Diff of the two buildlogs: -- --- b1/build.log 2025-03-16 04:05:53.537511639 +0000 +++ b2/build.log 2025-03-16 04:07:08.910120320 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Mar 15 15:55:57 -12 2025 -I: pbuilder-time-stamp: 1742097357 +I: Current time: Sun Apr 19 00:28:55 +14 2026 +I: pbuilder-time-stamp: 1776508135 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -29,52 +29,84 @@ dpkg-source: info: applying cpuid I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3576685/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/748710/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 Apr 18 10:29 /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/748710/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/748710/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='unstable' - 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fe30eabfbb2744f8b51d95895514ad3f' - 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='3576685' - PS1='# ' - PS2='> ' + INVOCATION_ID=8896b1b46ae74b94a48b1b2003b02bc2 + 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=748710 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.SmMyB0Pz/pbuilderrc_Rhc0 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SmMyB0Pz/b1 --logfile b1/build.log canu_2.2+dfsg-5.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.SmMyB0Pz/pbuilderrc_6rbh --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SmMyB0Pz/b2 --logfile b2/build.log canu_2.2+dfsg-5.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 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3576685/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/748710/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -185,7 +217,7 @@ Get: 61 http://deb.debian.org/debian unstable/main amd64 libsnappy-dev amd64 1.2.1-1+b1 [44.1 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libssw-java amd64 1.1-15+b2 [18.6 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 mhap all 2.1.3+dfsg-3 [160 kB] -Fetched 102 MB in 7s (13.7 MB/s) +Fetched 102 MB in 4s (24.1 MB/s) Preconfiguring packages ... Selecting previously unselected package libpipeline1:amd64. (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 ... 19785 files and directories currently installed.) @@ -623,7 +655,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/canu-2.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../canu_2.2+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/748710/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/748710/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/canu-2.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../canu_2.2+dfsg-5_source.changes dpkg-buildpackage: info: source package canu dpkg-buildpackage: info: source version 2.2+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -648,11 +684,11 @@ make[1]: Entering directory '/build/reproducible-path/canu-2.2+dfsg' rm -Rf src/utility/src/utility/libbacktrace src/stores/libsnappy dh_auto_build - cd src && make -j20 "INSTALL=install --strip-program=true" + cd src && make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/canu-2.2+dfsg/src' -/bin/sh: 1: git: not found +/bin/sh: line 1: git: command not found Building release v2.2 -For 'Linux' '6.1.0-32-amd64' as 'amd64' into '/build/reproducible-path/canu-2.2+dfsg/build/{bin,obj}'. +For 'Linux' '6.12.12+bpo-amd64' as 'amd64' into '/build/reproducible-path/canu-2.2+dfsg/build/{bin,obj}'. Using '/usr/bin/g++' version '14'. Using user-supplied CXXFLAGS '-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection'. @@ -676,6 +712,36 @@ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-reader.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-block.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer-stream.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits-wordArray.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/hexDump.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/md5.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/mt19937ar.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/speedCounter.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sweatShop.C +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cpuid.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/memory.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/memory.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_trace.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qx_dispatch.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qb_de_dispatch.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qe_db_dispatch.c +cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cigar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cigar.c +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C +utility/src/utility/kmers-writer.C:55:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] + 55 | #warning how to set prefix size for streaming operations? + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C utility/src/utility/files-memoryMapped.C: In constructor 'memoryMappedFile::memoryMappedFile(const char*, memoryMappedFileType)': utility/src/utility/files-memoryMapped.C:70:9: warning: ignoring return value of 'ssize_t read(int, void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 70 | read(_fd, _data, _length); @@ -684,19 +750,6 @@ utility/src/utility/files-memoryMapped.C:96:10: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | write(_fd, _data, _length), close(_fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers-writer.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/kmers.C -utility/src/utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': -utility/src/utility/files.C:299:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 299 | symlink(pathToFile, pathToLink); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -utility/src/utility/files.C: In function 'void AS_UTL_loadFileList(const char*, std::vector&)': -utility/src/utility/files.C:722:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 722 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -utility/src/utility/files.C:728:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 728 | fgets(line, FILENAME_MAX, F); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ utility/src/utility/system-stackTrace.C: In function 'void AS_UTL_catchCrash(int, siginfo_t*, void*)': utility/src/utility/system-stackTrace.C:40:30: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result] 40 | #define WRITE_STRING(S) write(2, S, strlen(S)) @@ -716,9 +769,18 @@ utility/src/utility/system-stackTrace.C:81:3: note: in expansion of macro 'WRITE_STRING' 81 | WRITE_STRING("'; backtrace (libbacktrace):\n"); | ^~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/bits-wordArray.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/hexDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/hexDump.