Diff of the two buildlogs: -- --- b1/build.log 2024-04-24 18:56:19.392784340 +0000 +++ b2/build.log 2024-04-24 19:28:09.335308304 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 24 06:42:35 -12 2024 -I: pbuilder-time-stamp: 1713984155 +I: Current time: Thu Apr 25 08:56:44 +14 2024 +I: pbuilder-time-stamp: 1713985004 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ 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/20637/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2713/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 24 18:57 /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/2713/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2713/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a31cfa771abe4e10b184537360105fd0' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='20637' - PS1='# ' - PS2='> ' + INVOCATION_ID=df1a5de6ef444db883562d7c08bdf4d2 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2713 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.OXy3r1vt/pbuilderrc_QaCN --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.OXy3r1vt/b1 --logfile b1/build.log libmems_1.6.0+4725-10.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OXy3r1vt/pbuilderrc_pgMs --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.OXy3r1vt/b2 --logfile b2/build.log libmems_1.6.0+4725-10.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32a 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:14 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20637/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:13 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2713/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -187,7 +219,7 @@ Get: 54 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-1+b2 [28.9 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-1+b2 [26.2 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf pkg-config armhf 1.8.1-1+b2 [14.0 kB] -Fetched 43.2 MB in 1s (36.0 MB/s) +Fetched 43.2 MB in 2s (17.7 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 ... 19637 files and directories currently installed.) @@ -426,7 +458,11 @@ 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/2713/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2713/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 @@ -669,19 +705,24 @@ config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build - make -j3 + make -j4 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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from MatchFinder.cpp:13: @@ -723,64 +764,6 @@ In file included from /usr/include/c++/13/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, - from ../libMems/SortedMerList.h:19, - from ../libMems/MatchFinder.h:16: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const' at MatchFinder.cpp:110:25: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const' at MatchFinder.cpp:123:25: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o -In file included from /usr/include/c++/13/vector:72, - from /usr/include/libGenome/gnGenomeSpec.h:21, - from /usr/include/libGenome/gnSequence.h:27, - from ../libMems/SortedMerList.h:19, - from ../libMems/MatchFinder.h:16: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', - inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'virtual void mems::MatchFinder::FindMatchSeeds(const std::vector&)' at MatchFinder.cpp:145:23: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'virtual void mems::MatchFinder::FindMatchSeeds()' at MatchFinder.cpp:132:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o -In file included from /usr/include/c++/13/vector:72, - from /usr/include/libGenome/gnGenomeSpec.h:21, - from /usr/include/libGenome/gnSequence.h:27, from ../libMems/MemorySML.h:16, from MemorySML.cpp:13: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::bmer&}; _Tp = mems::bmer; _Alloc = std::allocator]': @@ -838,12 +821,63 @@ 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/libGenome/gnGenomeSpec.h:21, + from /usr/include/libGenome/gnSequence.h:27, + from ../libMems/SortedMerList.h:19, + from ../libMems/MatchFinder.h:16: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const' at MatchFinder.cpp:110:25: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'virtual void mems::MatchFinder::GetBreakpoint(uint32, gnSeqI, std::vector&) const' at MatchFinder.cpp:123:25: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/libGenome/gnGenomeSpec.h:21, + from /usr/include/libGenome/gnSequence.h:27, + from ../libMems/SortedMerList.h:19, + from ../libMems/MatchFinder.h:16: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', + inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'virtual void mems::MatchFinder::FindMatchSeeds(const std::vector&)' at MatchFinder.cpp:145:23: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'virtual void mems::MatchFinder::FindMatchSeeds()' at MatchFinder.cpp:132:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 In file included from /usr/include/c++/13/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, @@ -917,26 +951,9 @@ /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/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(); - | ~~~~~~~~~~~~~~~~^~ -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(); } - | ^~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o In file included from /usr/include/c++/13/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, @@ -965,11 +982,13 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'virtual void mems::FileSML::LoadFile(const std::string&)' at FileSML.cpp:107:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1075,6 +1094,25 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from ../libMems/MatchList.h:25, + 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(); + | ~~~~~~~~~~~~~~~~^~ +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 member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void mems::maskNNNNN(const genome::gnSequence&, genome::gnSequence&, std::vector&, int)' at FileSML.cpp:258:27: @@ -1130,6 +1168,15 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', + inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, @@ -1139,12 +1186,7 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', - inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: @@ -1161,20 +1203,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o twister.lo twister.c -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o twister.lo twister.