Diff of the two buildlogs: -- --- b1/build.log 2024-01-09 17:01:40.797597391 +0000 +++ b2/build.log 2024-01-09 17:02:49.138904921 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 9 04:59:56 -12 2024 -I: pbuilder-time-stamp: 1704819596 +I: Current time: Tue Feb 11 13:24:39 +14 2025 +I: pbuilder-time-stamp: 1739229879 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: copying [./centrifuge_1.0.3-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZG_Xb2kx/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.Jh_9FP1n/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 9 17:01:32 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" @@ -37,51 +37,82 @@ dpkg-source: info: applying fix_arm_build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/24672/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1348/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-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 Feb 10 23:24 /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/1348/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1348/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,-fixfilepath parallel=8 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + 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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='0c83752aa7a549a1986df08e2a37041a' - 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='24672' - PS1='# ' - PS2='> ' + INVOCATION_ID=003b62b829ef46e5b1bb83472969a177 + 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=1348 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.vOtksyuj/pbuilderrc_E6pw --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.vOtksyuj/b1 --logfile b1/build.log centrifuge_1.0.3-8.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://78.137.99.97:3128' + 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.vOtksyuj/pbuilderrc_gX2P --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.vOtksyuj/b2 --logfile b2/build.log centrifuge_1.0.3-8.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://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash @@ -141,7 +172,7 @@ -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 7 09:27 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 10 23:24 sh -> /bin/bash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su @@ -167,7 +198,7 @@ -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/24672/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1348/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -269,7 +300,7 @@ Get: 58 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 59 http://deb.debian.org/debian bullseye/main i386 libjellyfish-2.0-2 i386 2.3.0-10 [71.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main i386 jellyfish i386 2.3.0-10 [769 kB] -Fetched 27.4 MB in 8s (3429 kB/s) +Fetched 27.4 MB in 0s (82.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17763 files and directories currently installed.) @@ -477,8 +508,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Jan 9 17:00:23 UTC 2024. -Universal Time is now: Tue Jan 9 17:00:23 UTC 2024. +Local time is now: Mon Feb 10 23:24:56 UTC 2025. +Universal Time is now: Mon Feb 10 23:24:56 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjellyfish-2.0-2:i386 (2.3.0-10) ... @@ -533,7 +564,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/centrifuge-1.0.3/ && 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 > ../centrifuge_1.0.3-8_source.changes +I: user script /srv/workspace/pbuilder/1348/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1348/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/centrifuge-1.0.3/ && 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 > ../centrifuge_1.0.3-8_source.changes dpkg-buildpackage: info: source package centrifuge dpkg-buildpackage: info: source version 1.0.3-8 dpkg-buildpackage: info: source distribution unstable @@ -543,7 +578,7 @@ debian/rules clean dh clean --with python3 dh_auto_clean - make -j8 clean + make -j15 clean make[1]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' rm -f centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge-build-bin-debug centrifuge-class-debug centrifuge-inspect-bin-debug \ centrifuge-build-bin.exe centrifuge-class.exe centrifuge-inspect-bin.exe centrifuge-build-bin-debug.exe centrifuge-class-debug.exe centrifuge-inspect-bin-debug.exe \ @@ -560,7 +595,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' dh_auto_build -- BITS=32 BITS_FLAG= - make -j8 "INSTALL=install --strip-program=true" BITS=32 BITS_FLAG= + make -j15 "INSTALL=install --strip-program=true" BITS=32 BITS_FLAG= make[2]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' /usr/bin/g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 \"" \ -fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -fdebug-prefix-map=/build/reproducible-path/centrifuge-1.0.3=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ @@ -657,6 +692,23 @@ multikey_qsort.h:496:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from blockwise_sa.h:29, + from bt2_idx.h:44, + from hier_idx.h:24, + from centrifuge_inspect.cpp:28: +diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': +diff_sample.h:175:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; + | ^~ +diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; + | ^~~~~ +diff_sample.h:176:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; + | ^~ +diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; + | ^~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, @@ -689,23 +741,15 @@ multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK' 1066 | OFF_MASK, begin, end); | ^~~~~~~~ -In file included from blockwise_sa.h:29, - from bt2_idx.h:44, +In file included from bt2_idx.h:44, from hier_idx.h:24, from centrifuge_inspect.cpp:28: -diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)': -diff_sample.h:175:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; - | ^~ -diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; - | ^~~~~ -diff_sample.h:176:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; - | ^~ -diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; - | ^~~~~ +blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]': +blockwise_sa.h:491:52: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] + 491 | this->verbose(), this->sanityCheck()); + | ^ +blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]': +blockwise_sa.h:491:52: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]': multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]' multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]' @@ -752,15 +796,6 @@ bt2_idx.h:3641:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] 3641 | for(size_t k = 0; k < kmer_size; k++) { | ~~^~~~~~~~~~~ -In file included from bt2_idx.h:44, - from hier_idx.h:24, - from centrifuge_inspect.cpp:28: -blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]': -blockwise_sa.h:491:52: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] - 491 | this->verbose(), this->sanityCheck()); - | ^ -blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]': -blockwise_sa.h:491:52: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] In file included from blockwise_sa.h:29, from bt2_idx.h:44, from centrifuge_build.cpp:27: @@ -901,12 +936,40 @@ multikey_qsort.h:1155:49: note: in expansion of macro 'OFF_MASK' 1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from ds.h:32, + from sequence_io.h:28, + from multikey_qsort.h:24, + from diff_sample.h:26, + from blockwise_sa.h:29, + from bt2_idx.h:44, + from centrifuge.cpp:34: +multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]': +blockwise_sa.h:485:56: required from here +btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] + 25 | #define OFF_MASK 0xffffffffffffffff + | ^~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:63: note: in expansion of macro 'OFF_MASK' + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ^~~~~~~~ btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1164:49: note: in expansion of macro 'OFF_MASK' 1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ +In file included from diff_sample.h:26, + from blockwise_sa.h:29, + from bt2_idx.h:44, + from centrifuge.cpp:34: +multikey_qsort.h:764:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] + 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multikey_qsort.h:764:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] +multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]': +blockwise_sa.h:491:52: required from here +multikey_qsort.h:496:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] + 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]': multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]' multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]' @@ -955,34 +1018,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro 'OFF_MASK' 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from ds.h:32, - from sequence_io.h:28, - from multikey_qsort.h:24, - from diff_sample.h:26, - from blockwise_sa.h:29, - from bt2_idx.h:44, - from centrifuge.cpp:34: -multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]': -blockwise_sa.h:485:56: required from here -btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] - 25 | #define OFF_MASK 0xffffffffffffffff - | ^~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:63: note: in expansion of macro 'OFF_MASK' - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ^~~~~~~~ -In file included from diff_sample.h:26, - from blockwise_sa.h:29, - from bt2_idx.h:44, - from centrifuge.cpp:34: -multikey_qsort.h:764:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] - 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multikey_qsort.h:764:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] -multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]': -blockwise_sa.h:491:52: required from here -multikey_qsort.h:496:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] - 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from centrifuge.cpp:47: classifier.h: In instantiation of 'int Classifier::go(const Scoring&, const Ebwt&, const Ebwt&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]': centrifuge.cpp:2660:94: required from here @@ -1070,13 +1105,6 @@ multikey_qsort.h:1007:48: note: in expansion of macro 'OFF_MASK' 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ -In file included from centrifuge.cpp:41: -aln_sink.h: In instantiation of 'void AlnSinkSam::appendMate(Ebwt&, BTString&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable; TReadId = long long unsigned int; size_t = unsigned int]': -aln_sink.h:1407:9: required from 'void AlnSinkSam::append(BTString&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, bool, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable; size_t = unsigned int; TReadId = long long unsigned int]' -aln_sink.h:1392:15: required from here -aln_sink.h:2302:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] - 2302 | for (int i=0; i < this->tab_fmt_cols_.size(); ++i) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, @@ -1140,6 +1168,13 @@ multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK' 1066 | OFF_MASK, begin, end); | ^~~~~~~~ +In file included from centrifuge.cpp:41: +aln_sink.h: In instantiation of 'void AlnSinkSam::appendMate(Ebwt&, BTString&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable; TReadId = long long unsigned int; size_t = unsigned int]': +aln_sink.h:1407:9: required from 'void AlnSinkSam::append(BTString&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, bool, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable; size_t = unsigned int; TReadId = long long unsigned int]' +aln_sink.h:1392:15: required from here +aln_sink.h:2302:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] + 2302 | for (int i=0; i < this->tab_fmt_cols_.size(); ++i) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]': multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]' multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]' @@ -1506,7 +1541,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' dh_auto_install -- prefix=/usr/lib/centrifuge - make -j8 install DESTDIR=/build/reproducible-path/centrifuge-1.0.3/debian/centrifuge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" prefix=/usr/lib/centrifuge + make -j15 install DESTDIR=/build/reproducible-path/centrifuge-1.0.3/debian/centrifuge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" prefix=/usr/lib/centrifuge make[2]: Entering directory '/build/reproducible-path/centrifuge-1.0.3' mkdir -p /build/reproducible-path/centrifuge-1.0.3/debian/centrifuge/usr/lib/centrifuge/bin mkdir -p /build/reproducible-path/centrifuge-1.0.3/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices @@ -1567,12 +1602,14 @@ 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/1348/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1348/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/24672 and its subdirectories -I: Current time: Tue Jan 9 05:01:40 -12 2024 -I: pbuilder-time-stamp: 1704819700 +I: removing directory /srv/workspace/pbuilder/1348 and its subdirectories +I: Current time: Tue Feb 11 13:25:44 +14 2025 +I: pbuilder-time-stamp: 1739229944