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C +utility/src/utility/files.C: In function 'void AS_UTL_symlink(const char*, const char*)': +utility/src/utility/files.C:299:10: warning: ignoring return value of 'int symlink(const char*, const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 299 | symlink(pathToFile, pathToLink); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +utility/src/utility/files.C: In function 'void AS_UTL_loadFileList(const char*, std::vector&)': +utility/src/utility/files.C:722:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 722 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +utility/src/utility/files.C:728:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 728 | fgets(line, FILENAME_MAX, F); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ utility/src/utility/logging.C: In member function 'void logFileInstance::rotate()': utility/src/utility/logging.C:157:46: warning: '.' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 157 | snprintf(_filePrefix, FILENAME_MAX, "%s.%03u.%s", _prefix, _order, _name); @@ -787,11 +849,16 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -utility/src/utility/kmers-writer.C:55:2: warning: #warning how to set prefix size for streaming operations? [-Wcpp] - 55 | #warning how to set prefix size for streaming operations? - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/md5.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/md5.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/mt19937ar.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C utility/src/utility/kmers-reader.C: In member function 'void merylFileReader::initializeFromMasterIndex(bool, bool, bool)': utility/src/utility/kmers-reader.C:133:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 133 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _inName); @@ -809,16 +876,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/speedCounter.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/utility/sweatShop.C -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cpuid.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/memory.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/memory.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_trace.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qx_dispatch.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qb_de_dispatch.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/sg_qe_db_dispatch.c -cc -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cigar.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utility/src/parasail/cigar.c utility/src/utility/kmers-writer.C: In destructor 'merylFileWriter::~merylFileWriter()': utility/src/utility/kmers-writer.C:144:32: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 144 | snprintf(N, FILENAME_MAX, "%s/merylIndex", _outName); @@ -836,64 +893,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/computeGlobalScore.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqCache.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqLibrary.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadData.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadDataWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqReadDataWriter.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStore.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreBlob.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreConstructor.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/sqStoreInfo.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovOverlap.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStore.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreWriter.C -stores/ovOverlap.C:201:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] - 201 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFilter.C stores/ovStoreWriter.C:33:2: warning: #warning not failing if a valid store [-Wcpp] 33 | #warning not failing if a valid store | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreFile.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/ovStoreHistogram.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgStore.C -stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': -stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] - 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 59 | dat.ovl.ahg5, dat.ovl.ahg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] - 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 59 | dat.ovl.ahg5, dat.ovl.ahg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] - 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 60 | dat.ovl.bhg5, dat.ovl.bhg3, - | ~~~~~~~~~~~~ - | | - | int -stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] - 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 60 | dat.ovl.bhg5, dat.ovl.bhg3, - | ~~~~~~~~~~~~ - | | - | int -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTig.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/objectStore.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C +stores/ovOverlap.C:201:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp] + 201 | #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C In file included from stores/sqStoreBlob.C:18: In function 'void makeBlobName(const char*, uint32, char*)', inlined from 'void sqStoreBlobWriter::writeData(sqReadDataWriter*)' at stores/sqStoreBlob.C:65:17: @@ -913,8 +931,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C +In function 'void makeBlobName(const char*, uint32, char*)', + inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:113:17: +stores/sqStore.H:106:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 106 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); +stores/sqStore.H:106:36: note: directive argument in the range [1, 65535] +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void makeBlobName(const char*, uint32, char*)' at stores/sqStore.H:106:11, + inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:113:17: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C stores/sqStoreConstructor.C: In destructor 'sqStore::~sqStore()': stores/sqStoreConstructor.C:329:32: warning: '/version.' directive output may be truncated writing 9 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 329 | snprintf(No, FILENAME_MAX, "%s/version.%03" F_U32P, sqStore_path(), V); @@ -1152,69 +1187,44 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In function 'void makeBlobName(const char*, uint32, char*)', - inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:113:17: -stores/sqStore.H:106:36: warning: '/blobs.' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 106 | snprintf(blobName, FILENAME_MAX, "%s/blobs.%04" F_U32P , storePath, blobNumber); -stores/sqStore.H:106:36: note: directive argument in the range [1, 65535] -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void makeBlobName(const char*, uint32, char*)' at stores/sqStore.H:106:11, - inlined from 'readBuffer* sqStoreBlobReader::getBuffer(sqReadMeta*)' at stores/sqStoreBlob.C:113:17: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4109 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/objectStore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap stores/objectStore.