Diff of the two buildlogs: -- --- b1/build.log 2024-05-14 01:23:36.480697316 +0000 +++ b2/build.log 2024-05-14 01:24:21.346788416 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 13 13:21:38 -12 2024 -I: pbuilder-time-stamp: 1715649698 +I: Current time: Mon Jun 16 21:46:40 +14 2025 +I: pbuilder-time-stamp: 1750060000 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/2255787/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3561552/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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 Jun 16 07:46 /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/3561552/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3561552/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='c3d8fe73b7424e569dadfc903913cb0e' - 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='2255787' - PS1='# ' - PS2='> ' + INVOCATION_ID=d997eeea3dcc4b25b0682f37c8618d18 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=3561552 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.tgvLtiMW/pbuilderrc_u4nJ --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.tgvLtiMW/b1 --logfile b1/build.log maq_0.7.1-9.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.tgvLtiMW/pbuilderrc_obmD --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.tgvLtiMW/b2 --logfile b2/build.log maq_0.7.1-9.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 13 11:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2255787/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 14 18:01 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3561552/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 amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] -Fetched 20.0 MB in 0s (41.9 MB/s) +Fetched 20.0 MB in 0s (77.8 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 ... 19699 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/3561552/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3561552/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 -j20 + make -j42 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' @@ -370,25 +406,52 @@ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o merge.o merge.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o match.o match.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o sort_mapping.o sort_mapping.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o assemble.o assemble.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o mapcheck.o mapcheck.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o get_pos.o get_pos.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o aux_utils.o aux_utils.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o subsnp.o subsnp.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o pair_stat.o pair_stat.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o indel_soa.o indel_soa.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o maqmap.o maqmap.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o maqmap_conv.o maqmap_conv.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o altchr.o altchr.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o rmdup.o rmdup.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o simulate.o simulate.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o indel_pe.o indel_pe.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o indel_call.o indel_call.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o eland2maq.o eland2maq.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o csmap2ntmap.o csmap2ntmap.cc +gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o break_pair.o break_pair.c +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o glfgen.o glfgen.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); @@ -412,12 +475,15 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o indel_soa.o indel_soa.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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; + | ^ +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")); + | ^~ 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"); @@ -474,31 +540,6 @@ /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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o maqmap.o maqmap.c -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o maqmap_conv.o maqmap_conv.c -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; - | ~~~~^~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o altchr.o altchr.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o rmdup.o rmdup.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o simulate.o simulate.c -indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': -indel_soa.cc:42:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] - 42 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; - | ~~^~ -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o indel_pe.o indel_pe.cc -gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o stdaln.o stdaln.c -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o indel_call.o indel_call.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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"); @@ -520,66 +561,13 @@ /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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o eland2maq.o eland2maq.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; - | ~~^~~~~~~~~~ -match.cc:61:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] - 61 | x = x + (x >> 32) & 0x0000007F; - | ~~^~~~~~~~~~~ -match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)': -match.cc:67:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] - 67 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; - | ~~^~~~~~~~~~ -match.cc:70:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] - 70 | x = x + (x >> 32) & 0x0000007F; - | ~~^~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -match.cc: In function 'void process_candidate(const required_option_t*, int, bit64_t, match_data_t*, ref_canlist_t*)': -match.cc:284:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ref_canlist_t'; use assignment or value-initialization instead [-Wclass-memaccess] - 284 | memset(list, 0, sizeof(ref_canlist_t)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -match.cc:49:16: note: 'struct ref_canlist_t' declared here - 49 | typedef struct { - | ^ -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o csmap2ntmap.o csmap2ntmap.cc -match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)': -match.cc:292:17: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] - 292 | bit32_t n_reads; - | ^~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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); - | ^~ -In file included from /usr/include/stdio.h:964, - from rbcc.cc:7: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'hash_map_char* cns_load_dbSNP(FILE*)' at rbcc.cc:21:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o break_pair.o break_pair.c -g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o glfgen.o glfgen.