Diff of the two buildlogs: -- --- b1/build.log 2024-03-25 07:44:14.397375235 +0000 +++ b2/build.log 2024-03-25 07:45:35.117924799 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 24 19:41:47 -12 2024 -I: pbuilder-time-stamp: 1711352507 +I: Current time: Mon Mar 25 21:44:26 +14 2024 +I: pbuilder-time-stamp: 1711352666 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -30,52 +30,84 @@ dpkg-source: info: applying mayhem.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/7821/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/32453/tmp/hooks/D01_modify_environment starting +debug: Running on virt32z. +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 Mar 25 07:44 /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/32453/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/32453/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='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='f0effb69cdc84aca99b909f22fbbbefa' - 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='7821' - PS1='# ' - PS2='> ' + INVOCATION_ID=adb487d5199b44f2ad3b6ea94dd69e3d + 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=32453 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.4l1GFUXO/pbuilderrc_rCKp --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4l1GFUXO/b1 --logfile b1/build.log maq_0.7.1-9.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.4l1GFUXO/pbuilderrc_1TPd --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4l1GFUXO/b2 --logfile b2/build.log maq_0.7.1-9.dsc' + SUDO_GID=110 + SUDO_UID=103 + 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 virt64b 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 23 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/7821/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 22 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/32453/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.14.1 [890 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg-3+b1 [904 kB] -Fetched 19.2 MB in 1s (32.3 MB/s) +Fetched 19.2 MB in 0s (85.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19577 files and directories currently installed.) @@ -283,7 +315,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/maq-0.7.1/ && 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 > ../maq_0.7.1-9_source.changes +I: user script /srv/workspace/pbuilder/32453/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/32453/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/maq-0.7.1/ && 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 > ../maq_0.7.1-9_source.changes dpkg-buildpackage: info: source package maq dpkg-buildpackage: info: source version 0.7.1-9 dpkg-buildpackage: info: source distribution unstable @@ -358,7 +394,7 @@ config.status: creating Makefile config.status: creating config.h dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' make all-am make[2]: Entering directory '/build/reproducible-path/maq-0.7.1' @@ -366,6 +402,7 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o const.o const.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o seq.o seq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o bfa.o bfa.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o read.o read.cc bfa.c: In function 'nst_load_bfa1': bfa.c:31:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 31 | fread(bfa1->name, sizeof(char), len, fp); @@ -389,9 +426,9 @@ bfa.c:48:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 48 | fread(&len, sizeof(int), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o read.o read.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fasta2bfa.o fasta2bfa.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o fastq2bfq.o fastq2bfq.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o merge.o merge.cc fastq2bfq.c: In function 'fastq2bfq': fastq2bfq.c:30:12: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 30 | fp = gzopen(str, "w"); @@ -448,14 +485,18 @@ /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o merge.o merge.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o match_aux.o match_aux.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o match.o match.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o sort_mapping.o sort_mapping.cc +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o assemble.o assemble.cc match.cc: In function 'int alt_cal_mm(bit64_t)': match.cc:58:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 58 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; | ~~^~~~~~~~~~ +sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': +sort_mapping.cc:59:75: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] + 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); + | ~~~~~~^~~~~~~~~ match.cc:61:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 61 | x = x + (x >> 32) & 0x0000007F; | ~~^~~~~~~~~~~ @@ -477,15 +518,10 @@ match.cc:292:17: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] 292 | bit32_t n_reads; | ^~~~~~~ -sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': -sort_mapping.cc:59:75: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] - 59 | p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); - | ~~~~~~^~~~~~~~~ match.cc: In function 'int ma_match(int, char**)': match.cc:525:31: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 525 | fscanf(tmpfp, "%s", adaptor); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o assemble.o assemble.cc assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': assemble.cc:106:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 106 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; @@ -494,12 +530,12 @@ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o get_pos.o get_pos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o assopt.o assopt.