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C -stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': -stores/ovStoreWriter.C:190:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 190 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); - | ^~~~~~~ -In file included from /usr/include/stdio.h:970, - from utility/src/utility/types.H:48, - from utility/src/utility/runtime.H:26, - from stores/ovStore.H:21, - from stores/ovStoreWriter.C:18: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)' at stores/ovStoreWriter.C:190:13: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': -stores/ovStoreWriter.C:199:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 199 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); - | ^~~~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)' at stores/ovStoreWriter.C:199:13: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': -stores/ovStoreWriter.C:222:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 222 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); - | ^~~~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)' at stores/ovStoreWriter.C:222:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/dumpBlob.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreBuild.C +stores/ovOverlap.C: In member function 'char* ovOverlap::toString(char*, ovOverlapDisplayType, bool)': +stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] + 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 59 | dat.ovl.ahg5, dat.ovl.ahg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] + 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 59 | dat.ovl.ahg5, dat.ovl.ahg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] + 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 60 | dat.ovl.bhg5, dat.ovl.bhg3, + | ~~~~~~~~~~~~ + | | + | int +stores/ovOverlap.C:55:20: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] + 55 | sprintf(str, "%10" F_U32P " %10" F_U32P " %c %6" F_U32P " %6" F_OVP " %6" F_OVP " %6" F_OVP " %6" F_OVP " %7.6f %s %s %s%s", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 60 | dat.ovl.bhg5, dat.ovl.bhg3, + | ~~~~~~~~~~~~ + | | + | int +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreConfig.C stores/ovStoreHistogram.C: In member function 'void ovErateLengthHistogram::addOverlap(ovOverlap*)': stores/ovStoreHistogram.C:337:21: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'int' [-Wformat=] 337 | fprintf(stderr, "BOGUS overlap - id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP " -- id %8u (len %6d) hangs %6" F_OVP " %6" F_OVP "%s\n", @@ -1246,57 +1256,49 @@ | ~~~~~~~~~~~~~~~~~~~~~ | | | int -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': -stores/ovStoreWriter.C:306:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 306 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); - | ^ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)' at stores/ovStoreWriter.C:306:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -stores/ovStore.H: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': -stores/ovStore.H:88:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 88 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); - | ^ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreBucketizer.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreSorter.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreIndexer.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreDump.C +stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': +stores/ovStoreWriter.C:190:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 190 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, i, _sliceNum); + | ^~~~~~~ +In file included from /usr/include/stdio.h:970, + from utility/src/utility/types.H:48, + from utility/src/utility/runtime.H:26, + from stores/ovStore.H:21, + from stores/ovStoreWriter.C:18: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void ovStoreInfo::save(const char*, uint32, bool)' at stores/ovStore.H:88:15, - inlined from 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)' at stores/ovStoreWriter.C:311:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 + inlined from 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)' at stores/ovStoreWriter.C:190:13: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C -stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': -stores/ovStoreWriter.C:366:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] - 366 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); - | ^ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C +stores/ovStoreWriter.C: In member function 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)': +stores/ovStoreWriter.C:199:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 199 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/sliceSizes", _storePath, i); + | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void ovStoreSliceWriter::mergeInfoFiles()' at stores/ovStoreWriter.C:366:13: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + inlined from 'uint64 ovStoreSliceWriter::loadBucketSizes(uint64*)' at stores/ovStoreWriter.C:199:13: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 23 and 4125 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': -stores/ovStore.H:86:39: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 86 | snprintf(name, FILENAME_MAX, "%s/info", path); - | ^~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreStats.C +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)': +stores/ovStoreWriter.C:222:35: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 222 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bucket, _sliceNum); + | ^~~~~~~ In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void ovStoreInfo::save(const char*, uint32, bool)' at stores/ovStore.H:86:15, - inlined from 'void ovStoreSliceWriter::mergeInfoFiles()' at stores/ovStoreWriter.C:389:12: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 + inlined from 'void ovStoreSliceWriter::loadOverlapsFromBucket(uint32, uint64, ovOverlap*, uint64&)' at stores/ovStoreWriter.C:222:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 22 and 4130 bytes into a destination of size 4096 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, @@ -1355,6 +1357,33 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': +stores/ovStoreWriter.C:306:40: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 306 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, _sliceNum); + | ^ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)' at stores/ovStoreWriter.C:306:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +stores/ovStore.H: In member function 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)': +stores/ovStore.H:88:39: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 88 | snprintf(name, FILENAME_MAX, "%s/%04u.info", path, index); + | ^ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void ovStoreInfo::save(const char*, uint32, bool)' at stores/ovStore.H:88:15, + inlined from 'void ovStoreSliceWriter::writeOverlaps(ovOverlap*, uint64)' at stores/ovStoreWriter.C:311:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 11 and 4113 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ stores/tgStore.C: In member function 'void tgStore::dumpMASR(tgStoreEntry*&, uint32&, uint32)': stores/tgStore.C:571:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 571 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.tig", _path, V); @@ -1419,6 +1448,63 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/sqStoreCreate.C +stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': +stores/tgTig.C:537:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 537 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ +stores/tgTig.C:667:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 667 | fgets(LINE, LINEmax, F); LINEnum++; + | ~~~~~^~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Iseqrequester/src/seqrequester stores/sqStoreDumpMetaData.C +stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': +stores/tgStore.C:672:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 672 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); + | ^~~~~~~~ +stores/tgStore.C:672:33: note: using the range [-2147483648, 2147483647] for directive argument + 672 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); + | ^~~~~~~~~~~~~~~~~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'FILE* tgStore::openDB(uint32)' at stores/tgStore.C:672:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Iseqrequester/src/seqrequester seqrequester/src/seqrequester/summarize.C +stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': +stores/ovStoreWriter.C:366:42: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] + 366 | snprintf(indexName, FILENAME_MAX, "%s/%04u.index", _storePath, ss); + | ^ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void ovStoreSliceWriter::mergeInfoFiles()' at stores/ovStoreWriter.C:366:13: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4114 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +stores/ovStore.H: In member function 'void ovStoreSliceWriter::mergeInfoFiles()': +stores/ovStore.H:86:39: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 86 | snprintf(name, FILENAME_MAX, "%s/info", path); + | ^~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void ovStoreInfo::save(const char*, uint32, bool)' at stores/ovStore.H:86:15, + inlined from 'void ovStoreSliceWriter::mergeInfoFiles()' at stores/ovStoreWriter.C:389:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreCompress.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreDump.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgTigSizeAnalysis.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeOverlapSlice()': stores/ovStoreWriter.C:448:37: warning: '/bucket' directive output may be truncated writing 7 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 448 | snprintf(name, FILENAME_MAX, "%s/bucket%04u/slice%04u", _storePath, bb, _sliceNum); @@ -1432,6 +1518,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreLoad.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgTigDisplay.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/loadCorrectedReads.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::checkSortingIsComplete()': stores/ovStoreWriter.C:467:38: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 467 | snprintf(nameF, FILENAME_MAX, "%s/%04u.info", _storePath, i); @@ -1458,23 +1547,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -stores/tgStore.C: In member function 'FILE* tgStore::openDB(uint32)': -stores/tgStore.C:672:36: warning: '/seqDB.v' directive output may be truncated writing 8 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 672 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); - | ^~~~~~~~ -stores/tgStore.C:672:33: note: using the range [-2147483648, 2147483647] for directive argument - 672 | snprintf(_name, FILENAME_MAX, "%s/seqDB.v%03d.dat", _path, version); - | ^~~~~~~~~~~~~~~~~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'FILE* tgStore::openDB(uint32)' at stores/tgStore.C:672:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 16 and 4120 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/loadTrimmedReads.C stores/ovStoreWriter.C: In member function 'void ovStoreSliceWriter::removeAllIntermediateFiles()': stores/ovStoreWriter.C:499:37: warning: '/' directive output may be truncated writing 1 byte into a region of size between 0 and 4096 [-Wformat-truncation=] 499 | snprintf(name, FILENAME_MAX, "%s/%04u.index", _storePath, ss); @@ -1540,50 +1613,28 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C -stores/tgTig.C: In member function 'bool tgTig::loadLayout(FILE*)': -stores/tgTig.C:537:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 537 | fgets(LINE, LINEmax, F); LINEnum++; - | ~~~~~^~~~~~~~~~~~~~~~~~ -stores/tgTig.C:667:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 667 | fgets(LINE, LINEmax, F); LINEnum++; - | ~~~~~^~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/gfa.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/gfa.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/bed.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src -Iutility/src/utility -Iutility/src/parasail -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/liboverlap gfa/bed.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/dumpBlob/stores/dumpBlob.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/dumpBlob.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreBuild/stores/ovStoreBuild.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreBuild.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreConfig/stores/ovStoreConfig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreConfig.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreBucketizer/stores/ovStoreBucketizer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreBucketizer.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreSorter/stores/ovStoreSorter.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreSorter.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreIndexer/stores/ovStoreIndexer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreIndexer.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreDump/stores/ovStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreDump.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/ovStoreStats/stores/ovStoreStats.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/ovStoreStats.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreCreate/stores/sqStoreCreate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/sqStoreCreate.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/sqStoreDumpFASTQ.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Iseqrequester/src/seqrequester stores/sqStoreDumpMetaData.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Iseqrequester/src/seqrequester seqrequester/src/seqrequester/summarize.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreCompress.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgStoreDump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreDump.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgTigSizeAnalysis.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgStoreLoad.C -stores/tgStoreDump.C:643:2: warning: #warning replace this with genericStatistics [-Wcpp] - 643 | #warning replace this with genericStatistics - | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/tgTigDisplay.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/loadCorrectedReads/stores/loadCorrectedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/loadCorrectedReads.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/loadTrimmedReads/stores/loadTrimmedReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Istores -Iutility/src/utility -IoverlapBasedTrimming stores/loadTrimmedReads.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/loadErates/stores/loadErates.