Diff of the two buildlogs: -- --- b1/build.log 2024-04-04 01:05:20.486764810 +0000 +++ b2/build.log 2024-04-04 01:26:17.949408526 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 3 12:56:04 -12 2024 -I: pbuilder-time-stamp: 1712192164 +I: Current time: Thu Apr 4 15:06:16 +14 2024 +I: pbuilder-time-stamp: 1712192776 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying spdlog-1.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6727/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4726/tmp/hooks/D01_modify_environment starting +debug: Running on ff4a. +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 4 01:06 /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/4726/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4726/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='d798d96a1a5c458c9a5f5eb1f8b9f356' - 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='6727' - PS1='# ' - PS2='> ' + INVOCATION_ID=5ae880380f5e42ce93212aad0a9fff45 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4726 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.gffSj1r0/pbuilderrc_WhL4 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gffSj1r0/b1 --logfile b1/build.log hinge_0.5.0-7.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gffSj1r0/pbuilderrc_0LYo --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gffSj1r0/b2 --logfile b2/build.log hinge_0.5.0-7.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64c 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 1 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6727/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 2 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4726/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -360,7 +392,7 @@ Get: 211 http://deb.debian.org/debian trixie/main armhf python3-pysam armhf 0.22.0+ds-1+b1 [3781 kB] Get: 212 http://deb.debian.org/debian trixie/main armhf python3-pbcore all 2.1.2+dfsg-7 [2831 kB] Get: 213 http://deb.debian.org/debian trixie/main armhf python3-ujson armhf 5.9.0-1+b1 [24.0 kB] -Fetched 193 MB in 6s (34.7 MB/s) +Fetched 193 MB in 13s (15.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19637 files and directories currently installed.) @@ -1051,8 +1083,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Apr 4 00:57:43 UTC 2024. -Universal Time is now: Thu Apr 4 00:57:43 UTC 2024. +Local time is now: Thu Apr 4 01:09:20 UTC 2024. +Universal Time is now: Thu Apr 4 01:09:20 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1246,7 +1278,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/hinge-0.5.0/ && 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 > ../hinge_0.5.0-7_source.changes +I: user script /srv/workspace/pbuilder/4726/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4726/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/hinge-0.5.0/ && 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 > ../hinge_0.5.0-7_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-7 dpkg-buildpackage: info: source distribution unstable @@ -1340,7 +1376,7 @@ CMake that the project does not need compatibility with older versions. --- Configuring done (1.3s) +-- Configuring done (6.6s) CMake Warning (dev) at src/filter/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy @@ -1381,7 +1417,7 @@ /build/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp This warning is for project developers. Use -Wno-dev to suppress it. --- Generating done (0.1s) +-- Generating done (0.3s) CMake Warning: Manually-specified variables were not used by the project: @@ -1396,37 +1432,52 @@ -- Build files have been written to: /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/hinge-0.5.0 -B/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend -make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/CMakeFiles/man.dir/DependInfo.cmake "--color=" +make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake "--color=" +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build -make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build +make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' [ 3%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o -[ 6%] Generating hinge.1 -[ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin && /usr/bin/pandoc --from markdown --to man -s /build/reproducible-path/hinge-0.5.0/src/hinge.1.md -o hinge.1 cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/ini.c +[ 6%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/align.c +[ 10%] Generating hinge.1 +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin && /usr/bin/pandoc --from markdown --to man -s /build/reproducible-path/hinge-0.5.0/src/hinge.1.md -o hinge.1 +[ 13%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DB.c make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 13%] Built target man +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); @@ -1437,75 +1488,34 @@ /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Built target man -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 13%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/align.c -[ 17%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/lib/INIReader.cpp -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 40 [-Wfree-nonheap-object] - 533 | free(reads); - | ^~~~~~~~~~~ -In function 'Malloc', - inlined from 'Open_DB' at /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:525:29: -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' - 84 | if ((p = malloc(size)) == NULL) - | ^~~~~~~~~~~~ -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:1587:15: warning: 'free' called on pointer 'p' with nonzero offset 1 [-Wfree-nonheap-object] - 1587 | free(seq); - | ^~~~~~~~~ -In function 'Malloc', - inlined from 'Read_All_Sequences' at /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:1564:18: -/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' - 84 | if ((p = malloc(size)) == NULL) - | ^~~~~~~~~~~~ -[ 20%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/QV.c -/build/reproducible-path/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table': -/build/reproducible-path/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] - 164 | { uint64 symbol = (uint64) (node->lft); - | ^ -/build/reproducible-path/hinge-0.5.0/src/lib/QV.c: In function 'Huffman': -/build/reproducible-path/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] - 211 | node[value].lft = (HTree *) (uint64) i; - | ^ -[ 24%] Linking CXX static library libini.a -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 -/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o -/usr/bin/ranlib libini.a -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 24%] Built target ini -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 27%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o +[ 17%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/paf.c -[ 31%] Linking C static library libPAF.a +[ 20%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/lib/INIReader.cpp +[ 24%] Linking C static library libPAF.a cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 /usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /usr/bin/ranlib libPAF.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 31%] Built target PAF +[ 24%] Built target PAF make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 34%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o +[ 27%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/kmer_lookup.c +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 40 [-Wfree-nonheap-object] + 533 | free(reads); + | ^~~~~~~~~~~ +In function 'Malloc', + inlined from 'Open_DB' at /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:525:29: +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' + 84 | if ((p = malloc(size)) == NULL) + | ^~~~~~~~~~~~ /build/reproducible-path/hinge-0.5.0/src/lib/kmer_lookup.c: In function 'find_best_aln_range': /build/reproducible-path/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 347 | q_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); @@ -1520,50 +1530,76 @@ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ -[ 37%] Linking C static library libkmer_lookup.a +[ 31%] Linking C static library libkmer_lookup.a cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libkmer_lookup.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 41%] Linking C static library libDB.a -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake -[ 41%] Built target kmer_lookup +[ 31%] Built target kmer_lookup make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o -/usr/bin/ranlib libDB.a -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 44%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o +[ 34%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/DW_banded.c -[ 44%] Built target DB -[ 48%] Linking C static library libDW_banded.a +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:1587:15: warning: 'free' called on pointer 'p' with nonzero offset 1 [-Wfree-nonheap-object] + 1587 | free(seq); + | ^~~~~~~~~ +In function 'Malloc', + inlined from 'Read_All_Sequences' at /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:1564:18: +/build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' + 84 | if ((p = malloc(size)) == NULL) + | ^~~~~~~~~~~~ +[ 37%] Linking C static library libDW_banded.a cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /usr/bin/ranlib libDW_banded.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 48%] Built target DW_banded +[ 37%] Built target DW_banded make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 51%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o +[ 41%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/falcon.dir/falcon.c.o -MF CMakeFiles/falcon.dir/falcon.c.o.d -o CMakeFiles/falcon.dir/falcon.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/falcon.c -[ 55%] Linking C static library libfalcon.a +[ 44%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/reproducible-path/hinge-0.5.0/src/lib/QV.c +/build/reproducible-path/hinge-0.5.0/src/lib/QV.c: In function 'Build_Table': +/build/reproducible-path/hinge-0.5.0/src/lib/QV.c:164:23: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] + 164 | { uint64 symbol = (uint64) (node->lft); + | ^ +/build/reproducible-path/hinge-0.5.0/src/lib/QV.c: In function 'Huffman': +/build/reproducible-path/hinge-0.5.0/src/lib/QV.c:211:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] + 211 | node[value].lft = (HTree *) (uint64) i; + | ^ +[ 48%] Linking CXX static library libini.a +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 +/usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o +/usr/bin/ranlib libini.a +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 48%] Built target ini +[ 51%] Linking C static library libfalcon.a cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 /usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o /usr/bin/ranlib libfalcon.