Diff of the two buildlogs: -- --- b1/build.log 2023-04-22 04:53:28.991601986 +0000 +++ b2/build.log 2023-04-22 04:54:40.664424448 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 21 16:52:33 -12 2023 -I: pbuilder-time-stamp: 1682139153 +I: Current time: Sat May 25 01:16:31 +14 2024 +I: pbuilder-time-stamp: 1716549391 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./maq_0.7.1.orig.tar.gz] I: copying [./maq_0.7.1-9.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Nov 15 22:45:18 2020 -12 +gpgv: Signature made Tue Nov 17 00:45:18 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -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/5022/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1948/tmp/hooks/D01_modify_environment starting +debug: Running on codethink13-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 25 01:16 /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/1948/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1948/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='5022' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=1948 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.m76RX36P/pbuilderrc_Iais --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.m76RX36P/b1 --logfile b1/build.log maq_0.7.1-9.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.m76RX36P/pbuilderrc_UeI0 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.m76RX36P/b2 --logfile b2/build.log --extrapackages usrmerge maq_0.7.1-9.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink16-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 19 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/5022/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 23 06:50 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1948/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 bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 19.3 MB in 1s (14.8 MB/s) +Fetched 19.3 MB in 0s (46.3 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 ... 19616 files and directories currently installed.) @@ -282,8 +314,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/1948/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/1948/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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 @@ -369,30 +410,6 @@ 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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match_aux.o match_aux.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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:32:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:33:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 33 | fread(&bfa1->len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:35:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c:37:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -bfa.c: In function 'nst_bfa_len': -bfa.c:46:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 46 | fread(&len, sizeof(int), 1, fp); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match.o match.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"); @@ -450,11 +467,49 @@ /usr/include/zlib.h:1631:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); | ^~ +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:32:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 32 | fread(&bfa1->ori_len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:33:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 33 | fread(&bfa1->len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:35:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 35 | fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c:37:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 37 | fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +bfa.c: In function 'nst_bfa_len': +bfa.c:46:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 46 | fread(&len, sizeof(int), 1, fp); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pileup.o pileup.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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.c +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; + | ^~~~~ +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; + | ~~~~^~~~~~~~~ +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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c +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 alt_cal_mm(bit64_t)': match.cc:58:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] 58 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; @@ -480,25 +535,11 @@ 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); - | ~~~~~~^~~~~~~~~ -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; - | ~~~~^~~~~~~~~ -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc 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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc @@ -526,7 +567,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.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); @@ -540,8 +580,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': rbcc.cc:21:35: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 21 | sprintf(str1, "%s.%d", name, pos); @@ -557,7 +599,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c +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"); + | ^ +simulate.c:86:17: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] + 86 | gzwrite(fpout, fqc, sizeof(fqc_t)); + | ^~~~~ + | | + | struct gzFile_s ** +In file included from /usr/include/zlib.h:34, + from simulate.c:6: +/usr/include/zlib.h:1448:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' + 1448 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, voidpc buf, unsigned len)); + | ^~ 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); @@ -572,6 +627,14 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +simulate.c:87:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] + 87 | gzclose(fpout); + | ^~~~~ + | | + | struct gzFile_s ** +/usr/include/zlib.h:1631:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' + 1631 | ZEXTERN int ZEXPORT gzclose OF((gzFile file)); + | ^~ subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:186:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] 186 | sprintf(key, "%s.%d", name, i); @@ -588,31 +651,8 @@ | ~~~~~~~~~~~~~~~~~ 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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -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"); - | ^ -simulate.c:86:17: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] - 86 | gzwrite(fpout, fqc, sizeof(fqc_t)); - | ^~~~~ - | | - | struct gzFile_s ** -In file included from /usr/include/zlib.h:34, - from simulate.c:6: -/usr/include/zlib.h:1448:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' - 1448 | ZEXTERN int ZEXPORT gzwrite OF((gzFile file, voidpc buf, unsigned len)); - | ^~ -simulate.c:87:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] - 87 | gzclose(fpout); - | ^~~~~ - | | - | struct gzFile_s ** -/usr/include/zlib.h:1631:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' - 1631 | ZEXTERN int ZEXPORT gzclose OF((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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stdaln.o stdaln.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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc In file included from /usr/include/string.h:535, from maqmap.h:23, from simulate.c:11: @@ -627,12 +667,8 @@ simulate.c:381:19: note: 'tc' declared here 381 | int i, k, tc[2][2]; | ^~ +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/maq-0.7.1=. -fstack-protector-strong -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.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; - | ^ -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/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c rmdup.cc: In function 'void maq_rmdup_core(gzFile, gzFile)': rmdup.cc:46:32: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-truncation] 46 | strncpy(buf, name, tl-1); @@ -663,6 +699,11 @@ rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ +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; + | ^ +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/maq-0.7.1=. -fstack-protector-strong -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] @@ -725,11 +766,11 @@ make -j8 install DESTDIR=/build/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/maq-0.7.1' make[2]: Entering directory '/build/maq-0.7.1' -make[2]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/mkdir -p '/build/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/maq-0.7.1/debian/maq/usr/bin' +make[2]: Nothing to be done for 'install-data-am'. /usr/bin/install -c maq '/build/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/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' dh_install @@ -763,8 +804,8 @@ dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_arm64.deb'. dpkg-deb: building package 'maq' in '../maq_0.7.1-9_arm64.deb'. +dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../maq_0.7.1-9_arm64.buildinfo dpkg-genchanges --build=binary -O../maq_0.7.1-9_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -772,12 +813,14 @@ 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/1948/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1948/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/5022 and its subdirectories -I: Current time: Fri Apr 21 16:53:28 -12 2023 -I: pbuilder-time-stamp: 1682139208 +I: removing directory /srv/workspace/pbuilder/1948 and its subdirectories +I: Current time: Sat May 25 01:17:39 +14 2024 +I: pbuilder-time-stamp: 1716549459