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility stores/loadErates.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/meryl.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/meryl.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylCommandBuilder.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCommandBuilder.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylCountArray.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylCountArray.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylInput.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C +stores/tgStoreDump.C:643:2: warning: #warning replace this with genericStatistics [-Wcpp] + 643 | #warning replace this with genericStatistics + | ^~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countThreads.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-histogram.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-nextMer.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapCheck/overlapCheck.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTQ()': stores/sqStoreDumpFASTQ.C:70:36: warning: '.fastq' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 70 | snprintf(N, FILENAME_MAX, "%s.fastq%s", _p, _s); @@ -1614,6 +1665,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C stores/sqStoreDumpFASTQ.C: In member function 'FILE* libOutput::openFASTA()': stores/sqStoreDumpFASTQ.C:100:36: warning: '.fasta' directive output may be truncated writing 6 bytes into a region of size between 1 and 4096 [-Wformat-truncation=] 100 | snprintf(N, FILENAME_MAX, "%s.fasta%s", _p, _s); @@ -1640,13 +1692,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylInput.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylInput.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-count.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-count.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-countSimple.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countSimple.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-countThreads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-countThreads.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-histogram.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-histogram.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp-nextMer.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp-nextMer.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/meryl/meryl/src/meryl/merylOp.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -DCANU -Iutility/src/utility -Istores meryl/src/meryl/merylOp.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Imhap/liboverlap mhap/mhapConvert.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iminimap/liboverlap minimap/mmapConvert.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores correction/filterCorrectionOverlaps.C stores/loadErates.C: In member function 'void ovStore::addEvalues(std::vector&)': stores/loadErates.C:59:41: warning: '/evalues.WORKING' directive output may be truncated writing 16 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] 59 | snprintf(evalueTemp, FILENAME_MAX, "%s/evalues.WORKING", _storePath); @@ -1677,84 +1729,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapCheck/overlapCheck/overlapCheck.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapCheck/overlapCheck.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Build_Hash_Index.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Build_Hash_Index.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Find_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Find_Overlaps.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Output.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_Overlaps.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCore-Process_String_Overlaps.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapInCorePartition/overlapInCore/overlapInCorePartition.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapConvert/overlapInCore/overlapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapImport/overlapInCore/overlapImport.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapInCore/overlapImport.C -meryl/src/meryl/merylCommandBuilder.C: In member function 'void merylCommandBuilder::initialize(char*)': -meryl/src/meryl/merylCommandBuilder.C:160:41: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 160 | snprintf(_indexName, FILENAME_MAX, "%s/merylIndex", _optString); - | ^~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from utility/src/utility/types.H:48, - from utility/src/utility/runtime.H:26, - from meryl/src/meryl/meryl.H:22, - from meryl/src/meryl/merylCommandBuilder.C:19: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void merylCommandBuilder::initialize(char*)' at meryl/src/meryl/merylCommandBuilder.C:160:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/src/meryl/merylCommandBuilder.C: In member function 'void merylCommandBuilder::initialize(char*)': -meryl/src/meryl/merylCommandBuilder.C:161:41: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 161 | snprintf(_sqInfName, FILENAME_MAX, "%s/info", _optString); - | ^~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void merylCommandBuilder::initialize(char*)' at meryl/src/meryl/merylCommandBuilder.C:161:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -meryl/src/meryl/merylCommandBuilder.C: In member function 'void merylCommandBuilder::initialize(char*)': -meryl/src/meryl/merylCommandBuilder.C:162:41: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 162 | snprintf(_sqRdsName, FILENAME_MAX, "%s/reads", _optString); - | ^~~~~~ -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void merylCommandBuilder::initialize(char*)' at meryl/src/meryl/merylCommandBuilder.C:162:11: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapPair/overlapInCore/overlapPair.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/overlapPair.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/edalign/overlapInCore/edalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapInCore/edalign.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/mhapConvert/mhap/mhapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Imhap/liboverlap mhap/mhapConvert.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/mmapConvert/minimap/mmapConvert.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iminimap/liboverlap minimap/mmapConvert.C overlapInCore/overlapPair.C:463:2: warning: #warning do we need to check for contained too? [-Wcpp] 463 | #warning do we need to check for contained too? | ^~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores correction/filterCorrectionOverlaps.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns correction/generateCorrectionLayouts.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C overlapInCore/overlapInCore-Build_Hash_Index.C: In function 'void Mark_Skip_Kmers()': overlapInCore/overlapInCore-Build_Hash_Index.C:209:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 209 | fgets(line, 1024, F); | ~~~~~^~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/generateCorrectionLayouts/correction/generateCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns correction/generateCorrectionLayouts.