Diff of the two buildlogs: -- --- b1/build.log 2024-04-24 11:25:12.250273578 +0000 +++ b2/build.log 2024-04-24 11:28:21.806202203 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 23 23:19:40 -12 2024 -I: pbuilder-time-stamp: 1713957580 +I: Current time: Wed May 28 07:48:15 +14 2025 +I: pbuilder-time-stamp: 1748368095 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -37,54 +37,86 @@ dpkg-source: info: applying fix-system.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/62643/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/55342/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 27 17:48 /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/55342/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/55342/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='e1d56275471944e285c343b78dff3916' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='62643' - PS1='# ' - PS2='> ' + INVOCATION_ID=8391d316a7e242d0b2ac824f130ab8a7 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=55342 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.t8VXgS6A/pbuilderrc_9etw --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.t8VXgS6A/b1 --logfile b1/build.log libmems_1.6.0+4725-10.dsc' - SUDO_GID='112' - SUDO_UID='107' - 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.t8VXgS6A/pbuilderrc_lAXq --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.t8VXgS6A/b2 --logfile b2/build.log libmems_1.6.0+4725-10.dsc' + SUDO_GID=112 + SUDO_UID=107 + 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 ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:12 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/62643/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/55342/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -97,7 +129,7 @@ Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), d-shlibs (>= 0.106~), pkg-config, libgenome-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19876 files and directories currently installed.) +(Reading database ... 19706 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: @@ -190,10 +222,10 @@ Get: 54 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 pkg-config i386 1.8.1-1+b2 [14.0 kB] -Fetched 44.9 MB in 1s (32.2 MB/s) +Fetched 44.9 MB in 1s (57.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19876 files and directories currently installed.) +(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 ... 19706 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. @@ -429,7 +461,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libmems-1.6.0+4725/ && 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 > ../libmems_1.6.0+4725-10_source.changes +I: user script /srv/workspace/pbuilder/55342/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/55342/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libmems-1.6.0+4725/ && 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 > ../libmems_1.6.0+4725-10_source.changes dpkg-buildpackage: info: source package libmems dpkg-buildpackage: info: source version 1.6.0+4725-10 dpkg-buildpackage: info: source distribution unstable @@ -672,42 +708,86 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j11 + make -j21 make[1]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725' make all-recursive make[2]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725' Making all in libMems make[3]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome 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-DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. 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-fPIC -DPIC -o .libs/IntervalList.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 +In file included from /usr/include/c++/13/ext/hash_map:60, + from ../libMems/HomologyHMM/dptables.h:43, + from ../libMems/HomologyHMM/homology.h:27, + from ../libMems/Islands.h:25, + from Islands.cpp:13: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 +In file included from /usr/include/c++/13/ext/hash_map:60, + from ../libMems/HomologyHMM/dptables.h:43, + from ../libMems/HomologyHMM/homology.h:27, + from ../libMems/Islands.h:25, + from Aligner.cpp:10: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o twister.lo twister.c libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, - from ../libMems/Aligner.h:19, - from FileSML.cpp:12: + from ../libMems/MatchFinder.h:18, + from ../libMems/MemHash.h:20, + from MemHash.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -723,13 +803,18 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1 +In file included from /usr/include/c++/13/ext/hash_map:60, + from ../libMems/HomologyHMM/dptables.h:43, + from ../libMems/HomologyHMM/homology.h:27, + from ../libMems/Islands.h:25, + from ../libMems/ProgressiveAligner.h:21, + from Backbone.cpp:13: +/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] + 32 | #warning \ + | ^~~~~~~ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, - from ../libMems/MemHash.h:20, - from ../libMems/IntervalList.h:23, - from IntervalList.cpp:13: + from MatchFinder.