest); @@ -1764,6 +1798,7 @@ | | | | long int size_t {aka unsigned int} | %d +cc -c -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_KALLOC format.c -o format.o format.c: In function 'mm_write_sam3': format.c:391:36: warning: variable 'this_rev' set but not used [-Wunused-but-set-variable] 391 | int this_rid = -1, this_pos = -1, this_rev = 0; @@ -2921,7 +2956,7 @@ creating build creating build/temp.linux-armhf-3.9 creating build/temp.linux-armhf-3.9/python -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c align.c -o build/temp.linux-armhf-3.9/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c align.c -o build/temp.linux-armhf-3.9/align.o -DHAVE_KALLOC align.c: In function 'mm_get_hplen_back': align.c:346:29: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 346 | if (mm_seq4_get(mi->S, i) != c) break; @@ -2937,10 +2972,10 @@ align.c:672:44: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 672 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re; | ^ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c bseq.c -o build/temp.linux-armhf-3.9/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c chain.c -o build/temp.linux-armhf-3.9/chain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c esterr.c -o build/temp.linux-armhf-3.9/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c format.c -o build/temp.linux-armhf-3.9/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c bseq.c -o build/temp.linux-armhf-3.9/bseq.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c chain.c -o build/temp.linux-armhf-3.9/chain.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c esterr.c -o build/temp.linux-armhf-3.9/esterr.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c format.c -o build/temp.linux-armhf-3.9/format.o -DHAVE_KALLOC format.c: In function 'mm_event_identity': format.c:268:16: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 268 | for (i = 0; i < r->p->n_cigar; ++i) { @@ -2949,7 +2984,7 @@ format.c:391:36: warning: variable 'this_rev' set but not used [-Wunused-but-set-variable] 391 | int this_rid = -1, this_pos = -1, this_rev = 0; | ^~~~~~~~ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c hit.c -o build/temp.linux-armhf-3.9/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c hit.c -o build/temp.linux-armhf-3.9/hit.o -DHAVE_KALLOC hit.c: In function 'mm_hit_sort': hit.c:171:48: warning: variable 'no_cigar' set but not used [-Wunused-but-set-variable] 171 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; @@ -2972,7 +3007,7 @@ /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c index.c -o build/temp.linux-armhf-3.9/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c index.c -o build/temp.linux-armhf-3.9/index.o -DHAVE_KALLOC index.c: In function 'mm_idx_name2id': index.c:149:25: warning: operand of '?:' changes signedness from 'int' to 'uint32_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare] 149 | return k == kh_end(h)? -1 : kh_val(h, k); @@ -2997,13 +3032,13 @@ index.c:708:35: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 708 | if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1; | ^~ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c kalloc.c -o build/temp.linux-armhf-3.9/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c ksw2_extd2_sse.c -o build/temp.linux-armhf-3.9/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c ksw2_exts2_sse.c -o build/temp.linux-armhf-3.9/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c ksw2_extz2_sse.c -o build/temp.linux-armhf-3.9/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c ksw2_ll_sse.c -o build/temp.linux-armhf-3.9/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c kthread.c -o build/temp.linux-armhf-3.9/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c map.c -o build/temp.linux-armhf-3.9/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c kalloc.c -o build/temp.linux-armhf-3.9/kalloc.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_extd2_sse.c -o build/temp.linux-armhf-3.9/ksw2_extd2_sse.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_exts2_sse.c -o build/temp.linux-armhf-3.9/ksw2_exts2_sse.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_extz2_sse.c -o build/temp.linux-armhf-3.9/ksw2_extz2_sse.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c ksw2_ll_sse.c -o build/temp.linux-armhf-3.9/ksw2_ll_sse.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c kthread.c -o build/temp.linux-armhf-3.9/kthread.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c map.c -o build/temp.linux-armhf-3.9/map.o -DHAVE_KALLOC map.c: In function 'mm_dust_minier': map.c:52:42: warning: operand of '?:' changes signedness from 'int32_t' {aka 'int'} to 'uint64_t' {aka 'const long long unsigned int'} due to unsignedness of other operand [-Wsign-compare] 52 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32; @@ -3030,13 +3065,13 @@ | | | | long int size_t {aka unsigned int} | %d -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c misc.c -o build/temp.linux-armhf-3.9/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c options.c -o build/temp.linux-armhf-3.9/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c pe.c -o build/temp.linux-armhf-3.9/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c python/mappy.c -o build/temp.linux-armhf-3.9/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c sdust.c -o build/temp.linux-armhf-3.9/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c sketch.c -o build/temp.linux-armhf-3.9/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ -arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -Isse2neon/ -I/usr/include/python3.9 -c splitidx.c -o build/temp.linux-armhf-3.9/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -D__SSE2__ +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c misc.c -o build/temp.linux-armhf-3.9/misc.