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/generateCorrectionLayouts/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/filterCorrectionLayouts/correction/filterCorrectionLayouts.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores correction/filterCorrectionLayouts.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/falconsense/correction/falconsense.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns correction/falconsense.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/falconsense/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns utgcns/stashContains.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/errorEstimate/correction/errorEstimate.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns haplotyping/splitHaplotype.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-bestEdge.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-largestCovered.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-workUnit.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-subReads.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-trimBad.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustNormal.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustFlipped.C overlapInCore/edalign.C: In function 'bool readLine(FILE*, char*, int32, int32&, splitToWords&)': overlapInCore/edalign.C:30:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets(line, lineMax, file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitHaplotype/haplotyping/splitHaplotype.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -Iutgcns haplotyping/splitHaplotype.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/mergeRanges.C overlapInCore/overlapImport.C: In function 'int main(int, char**)': overlapInCore/overlapImport.C:254:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 254 | fgets(S, 1024, in->file()); @@ -1762,41 +1764,8 @@ overlapInCore/overlapImport.C:284:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fgets(S, 1024, in->file()); | ~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads-bestEdge.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-bestEdge.C -minimap/mmapConvert.C: In function 'int main(int, char**)': -minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] - 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~ - | | - | int -minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] - 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, - | ~~~~~~~~~~~~~~~ - | | - | int -minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] - 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, - | ~~~~~~~~~~~~~~~ - | | - | int -minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] - 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -...... - 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, - | ~~~~~~~~~~~~~~~ - | | - | int +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C +g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C mhap/mhapConvert.C: In function 'int main(int, char**)': mhap/mhapConvert.C:147:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] 147 | fprintf(stderr, "%s\nINVALID OVERLAP read " F_U32 " (len %d) and read " F_U32 " (len %d) hangs " F_OV "/" F_OV " and " F_OV "/" F_OV "%s\n", @@ -1830,32 +1799,87 @@ | ~~~~~~~~~~~~~~~ | | | int -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/trimReads/overlapBasedTrimming/trimReads-largestCovered.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/trimReads-largestCovered.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-workUnit.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-workUnit.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-subReads.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-subReads.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/splitReads-trimBad.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/splitReads-trimBad.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustNormal.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustNormal.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/splitReads/overlapBasedTrimming/adjustFlipped.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/adjustFlipped.C -In file included from overlapBasedTrimming/trimReads.C:19: -overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(const char*, const char*, uint32)': -overlapBasedTrimming/trimStat.H:69:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | system(N); - | ~~~~~~^~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/mergeRanges/overlapBasedTrimming/mergeRanges.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapBasedTrimming/mergeRanges.C -correction/falconsense.C: In function 'void loadReadList(const char*, uint32, uint32, std::set&)': -correction/falconsense.C:64:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 64 | for (fgets(L, 1024, R); - | ~~~~~^~~~~~~~~~~~ -correction/falconsense.C:66:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 66 | fgets(L, 1024, R)) { - | ~~~~~^~~~~~~~~~~~ -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/overlapAlign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/overlapAlign.C -g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeOverlapAlignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeOverlapAlignment.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/trimRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/trimRead.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/clearRangeFile.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/clearRangeFile.C +minimap/mmapConvert.C: In function 'int main(int, char**)': +minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'int' [-Wformat=] + 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~ + | | + | int +minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 8 has type 'int' [-Wformat=] + 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 130 | ov.dat.ovl.ahg5, ov.dat.ovl.ahg3, + | ~~~~~~~~~~~~~~~ + | | + | int +minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 9 has type 'int' [-Wformat=] + 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, + | ~~~~~~~~~~~~~~~ + | | + | int +minimap/mmapConvert.C:127:25: warning: format '%lu' expects argument of type 'long unsigned int', but argument 10 has type 'int' [-Wformat=] + 127 | fprintf(stderr, "INVALID OVERLAP " F_U32 " (len %6d) " F_U32 " (len %6d) hangs " F_OV " " F_OV " - " F_OV " " F_OV "%s\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +...... + 131 | ov.dat.ovl.bhg5, ov.dat.ovl.bhg3, + | ~~~~~~~~~~~~~~~ + | | + | int g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/overlapAlign/overlapAlign/computeAlignments.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib overlapAlign/computeAlignments.