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 55%] Built target falcon +[ 51%] Built target falcon +[ 55%] Linking C static library libDB.a +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 +/usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o +/usr/bin/ranlib libDB.a +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 55%] Built target DB [ 58%] Linking C static library libLA.a cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LA.dir/link.txt --verbose=1 @@ -1594,48 +1630,36 @@ make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend -make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend -make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/filter /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake "--color=" +make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/maximal /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake "--color=" +make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake "--color=" +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build +make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 68%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/filter/filter.cpp make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -[ 75%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o +[ 72%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/maximal/maximal.cpp -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/filter/filter.cpp +[ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp -/build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp: In function 'int draft_assembly_ctg(std::vector >&, LAInterface&, std::vector&, std::unordered_map >&, std::unordered_map > >&, std::vector&, int, int, int, int, int, bool, bool, std::string&)': -/build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp:514:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector > >::size_type' {aka 'unsigned int'} [-Wformat=] - 514 | printf("In total %lu lanes\n", lanes.size()); - | ~~^ ~~~~~~~~~~~~ - | | | - | long unsigned int std::vector > >::size_type {aka unsigned int} - | %u -[ 79%] Linking CXX executable get_maximal_reads -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 79%] Built target get_maximal_reads -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build -make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o +[ 79%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp /build/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp: In function 'int main(int, char**)': /build/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp:126:15: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] @@ -1651,24 +1675,36 @@ | | | | long unsigned int std::vector::size_type {aka unsigned int} | %u -[ 86%] Linking CXX executable Reads_filter -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz +[ 82%] Linking CXX executable consensus +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 86%] Built target Reads_filter +[ 82%] Built target consensus make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/layout /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 89%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o +[ 86%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/layout && /usr/bin/c++ -DBOOST_GRAPH_NO_LIB -DBOOST_REGEX_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp -[ 93%] Linking CXX executable consensus -cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a +/build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp: In function 'int draft_assembly_ctg(std::vector >&, LAInterface&, std::vector&, std::unordered_map >&, std::unordered_map > >&, std::vector&, int, int, int, int, int, bool, bool, std::string&)': +/build/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp:514:24: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector > >::size_type' {aka 'unsigned int'} [-Wformat=] + 514 | printf("In total %lu lanes\n", lanes.size()); + | ~~^ ~~~~~~~~~~~~ + | | | + | long unsigned int std::vector > >::size_type {aka unsigned int} + | %u +[ 89%] Linking CXX executable get_maximal_reads +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz +make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' +[ 89%] Built target get_maximal_reads +[ 93%] Linking CXX executable Reads_filter +cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' -[ 93%] Built target consensus +[ 93%] Built target Reads_filter [ 96%] Linking CXX executable draft_assembly cd /build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/draft_assembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/draft_assembly.dir/draft.cpp.o -o draft_assembly -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libfalcon.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a @@ -1686,7 +1722,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/hinge/ - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/hinge-0.5.0 -B/build/reproducible-path/hinge-0.5.0/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -1697,61 +1733,61 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py +-- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh --- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter @@ -1781,16 +1817,16 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/draft_assembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/get_maximal_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/hinging contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/Reads_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/get_maximal_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/hinge/usr/lib/hinge/draft_assembly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-7_armhf.deb'. dpkg-deb: building package 'hinge' in '../hinge_0.5.0-7_armhf.deb'. +dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-7_armhf.deb'. dpkg-genbuildinfo --build=binary -O../hinge_0.5.0-7_armhf.buildinfo dpkg-genchanges --build=binary -O../hinge_0.5.0-7_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1798,12 +1834,14 @@ 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/4726/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4726/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/6727 and its subdirectories -I: Current time: Wed Apr 3 13:05:11 -12 2024 -I: pbuilder-time-stamp: 1712192711 +I: removing directory /srv/workspace/pbuilder/4726 and its subdirectories +I: Current time: Thu Apr 4 15:26:13 +14 2024 +I: pbuilder-time-stamp: 1712193973