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); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for 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; - | ^ -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")); - | ^~ +indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': +indel_soa.cc:42:61: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] + 42 | if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; + | ~~^~ +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; + | ~~^~ In file included from /usr/include/string.h:548, from maqmap.h:23, from simulate.c:11: @@ -598,6 +586,46 @@ mapcheck.cc:60:24: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] 60 | FILE *fp_bfa, *fpout; | ^~~~~ +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); + | ~~~~~~^~~~~~~~~ +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; + | ~~~~^~~~~~~~~ +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); + | ^~ +In file included from /usr/include/stdio.h:964, + from subsnp.cc:2: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'hash_map_char* ma_load_snp(FILE*)' at subsnp.cc:20:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +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; + | ~~~~^~~~~~~~~ +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); + | ^~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'hash_set_char* ma_load_snp_set(FILE*)' at subsnp.cc:35:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ 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); @@ -628,35 +656,39 @@ rmdup.cc:42:40: note: length computed here 42 | int c1, c2, tl = strlen(name); | ~~~~~~^~~~~~ -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; - | ~~~~^~~~~~~~~ -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); - | ~~~~~~^~~~~~~~~ -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); - | ^~ +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; + | ~~^~~~~~~~~~ +match.cc:61:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] + 61 | x = x + (x >> 32) & 0x0000007F; + | ~~^~~~~~~~~~~ +match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)': +match.cc:67:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] + 67 | x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; + | ~~^~~~~~~~~~ +match.cc:70:15: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] + 70 | x = x + (x >> 32) & 0x0000007F; + | ~~^~~~~~~~~~~ +match.cc: In function 'void process_candidate(const required_option_t*, int, bit64_t, match_data_t*, ref_canlist_t*)': +match.cc:284:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ref_canlist_t'; use assignment or value-initialization instead [-Wclass-memaccess] + 284 | memset(list, 0, sizeof(ref_canlist_t)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +match.cc:49:16: note: 'struct ref_canlist_t' declared here + 49 | typedef struct { + | ^ +match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)': +match.cc:292:17: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] + 292 | bit32_t n_reads; + | ^~~~~~~ +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); + | ^~ In file included from /usr/include/stdio.h:964, - from subsnp.cc:2: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'hash_map_char* ma_load_snp(FILE*)' at subsnp.cc:20:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -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); - | ^~ + from rbcc.cc:7: In function 'int sprintf(char*, const char*, ...)', - inlined from 'hash_set_char* ma_load_snp_set(FILE*)' at subsnp.cc:35:10: + inlined from 'hash_map_char* cns_load_dbSNP(FILE*)' at rbcc.cc:21:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -682,21 +714,10 @@ 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 ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -eland2maq.cc: In function 'void export2maq_core(FILE*, FILE*, gzFile)': -eland2maq.cc:563:35: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] - 563 | sprintf(str2, "%s_%d:%d:%d:%d:%d", str, ti[0], ti[1], ti[2], ti[3], ti[4]); - | ^~ -In file included from /usr/include/stdio.h:964, - from eland2maq.cc:9: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'void export2maq_core(FILE*, FILE*, gzFile)' at eland2maq.cc:563:10: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1084 bytes into a destination of size 1024 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +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); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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); @@ -731,22 +752,37 @@ stdaln.c:726:17: note: in expansion of macro 'MYFREE' 726 | MYFREE(s_array[i]); | ^~~~~~ +eland2maq.cc: In function 'void export2maq_core(FILE*, FILE*, gzFile)': +eland2maq.cc:563:35: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] + 563 | sprintf(str2, "%s_%d:%d:%d:%d:%d", str, ti[0], ti[1], ti[2], ti[3], ti[4]); + | ^~ +In file included from /usr/include/stdio.h:964, + from eland2maq.cc:9: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'void export2maq_core(FILE*, FILE*, gzFile)' at eland2maq.cc:563:10: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 11 and 1084 bytes into a destination of size 1024 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ g++ -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/maq-0.7.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz 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 -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 + make -j42 check "TESTSUITEFLAGS=-j42 --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 -j20 install DESTDIR=/build/reproducible-path/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no + make -j42 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' +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/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/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' @@ -782,8 +818,8 @@ 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_amd64.deb'. dpkg-deb: building package 'maq' in '../maq_0.7.1-9_amd64.deb'. +dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-9_amd64.deb'. dpkg-genbuildinfo --build=binary -O../maq_0.7.1-9_amd64.buildinfo dpkg-genchanges --build=binary -O../maq_0.7.1-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -791,12 +827,14 @@ 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/3561552/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3561552/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/2255787 and its subdirectories -I: Current time: Mon May 13 13:23:35 -12 2024 -I: pbuilder-time-stamp: 1715649815 +I: removing directory /srv/workspace/pbuilder/3561552 and its subdirectories +I: Current time: Mon Jun 16 21:47:20 +14 2025 +I: pbuilder-time-stamp: 1750060040