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc mapcheck.cc: In function 'int ma_mapcheck(int, char**)': mapcheck.cc:60:24: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] 60 | FILE *fp_bfa, *fpout; | ^~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': @@ -517,7 +553,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc subsnp.cc: In function 'hash_map_char* ma_load_snp(FILE*)': subsnp.cc:20:34: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 20 | sprintf(key, "%s.%d", name, pos); @@ -533,6 +568,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc subsnp.cc: In function 'hash_set_char* ma_load_snp_set(FILE*)': subsnp.cc:35:34: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 35 | sprintf(key, "%s.%d", name, pos); @@ -554,6 +590,9 @@ indel_soa.cc:56:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] 56 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; | ~~^~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o altchr.o altchr.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o submap.o submap.c subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:190:42: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 190 | sprintf(key, "%s.%d", name, pos); @@ -582,11 +621,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o altchr.o altchr.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o submap.o submap.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o simulate.o simulate.c +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o genran.o genran.c +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc simulate.c: In function 'maq_simutrain': simulate.c:83:15: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 83 | fpout = gzopen(argv[1], "w"); @@ -608,6 +646,7 @@ /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stdaln.o stdaln.c In file included from /usr/include/string.h:535, from maqmap.h:23, from simulate.c:11: @@ -622,8 +661,10 @@ simulate.c:381:19: note: 'tc' declared here 381 | int i, k, tc[2][2]; | ^~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o genran.o genran.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc +stdaln.c: In function 'aln_local_core': +stdaln.c:534:32: warning: variable 'b' set but not used [-Wunused-but-set-variable] + 534 | int gap_open, gap_ext, b; + | ^ rmdup.cc: In function 'void maq_rmdup_core(gzFile, gzFile)': rmdup.cc:46:32: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound depends on the length of the source argument [-Wstringop-truncation] 46 | strncpy(buf, name, tl-1); @@ -654,11 +695,6 @@ rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o stdaln.o stdaln.c -stdaln.c: In function 'aln_local_core': -stdaln.c:534:32: warning: variable 'b' set but not used [-Wunused-but-set-variable] - 534 | int gap_open, gap_ext, b; - | ^ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc @@ -669,12 +705,6 @@ 726 | MYFREE(s_array[i]); | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o break_pair.o break_pair.c -In file included from break_pair.c:2: -break_pair.c: In function 'breakpair': -break_pair.c:16:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] - 16 | assert(fp = gzopen(str, "r")); - | ^~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc eland2maq.cc: In function 'void eland2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:88:23: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 88 | fscanf(fp_eland, "%s", str); @@ -693,6 +723,12 @@ eland2maq.cc:323:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | fgets( str2, 4096, fp_novo ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc +In file included from break_pair.c:2: +break_pair.c: In function 'breakpair': +break_pair.c:16:16: warning: suggest parentheses around assignment used as truth value [-Wparentheses] + 16 | assert(fp = gzopen(str, "r")); + | ^~ glfgen.cc: In function 'glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)': glfgen.cc:43:77: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] 43 | if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; @@ -716,18 +752,18 @@ make[2]: Leaving directory '/build/reproducible-path/maq-0.7.1' make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' make[1]: Leaving directory '/build/reproducible-path/maq-0.7.1' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/maq/ - make -j3 install DESTDIR=/build/reproducible-path/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/reproducible-path/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/maq-0.7.1' make[2]: Entering directory '/build/reproducible-path/maq-0.7.1' /usr/bin/mkdir -p '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' - /usr/bin/mkdir -p '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' make[2]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/reproducible-path/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/reproducible-path/maq-0.7.1' @@ -772,12 +808,14 @@ 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/32453/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/32453/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/7821 and its subdirectories -I: Current time: Sun Mar 24 19:44:10 -12 2024 -I: pbuilder-time-stamp: 1711352650 +I: removing directory /srv/workspace/pbuilder/32453 and its subdirectories +I: Current time: Mon Mar 25 21:45:31 +14 2024 +I: pbuilder-time-stamp: 1711352731