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 ../libMems/MemHash.h:20, @@ -1196,6 +1230,10 @@ 1127 | path leaf() const { return filename(); } | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o In file included from ../libMems/MatchList.h:25, from MatchList.cpp:13: ../libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)': @@ -1214,8 +1252,6 @@ 1127 | path leaf() const { return filename(); } | ^~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 In file included from /usr/include/c++/13/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, @@ -1225,7 +1261,7 @@ /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 \ | ^~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from /usr/include/c++/13/ext/hash_map:60, from ../libMems/HomologyHMM/dptables.h:43, @@ -1274,6 +1310,8 @@ ../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/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o In file included from ../libMems/MatchList.h:25, from ../libMems/MatchFinder.h:18, from ../libMems/MemHash.h:20, @@ -1315,8 +1353,28 @@ ../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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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(); } + | ^~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, @@ -1344,31 +1402,36 @@ /usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -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(); } - | ^~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/libGenome/gnGenomeSpec.h:21, + from /usr/include/libGenome/gnSequence.h:27, + from ../libMems/SortedMerList.h:19, + from ../libMems/MatchFinder.h:16: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', + inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /usr/include/libGenome/gnGenomeSpec.h:21, + from /usr/include/libGenome/gnSequence.h:27, + from ../libMems/GappedAlignment.h:17, + from GappedAlignment.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, @@ -1414,28 +1477,42 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/libGenome/gnGenomeSpec.h:21, - from /usr/include/libGenome/gnSequence.h:27, - from ../libMems/SortedMerList.h:19, - from ../libMems/MatchFinder.h:16: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:934:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', - inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:187:16: +/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1532 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:129:16: +/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1532 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:138:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GappedAlignment&}; _Tp = mems::GappedAlignment; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1454,6 +1531,7 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void mems::addUnalignedIntervals(IntervalList&, std::set, std::vector)' at Islands.cpp:244:25: @@ -1483,6 +1561,11 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', + inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1500,11 +1583,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', - inlined from 'void mems::HybridAbstractMatch::SetStart(uint, int64) [with unsigned int FIXED_SEQ_COUNT = 2; int64Alloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/HybridAbstractMatch.h:197:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1534,11 +1612,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, @@ -1550,13 +1629,14 @@ 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void mems::Aligner::Recursion(mems::MatchList&, mems::Match*, mems::Match*, boolean)' at Aligner.cpp:1128:19: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -1573,6 +1653,15 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from ../libMems/Matrix.h:19, + from ../libMems/NumericMatrix.h:16, + from ../libMems/MuscleInterface.h:16, + from MuscleInterface.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -1621,20 +1710,22 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', inlined from 'void mems::computeLCBAdjacencies_v2(std::vector >*> >&, std::vector >&, std::vector&)' at Aligner.cpp:635:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/libGenome/gnGenomeSpec.h:21, - from /usr/include/libGenome/gnSequence.h:27, - from ../libMems/GappedAlignment.h:17, - from GappedAlignment.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::LCB*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::LCB*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::LCB*; _Tp = mems::LCB]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, @@ -1643,27 +1734,6 @@ /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:313:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:315:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: @@ -1690,86 +1760,23 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', - inlined from 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector >*> >&, boolean, std::ostream*)' at Aligner.cpp:2130:28: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', - inlined from 'void mems::Aligner::align(mems::MatchList&, mems::IntervalList&, double, double, boolean, boolean, boolean, std::string)' at Aligner.cpp:2273:26: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o -In file included from /usr/include/c++/13/vector:72, - from ../libMems/Matrix.h:19, - from ../libMems/NumericMatrix.h:16, - from ../libMems/MuscleInterface.h:16, - from MuscleInterface.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:187:16: -/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1532 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:129:16: -/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1532 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:138:20: + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:313:17: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:315:17: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'virtual boolean mems::MuscleInterface::Align(mems::GappedAlignment&, mems::Match*, mems::Match*, std::vector&)' at MuscleInterface.cpp:451:20: @@ -1816,6 +1823,35 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', + inlined from 'void mems::Aligner::RecursiveAnchorSearch(mems::MatchList&, gnSeqI, std::vector >*> >&, boolean, std::ostream*)' at Aligner.cpp:2130:28: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', + inlined from 'void mems::Aligner::align(mems::MatchList&, mems::IntervalList&, double, double, boolean, boolean, boolean, std::string)' at Aligner.cpp:2273:26: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 In file included from /usr/include/c++/13/vector:72, from /usr/include/libGenome/gnGenomeSpec.h:21, from /usr/include/libGenome/gnSequence.h:27, @@ -1831,21 +1867,10 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.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 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 /usr/include/c++/13/vector:72, from ../libMems/RepeatMatch.h:18, from RepeatMatch.cpp:13: @@ -1860,6 +1885,50 @@ 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.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 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 \ + | ^~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.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 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 \ + | ^~~~~~~ +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 ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17: @@ -1899,40 +1968,6 @@ ../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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.