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -745,11 +830,44 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp In file included from ../libMems/MatchList.h:25, - from ../libMems/MatchFinder.h:18, - from ../libMems/MemHash.h:20, - from MemHash.cpp:13: + from MatchList.cpp:13: +../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': +../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 82 | dir = path.branch_path().string(); + | ~~~~~~~~~~~~~~~~^~ +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from ../libMems/Files.h:23: +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 86 | name = path.leaf().string(); + | ~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +In file included from ../libMems/MatchList.h:25, + from ../libMems/RepeatMatchList.h:21, + from RepeatMatchList.cpp:13: +../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': +../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 82 | dir = path.branch_path().string(); + | ~~~~~~~~~~~~~~~~^~ +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from ../libMems/Files.h:23: +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 86 | name = path.leaf().string(); + | ~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ +In file included from ../libMems/MatchList.h:25, + from ../libMems/Aligner.h:19, + from FileSML.cpp:12: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -765,10 +883,11 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, - from MatchFinder.cpp:13: + from ../libMems/MemHash.h:20, + from ../libMems/IntervalList.h:23, + from ../libMems/Islands.h:18: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -787,8 +906,8 @@ In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, - from ../libMems/RepeatHash.h:16, - from RepeatHash.cpp:13: + from ../libMems/MaskedMemHash.h:16, + from MaskedMemHash.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -804,26 +923,11 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 -In file included from /usr/include/c++/13/ext/hash_map:60, - from ../libMems/HomologyHMM/dptables.h:43, - from ../libMems/HomologyHMM/homology.h:27, - from ../libMems/Islands.h:25, - from Aligner.cpp:10: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ In file included from ../libMems/MatchList.h:25, - from MatchList.cpp:13: + from ../libMems/MatchFinder.h:18, + from ../libMems/MemHash.h:20, + from ../libMems/RepeatHash.h:16, + from RepeatHash.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -839,18 +943,6 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -In file included from /usr/include/c++/13/ext/hash_map:60, - from ../libMems/HomologyHMM/dptables.h:43, - from ../libMems/HomologyHMM/homology.h:27, - from ../libMems/Islands.h:25, - from Islands.cpp:13: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from Aligner.cpp:9: @@ -869,12 +961,11 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, from ../libMems/IntervalList.h:23, - from ../libMems/Islands.h:18: + from IntervalList.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -890,6 +981,7 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -911,7 +1003,9 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -933,56 +1027,28 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o -In file included from ../libMems/MatchList.h:25, - from ../libMems/MatchFinder.h:18, - from ../libMems/MemHash.h:20, - from ../libMems/MaskedMemHash.h:16, - from MaskedMemHash.cpp:13: -../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': -../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 82 | dir = path.branch_path().string(); - | ~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from ../libMems/Files.h:23: -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 86 | name = path.leaf().string(); - | ~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 In file included from /usr/include/c++/13/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, - from Backbone.cpp:13: + from ProgressiveAligner.cpp:14: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o In file included from ../libMems/MatchList.h:25, - from ../libMems/RepeatMatchList.h:21, - from RepeatMatchList.cpp:13: + from ../libMems/MatchFinder.h:18, + from ../libMems/MemHash.h:20, + from ../libMems/PairwiseMatchFinder.h:16, + from PairwiseMatchFinder.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': ../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] 82 | dir = path.branch_path().string(); @@ -998,10 +1064,9 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17: @@ -1020,36 +1085,16 @@ /usr/include/boost/filesystem/path.hpp:1127:10: note: declared here 1127 | path leaf() const { return filename(); } | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o -In file included from ../libMems/MatchList.h:25, - from ../libMems/MatchFinder.h:18, - from ../libMems/MemHash.h:20, - from ../libMems/PairwiseMatchFinder.h:16, - from PairwiseMatchFinder.cpp:13: -../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': -../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 82 | dir = path.branch_path().string(); - | ~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from ../libMems/Files.h:23: -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 86 | name = path.leaf().string(); - | ~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ In file included from /usr/include/c++/13/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, - from ProgressiveAligner.cpp:14: + from GreedyBreakpointElimination.cpp:7: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1071,15 +1116,12 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 In file included from /usr/include/c++/13/ext/hash_map:60, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, @@ -1087,6 +1129,25 @@ /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 +In file included from ../libMems/MatchList.h:25, + from ../libMems/Aligner.h:19, + from ../libMems/ProgressiveAligner.h:17: +../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': +../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 82 | dir = path.branch_path().string(); + | ~~~~~~~~~~~~~~~~^~ +In file included from /usr/include/boost/filesystem/operations.hpp:20, + from ../libMems/Files.h:23: +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 86 | name = path.leaf().string(); + | ~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ In file included from HomologyHMM/algebras.cc:27: HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1108,17 +1169,16 @@ HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o In file included from /usr/include/c++/13/ext/hash_map:60, - from ../libMems/HomologyHMM/dptables.h:43, - from ../libMems/HomologyHMM/homology.h:27, - from ../libMems/Islands.h:25, - from ../libMems/ProgressiveAligner.h:21, - from GreedyBreakpointElimination.cpp:7: + from HomologyHMM/dptables.h:43, + from HomologyHMM/homology.h:27, + from HomologyHMM/homologymain.cc:21: /usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 In file included from HomologyHMM/homology.h:28: HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1140,6 +1200,24 @@ HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ +In file included from ../libMems/SeedOccurrenceList.h:9, + from ../libMems/GreedyBreakpointElimination.h:13, + from GreedyBreakpointElimination.cpp:6: +../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': +../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 82 | dir = path.branch_path().string(); + | ~~~~~~~~~~~~~~~~^~ +In file included from /usr/include/boost/filesystem.hpp:16, + from ../libMems/SeedOccurrenceList.h:7: +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] + 86 | name = path.leaf().string(); + | ~~~~~~~~~^~ +/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here + 1127 | path leaf() const { return filename(); } + | ^~~~ HomologyHMM/homology.cc: In function 'Algebra Forward(HomologyDPTable**, Params, char*, int)': HomologyHMM/homology.cc:319:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 319 | register double iTempResult[1]; @@ -1165,73 +1243,6 @@ HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 673 | register double iTempResult[1]; | ^~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o -In file included from /usr/include/c++/13/ext/hash_map:60, - from HomologyHMM/dptables.h:43, - from HomologyHMM/homology.h:27, - from HomologyHMM/homologymain.cc:21: -/usr/include/c++/13/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] - 32 | #warning \ - | ^~~~~~~ -In file included from ../libMems/MatchList.h:25, - from ../libMems/Aligner.h:19, - from ../libMems/ProgressiveAligner.h:17: -../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': -../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 82 | dir = path.branch_path().string(); - | ~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem/operations.hpp:20, - from ../libMems/Files.h:23: -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 86 | name = path.leaf().string(); - | ~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -In file included from HomologyHMM/homology.h:28: -HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': -HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 190 | register BFloat a( 0.0, 0 ); - | ^ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 209 | register BFloat sf(a.f*b.f,a.e+b.e); - | ^~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 216 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 229 | register double mantisse = a.f*b; - | ^~~~~~~~ -HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 236 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ -In file included from ../libMems/SeedOccurrenceList.h:9, - from ../libMems/GreedyBreakpointElimination.h:13, - from GreedyBreakpointElimination.cpp:6: -../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': -../libMems/Files.h:82:31: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 82 | dir = path.branch_path().string(); - | ~~~~~~~~~~~~~~~~^~ -In file included from /usr/include/boost/filesystem.hpp:16, - from ../libMems/SeedOccurrenceList.h:7: -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -../libMems/Files.h:86:25: warning: 'boost::filesystem::path boost::filesystem::path::leaf() const' is deprecated: Use path::filename() instead [-Wdeprecated-declarations] - 86 | name = path.leaf().string(); - | ~~~~~~~~~^~ -/usr/include/boost/filesystem/path.hpp:1127:10: note: declared here - 1127 | path leaf() const { return filename(); } - | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 In file included from ../libMems/HomologyHMM/homology.h:28: ../libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': ../libMems/HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] @@ -1274,16 +1285,38 @@ ../libMems/HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 236 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 +In file included from HomologyHMM/homology.h:28: +HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)': +HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 190 | register BFloat a( 0.0, 0 ); + | ^ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 209 | register BFloat sf(a.f*b.f,a.e+b.e); + | ^~ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 216 | register double mantisse = a.f*b; + | ^~~~~~~~ +HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 229 | register double mantisse = a.f*b; + | ^~~~~~~~ +HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 236 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c dmSML/aPOSIXaio.c: In function 'QueryLastCompletePAIO': dmSML/aPOSIXaio.c:115:28: warning: passing argument 1 of 'aio_suspend' from incompatible pointer type [-Wincompatible-pointer-types] 115 | rval = aio_suspend(request_array, 1, &zero_wait); @@ -1298,16 +1331,18 @@ /usr/include/aio.h:202:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' 202 | extern int __REDIRECT_NTH (aio_suspend, | ^~~~~~~~~~~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o dmSML/util.c: In function 'removeFile': dmSML/util.c:127:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 127 | rm_cmd = Fmt( "/bin/rm -fv %s", filename ); @@ -1315,26 +1350,27 @@ dmSML/util.c:129:24: warning: assignment discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 129 | rm_cmd = Fmt( "/bin/rm -f %s", filename ); | ^ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/i386-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread +/bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2 -ffile-prefix-map=/build/reproducible-path/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/i386-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/i686-linux-gnu/13/../../../i386-linux-gnu/crti.o /usr/lib/gcc/i686-linux-gnu/13/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -lGenome -lMUSCLE -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc/i686-linux-gnu/13 -L/usr/lib/gcc/i686-linux-gnu/13/../../../i386-linux-gnu -L/usr/lib/gcc/i686-linux-gnu/13/../../../../lib -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/i686-linux-gnu/13/crtendS.o /usr/lib/gcc/i686-linux-gnu/13/../../../i386-linux-gnu/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems.so.1 -o .libs/libMems.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libMems.so.1" && ln -s "libMems.so.1.0.0" "libMems.so.1") libtool: link: (cd ".libs" && rm -f "libMems.so" && ln -s "libMems.so.1.0.0" "libMems.so") @@ -1347,7 +1383,7 @@ make[2]: Leaving directory '/build/reproducible-path/libmems-1.6.0+4725' make[1]: Leaving directory '/build/reproducible-path/libmems-1.6.0+4725' dh_auto_test - make -j11 check "TESTSUITEFLAGS=-j11 --verbose" VERBOSE=1 + make -j21 check "TESTSUITEFLAGS=-j21 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725' Making check in libMems make[2]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' @@ -1365,7 +1401,7 @@ make[2]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/build/reproducible-path/libmems-1.6.0+4725/libMems' /usr/bin/mkdir -p '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu' - /bin/bash ../libtool --mode=install /usr/bin/install -c libMems.la '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu' + /bin/sh ../libtool --mode=install /usr/bin/install -c libMems.la '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libMems.so.1.0.0 /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu/libMems.so.1.0.0 libtool: install: (cd /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libMems.so.1.0.0 libMems.so.1 || { rm -f libMems.so.1 && ln -s libMems.so.1.0.0 libMems.so.1; }; }) libtool: install: (cd /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libMems.so.1.0.0 libMems.so || { rm -f libMems.so && ln -s libMems.so.1.0.0 libMems.so; }; }) @@ -1441,9 +1477,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libmems-dev' in '../libmems-dev_1.6.0+4725-10_i386.deb'. dpkg-deb: building package 'libmems1t64-dbgsym' in '../libmems1t64-dbgsym_1.6.0+4725-10_i386.deb'. dpkg-deb: building package 'libmems1t64' in '../libmems1t64_1.6.0+4725-10_i386.deb'. +dpkg-deb: building package 'libmems-dev' in '../libmems-dev_1.6.0+4725-10_i386.deb'. dpkg-genbuildinfo --build=binary -O../libmems_1.6.0+4725-10_i386.buildinfo dpkg-genchanges --build=binary -O../libmems_1.6.0+4725-10_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1451,12 +1487,14 @@ 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/55342/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/55342/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/62643 and its subdirectories -I: Current time: Tue Apr 23 23:25:11 -12 2024 -I: pbuilder-time-stamp: 1713957911 +I: removing directory /srv/workspace/pbuilder/55342 and its subdirectories +I: Current time: Wed May 28 07:51:20 +14 2025 +I: pbuilder-time-stamp: 1748368280