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors.C +meryl/src/meryl/merylCommandBuilder.C: In member function 'void merylCommandBuilder::initialize(char*)': +meryl/src/meryl/merylCommandBuilder.C:160:41: warning: '/merylIndex' directive output may be truncated writing 11 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 160 | snprintf(_indexName, FILENAME_MAX, "%s/merylIndex", _optString); + | ^~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from utility/src/utility/types.H:48, + from utility/src/utility/runtime.H:26, + from meryl/src/meryl/meryl.H:22, + from meryl/src/meryl/merylCommandBuilder.C:19: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void merylCommandBuilder::initialize(char*)' at meryl/src/meryl/merylCommandBuilder.C:160:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4108 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/src/meryl/merylCommandBuilder.C: In member function 'void merylCommandBuilder::initialize(char*)': +meryl/src/meryl/merylCommandBuilder.C:161:41: warning: '/info' directive output may be truncated writing 5 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 161 | snprintf(_sqInfName, FILENAME_MAX, "%s/info", _optString); + | ^~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void merylCommandBuilder::initialize(char*)' at meryl/src/meryl/merylCommandBuilder.C:161:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 6 and 4102 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +meryl/src/meryl/merylCommandBuilder.C: In member function 'void merylCommandBuilder::initialize(char*)': +meryl/src/meryl/merylCommandBuilder.C:162:41: warning: '/reads' directive output may be truncated writing 6 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 162 | snprintf(_sqRdsName, FILENAME_MAX, "%s/reads", _optString); + | ^~~~~~ +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void merylCommandBuilder::initialize(char*)' at meryl/src/meryl/merylCommandBuilder.C:162:11: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 7 and 4103 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Analyze_Alignment.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Analyze_Alignment.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Output.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Output.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/findErrors/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C @@ -1866,6 +1890,11 @@ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/fixErrors/overlapErrorAdjustment/fixErrors.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapErrorAdjustment/fixErrors.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/fixErrors/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores overlapErrorAdjustment/correctOverlaps-Correct_Frags.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/findErrors-Dump/overlapErrorAdjustment/findErrors-Dump.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/findErrors-Dump.C +In file included from overlapBasedTrimming/trimReads.C:19: +overlapBasedTrimming/trimStat.H: In member function 'void trimStat::generatePlots(const char*, const char*, uint32)': +overlapBasedTrimming/trimStat.H:69:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | system(N); + | ~~~~~~^~~ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Correct_Frags.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Correct_Frags.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Read_Olaps.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Read_Olaps.C @@ -1873,6 +1902,13 @@ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/computeDiff.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/computeDiff.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/correctOverlaps/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/liboverlap overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/bogart.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/bogart.C +correction/falconsense.C: In function 'void loadReadList(const char*, uint32, uint32, std::set&)': +correction/falconsense.C:64:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 64 | for (fgets(L, 1024, R); + | ~~~~~^~~~~~~~~~~~ +correction/falconsense.C:66:13: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 66 | fgets(L, 1024, R)) { + | ~~~~~^~~~~~~~~~~~ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_AssemblyGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_AssemblyGraph.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_BestOverlapGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_BestOverlapGraph.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_ChunkGraph.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_ChunkGraph.C @@ -1892,29 +1928,6 @@ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_ReadInfo.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_ReadInfo.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SetParentAndHang.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SetParentAndHang.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SplitDiscontinuous.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitDiscontinuous.C -bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': -bogart/AS_BAT_Logging.C:115:36: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] - 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); - | ^~~~ -In member function 'void logFileInstance::open()', - inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:110:1: -bogart/AS_BAT_Logging.C:115:33: note: using the range [-2147483648, 2147483647] for directive argument - 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); - | ^~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:970, - from utility/src/utility/types.H:48, - from utility/src/utility/system.H:23, - from bogart/AS_BAT_Logging.C:18: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:115:11, - inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:110:1: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4116 bytes into a destination of size 4096 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_SplitTig_AtReadEnds.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_SplitTig_AtReadEnds.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_TigVector.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_TigVector.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/bogart/bogart/AS_BAT_Unitig.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores bogart/AS_BAT_Unitig.C @@ -1961,6 +1974,29 @@ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/stashContains.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/stashContains.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/utgcns/utgcns/unitigConsensus.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Iutility/src/parasail -Istores -Iutgcns/libpbutgcns -Iutgcns/libboost utgcns/unitigConsensus.C g++ -o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/alignGFA/gfa/alignGFA.