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 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 \ - | ^~~~~~~ -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(); } - | ^~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 In file included from ../libMems/MatchList.h:25, from ../libMems/Aligner.h:19, from ../libMems/ProgressiveAligner.h:17: @@ -1972,6 +2007,18 @@ ../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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from ../libMems/AbstractMatch.h:18, + from ../libMems/SparseAbstractMatch.h:18, + from ../libMems/Interval.h:18, + from ../libMems/SuperInterval.h:8, + from ../libMems/ProgressiveAligner.h:16: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from ../libMems/AbstractMatch.h:18, @@ -1983,13 +2030,41 @@ /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from ../libMems/AbstractMatch.h:17: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 195 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_equal_to_iter]': +/usr/include/c++/13/bits/stl_algo.h:905:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 905 | __unique(_ForwardIterator __first, _ForwardIterator __last, + | ^~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:905:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -1998,12 +2073,50 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from ../libMems/AbstractMatch.h:17: /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | __final_insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1854 | __final_insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | __final_insertion_sort(_RandomAccessIterator __first, @@ -2015,6 +2128,12 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 751 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, @@ -2024,20 +2143,17 @@ /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from ../libMems/AbstractMatch.h:17, - from ../libMems/SparseAbstractMatch.h:18, - from ../libMems/Interval.h:18, - from ../libMems/SuperInterval.h:8, - from SuperInterval.cpp:6: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2048,49 +2164,6 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:187:16: -/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1532 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:129:16: -/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1532 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:138:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:313:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:315:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2100,16 +2173,6 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:934:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2164,7 +2227,20 @@ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from ../libMems/AbstractMatch.h:17, + from ../libMems/SparseAbstractMatch.h:18, + from ../libMems/Interval.h:18, + from ../libMems/SuperInterval.h:8, + from SuperInterval.cpp:6: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2186,175 +2262,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from ../libMems/AbstractMatch.h:18, - from ../libMems/SparseAbstractMatch.h:18, - from ../libMems/Interval.h:18, - from ../libMems/SuperInterval.h:8, - from ../libMems/ProgressiveAligner.h:16: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from ../libMems/AbstractMatch.h:17: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 195 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function '_ForwardIterator std::__unique(_ForwardIterator, _ForwardIterator, _BinaryPredicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _BinaryPredicate = __gnu_cxx::__ops::_Iter_equal_to_iter]': -/usr/include/c++/13/bits/stl_algo.h:905:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 905 | __unique(_ForwardIterator __first, _ForwardIterator __last, - | ^~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:905:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | __final_insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1854 | __final_insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1854:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 751 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -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: -/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/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(); } - | ^~~~ -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] - 190 | register BFloat a( 0.0, 0 ); - | ^ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -../libMems/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); - | ^~ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 216 | register double mantisse = a.f*b; - | ^~~~~~~~ -../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 229 | register double mantisse = a.f*b; - | ^~~~~~~~ -../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -../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); - | ^~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const' at ../libMems/PairwiseMatchAdapter.h:90:16: @@ -2366,67 +2273,10 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator]', - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:287:24: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2436,46 +2286,50 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:187:16: +/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1532 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:129:16: +/usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1532 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:195:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:213:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:215:26: + inlined from 'void mems::SparseAbstractMatch::SetStart(uint, int64) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:138:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:221:25: + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:313:17: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1950 | std::__final_insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::makeAllPairwiseGenomeHSS(IntervalList&, std::vector*>&, std::vector*>&, pairwise_genome_hss_t&, const HssDetector*)' at Backbone.cpp:350:29: + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:315:17: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2488,6 +2342,16 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:934:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void mems::applyAncestralBreakpoints(const std::vector&, std::vector&, uint, Manipulator&) [with T = AbstractMatch*; Manipulator = GenericMatchSeqManipulator<>]' at ProgressiveAligner.cpp:265:6: @@ -2501,6 +2365,7 @@ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void mems::SparseAbstractMatch::SetLeftEnd(uint, gnSeqI) [with gnSeqIAlloc = std::allocator; uintAlloc = std::allocator]' at ../libMems/SparseAbstractMatch.h:182:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2516,11 +2381,6 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', - inlined from 'void mems::unalignIslands(IntervalList&, std::vector*>&, std::vector >*, std::allocator >*> > >&)' at Backbone.cpp:798:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:340:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -2540,32 +2400,20 @@ 1484 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::make_heap(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = mems::MoveScoreHeapComparator]', inlined from 'double