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c options.c -o build/temp.linux-armhf-3.9/options.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c pe.c -o build/temp.linux-armhf-3.9/pe.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c python/mappy.c -o build/temp.linux-armhf-3.9/python/mappy.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c sdust.c -o build/temp.linux-armhf-3.9/sdust.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c sketch.c -o build/temp.linux-armhf-3.9/sketch.o -DHAVE_KALLOC +arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-jS0VHk/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I. -I/usr/include/python3.9 -c splitidx.c -o build/temp.linux-armhf-3.9/splitidx.o -DHAVE_KALLOC arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/reproducible-path/minimap2-2.17+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.9/align.o build/temp.linux-armhf-3.9/bseq.o build/temp.linux-armhf-3.9/chain.o build/temp.linux-armhf-3.9/esterr.o build/temp.linux-armhf-3.9/format.o build/temp.linux-armhf-3.9/hit.o build/temp.linux-armhf-3.9/index.o build/temp.linux-armhf-3.9/kalloc.o build/temp.linux-armhf-3.9/ksw2_extd2_sse.o build/temp.linux-armhf-3.9/ksw2_exts2_sse.o build/temp.linux-armhf-3.9/ksw2_extz2_sse.o build/temp.linux-armhf-3.9/ksw2_ll_sse.o build/temp.linux-armhf-3.9/kthread.o build/temp.linux-armhf-3.9/map.o build/temp.linux-armhf-3.9/misc.o build/temp.linux-armhf-3.9/options.o build/temp.linux-armhf-3.9/pe.o build/temp.linux-armhf-3.9/python/mappy.o build/temp.linux-armhf-3.9/sdust.o build/temp.linux-armhf-3.9/sketch.o build/temp.linux-armhf-3.9/splitidx.o -lz -lm -lpthread -o /build/reproducible-path/minimap2-2.17+dfsg/.pybuild/cpython3_3.9/build/mappy.cpython-39-arm-linux-gnueabihf.so running build_scripts creating build/scripts-3.9 @@ -3048,32 +3083,32 @@ debian/rules:51: warning: overriding recipe for target 'override_dh_auto_clean' debian/rules:15: warning: ignoring old recipe for target 'override_dh_auto_clean' debian/test_script -[M::mm_idx_gen::0.005*1.56] collected minimizers -[M::mm_idx_gen::0.007*1.86] sorted minimizers -[M::main::0.007*1.86] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.008*1.78] mid_occ = 2 +[M::mm_idx_gen::0.054*0.42] collected minimizers +[M::mm_idx_gen::0.098*0.37] sorted minimizers +[M::main::0.099*0.37] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.102*0.39] mid_occ = 2 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.008*1.74] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 -[M::worker_pipeline::0.286*1.03] mapped 1 sequences +[M::mm_idx_stat::0.105*0.40] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 +[M::worker_pipeline::2.688*0.35] mapped 1 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa -[M::main] Real time: 0.290 sec; CPU: 0.297 sec; Peak RSS: 0.004 GB -[M::mm_idx_gen::0.006*1.58] collected minimizers -[M::mm_idx_gen::0.008*1.89] sorted minimizers -[M::main::0.013*1.54] loaded/built the index for 1 target sequence(s) +[M::main] Real time: 2.716 sec; CPU: 0.937 sec; Peak RSS: 0.003 GB +[M::mm_idx_gen::0.056*0.38] collected minimizers +[M::mm_idx_gen::0.101*0.34] sorted minimizers +[M::main::0.134*0.35] 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::0.013*1.52] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 +[M::mm_idx_stat::0.140*0.36] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa -[M::main] Real time: 0.015 sec; CPU: 0.022 sec; Peak RSS: 0.002 GB -[M::main::0.008*1.21] loaded/built the index for 1 target sequence(s) -[M::mm_mapopt_update::0.009*1.19] mid_occ = 2 +[M::main] Real time: 0.166 sec; CPU: 0.057 sec; Peak RSS: 0.002 GB +[M::main::0.060*0.44] loaded/built the index for 1 target sequence(s) +[M::mm_mapopt_update::0.068*0.43] mid_occ = 2 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 -[M::mm_idx_stat::0.009*1.18] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 -[M::worker_pipeline::0.291*1.01] mapped 1 sequences +[M::mm_idx_stat::0.076*0.42] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326 +[M::worker_pipeline::2.887*0.32] mapped 1 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa -[M::main] Real time: 0.294 sec; CPU: 0.297 sec; Peak RSS: 0.008 GB +[M::main] Real time: 2.920 sec; CPU: 0.930 sec; Peak RSS: 0.003 GB rm test.sam make[1]: Leaving directory '/build/reproducible-path/minimap2-2.17+dfsg' create-stamp debian/debhelper-build-stamp @@ -3145,11 +3180,11 @@ dpkg-gencontrol: warning: package python3-mappy: substitution variable ${python3:Versions} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'minimap2' in '../minimap2_2.17+dfsg-12_armhf.deb'. -dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.17+dfsg-12_armhf.deb'. dpkg-deb: building package 'python3-mappy-dbgsym' in '../python3-mappy-dbgsym_2.17+dfsg-12_armhf.deb'. -dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.17+dfsg-12_armhf.deb'. +dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.17+dfsg-12_armhf.deb'. +dpkg-deb: building package 'minimap2' in '../minimap2_2.17+dfsg-12_armhf.deb'. dpkg-deb: building package 'minimap2-dbgsym' in '../minimap2-dbgsym_2.17+dfsg-12_armhf.deb'. +dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.17+dfsg-12_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../minimap2_2.17+dfsg-12_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -3157,12 +3192,14 @@ 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/4567/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4567/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/2083 and its subdirectories -I: Current time: Sun Jan 7 22:17:57 -12 2024 -I: pbuilder-time-stamp: 1704709077 +I: removing directory /srv/workspace/pbuilder/4567 and its subdirectories +I: Current time: Tue Jan 9 01:02:42 +14 2024 +I: pbuilder-time-stamp: 1704711762