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/canu-2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -pthread -fopenmp -fPIC -DLIBBACKTRACE -I/build/reproducible-path/canu-2.2+dfsg/src -Iutility/src/utility -Istores -IoverlapInCore/libedlib gfa/alignGFA.C +bogart/AS_BAT_Logging.C: In member function 'void logFileInstance::open()': +bogart/AS_BAT_Logging.C:115:36: warning: '.num' directive output may be truncated writing 4 bytes into a region of size between 0 and 4096 [-Wformat-truncation=] + 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); + | ^~~~ +In member function 'void logFileInstance::open()', + inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:110:1: +bogart/AS_BAT_Logging.C:115:33: note: using the range [-2147483648, 2147483647] for directive argument + 115 | snprintf(_path, FILENAME_MAX, "%s.num%03d.log", _name, _part); + | ^~~~~~~~~~~~~~~~ +In file included from /usr/include/stdio.h:970, + from utility/src/utility/types.H:48, + from utility/src/utility/system.H:23, + from bogart/AS_BAT_Logging.C:18: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:115:11, + inlined from 'void logFileInstance::open()' at bogart/AS_BAT_Logging.C:110:1: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 12 and 4116 bytes into a destination of size 4096 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ cp -pf pipelines/canu.pl /build/reproducible-path/canu-2.2+dfsg/build/bin/canu cp -pf pipelines/canu-time.pl /build/reproducible-path/canu-2.2+dfsg/build/bin/canu-time cp -pf pipelines/draw-tig.pl /build/reproducible-path/canu-2.2+dfsg/build/bin/draw-tig @@ -1989,6 +2025,10 @@ cp -pf pipelines/canu/OverlapStore.pm /build/reproducible-path/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Report.pm /build/reproducible-path/canu-2.2+dfsg/build/lib/site_perl/canu/ cp -pf pipelines/canu/Unitig.pm /build/reproducible-path/canu-2.2+dfsg/build/lib/site_perl/canu/ +gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': +gfa/alignGFA.C:148:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 148 | system(Pname); + | ~~~~~~^~~~~~~ ar -rv /build/reproducible-path/canu-2.2+dfsg/build/lib/libcanu.a /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/runtime.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/align-parasail-driver.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/edlib.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-buffered.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-compressed.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-fasta-fastq.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/files-memoryMapped.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/logging.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/strings.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/system.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/system-stackTrace.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/sequence.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/types.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-exact.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-files.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-histogram.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-reader.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-block.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer-stream.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers-writer.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/kmers.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/bits-wordArray.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/hexDump.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/md5.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/mt19937ar.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/speedCounter.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/sweatShop.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cpuid.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/memory.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_trace.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qx_dispatch.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qb_de_dispatch.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/sg_qe_db_dispatch.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/parasail/cigar.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/computeGlobalScore.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqCache.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqLibrary.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadData.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqReadDataWriter.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStore.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreBlob.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreConstructor.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/sqStoreInfo.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovOverlap.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStore.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreWriter.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFilter.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreFile.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/ovStoreHistogram.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgStore.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTig.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/stores/objectStore.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/gfa.o /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/gfa/bed.o ar: creating /build/reproducible-path/canu-2.2+dfsg/build/lib/libcanu.a a - /build/reproducible-path/canu-2.2+dfsg/build/obj/lib/libcanu.a/utility/src/utility/runtime.o @@ -2080,10 +2120,6 @@ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/bin/sqStoreDumpFASTQ -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.2+dfsg/build/lib /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpFASTQ/stores/sqStoreDumpFASTQ.o -lcanu -lsnappy -lbacktrace g++ -o /build/reproducible-path/canu-2.2+dfsg/build/bin/sqStoreDumpMetaData -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.2+dfsg/build/lib /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/stores/sqStoreDumpMetaData.o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/sqStoreDumpMetaData/seqrequester/src/seqrequester/summarize.o -lcanu -lsnappy -lbacktrace g++ -o /build/reproducible-path/canu-2.2+dfsg/build/bin/tgStoreCompress -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.2+dfsg/build/lib /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreCompress/stores/tgStoreCompress.o -lcanu -lsnappy -lbacktrace -gfa/alignGFA.C: In function 'void dotplot(uint32, bool, char*, uint32, bool, char*)': -gfa/alignGFA.C:148:9: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 148 | system(Pname); - | ~~~~~~^~~~~~~ g++ -o /build/reproducible-path/canu-2.2+dfsg/build/bin/tgStoreDump -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.2+dfsg/build/lib /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgStoreDump.o /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreDump/stores/tgTigSizeAnalysis.o -lcanu -lsnappy -lbacktrace g++ -o /build/reproducible-path/canu-2.2+dfsg/build/bin/tgStoreLoad -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.2+dfsg/build/lib /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgStoreLoad/stores/tgStoreLoad.o -lcanu -lsnappy -lbacktrace g++ -o /build/reproducible-path/canu-2.2+dfsg/build/bin/tgTigDisplay -Wl,-z,relro -Wl,-z,now -pthread -fopenmp -lm -L/build/reproducible-path/canu-2.2+dfsg/build/lib /build/reproducible-path/canu-2.2+dfsg/build/obj/bin/tgTigDisplay/stores/tgTigDisplay.o -lcanu -lsnappy -lbacktrace @@ -2168,12 +2204,14 @@ 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/748710/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/748710/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/3576685 and its subdirectories -I: Current time: Sat Mar 15 16:05:52 -12 2025 -I: pbuilder-time-stamp: 1742097952 +I: removing directory /srv/workspace/pbuilder/748710 and its subdirectories +I: Current time: Sun Apr 19 00:30:07 +14 2026 +I: pbuilder-time-stamp: 1776508207