mems::greedySearch(SearchScorer&) [with SearchScorer = EvenFasterSumOfPairsBreakpointScorer]' at ../libMems/GreedyBreakpointElimination.h:794:16: /usr/include/c++/13/bits/stl_heap.h:413:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 413 | std::__make_heap(__first, __last, __cmp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from ../libMems/AbstractMatch.h:18, - from ../libMems/GreedyBreakpointElimination.h:8: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void mems::chooseNextAlignmentPair(PhyloTree&, node_id_t&, node_id_t&, node_id_t&)' at ProgressiveAligner.cpp:3127:22: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2576,97 +2424,57 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from ../libMems/AbstractMatch.h:17: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::GenericInterval, std::allocator > > >&}; _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const' at ../libMems/PairwiseMatchAdapter.h:90:16: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const' at ../libMems/PairwiseMatchAdapter.h:91:16: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:934:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:313:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:315:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:934:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.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: +/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 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] + 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); + | ^~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, @@ -2687,20 +2495,11 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -2709,14 +2508,30 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.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/homology.cc:24: +/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 \ + | ^~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator]', - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:287:24: + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:287:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ @@ -2727,7 +2542,7 @@ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2736,7 +2551,7 @@ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ @@ -2747,19 +2562,120 @@ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ^~ +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]; + | ^~~~~~~~~~~ +HomologyHMM/homology.cc:321:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 321 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +HomologyHMM/homology.cc: In function 'Algebra Backward(HomologyBaumWelch&, HomologyDPTable*, HomologyDPTable**, Params, char*, int)': +HomologyHMM/homology.cc:417:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 417 | register double iTempResult[1]; + | ^~~~~~~~~~~ +HomologyHMM/homology.cc:419:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 419 | register bfloat iTempProb[3]; + | ^~~~~~~~~ +HomologyHMM/homology.cc: In function 'Algebra Viterbi_recurse(HomologyDPTable**, Params, char*, int)': +HomologyHMM/homology.cc:565:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 565 | register double iTempResult[1]; + | ^~~~~~~~~~~ +HomologyHMM/homology.cc:567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 567 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +HomologyHMM/homology.cc: In function 'Path& Viterbi_trace(HomologyDPTable*, Params, char*, int)': +HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 673 | register double iTempResult[1]; + | ^~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:195:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:213:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:215:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:221:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1950 | std::__final_insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:65: /usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::SuperInterval*]': /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +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(); } + | ^~~~ In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::SuperInterval*; bool _TrivialValueTypes = false]', inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::SuperInterval*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = mems::SuperInterval*; _Tp = mems::SuperInterval]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, @@ -2782,54 +2698,37 @@ | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:195:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:213:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:215:26: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:221:25: + inlined from 'void mems::makeAllPairwiseGenomeHSS(IntervalList&, std::vector*>&, std::vector*>&, pairwise_genome_hss_t&, const HssDetector*)' at Backbone.cpp:350:29: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, - inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator]', inlined from 'void PhyloTree::push_back(T&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:57:41, inlined from 'node_id_t mems::createAlignmentTreeRoot(PhyloTree&, node_id_t, node_id_t)' at ProgressiveAligner.cpp:3189:27: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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] + 190 | register BFloat a( 0.0, 0 ); + | ^ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +../libMems/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); + | ^~ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +../libMems/HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 216 | register double mantisse = a.f*b; + | ^~~~~~~~ +../libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +../libMems/HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 229 | register double mantisse = a.f*b; + | ^~~~~~~~ +../libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +../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); + | ^~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::AlignmentTreeNode; _Alloc = std::allocator]', inlined from 'void PhyloTree::readTree(std::istream&) [with T = mems::AlignmentTreeNode]' at ../libMems/PhyloTree.h:173:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 @@ -2850,11 +2749,25 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'mems::EvenFasterSumOfPairsBreakpointScorer::EvenFasterSumOfPairsBreakpointScorer(double, double, boost::multi_array, boost::multi_array, std::vector*>, mems::PairwiseLCBMatrix&, std::vector&, std::vector&, boost::multi_array&, boost::multi_array&, size_t, size_t, size_t, size_t)' at GreedyBreakpointElimination.cpp:368:18: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/backward/hashtable.h:62, + from /usr/include/c++/13/ext/hash_map:64: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void SimplePath::addEdge(int, double, std::vector&, int, int)' at HomologyHMM/homology.cc:248:20: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::GenericInterval<>; _Alloc = std::allocator >]', + inlined from 'void mems::unalignIslands(IntervalList&, std::vector*>&, std::vector >*, std::allocator >*> > >&)' at Backbone.cpp:798:23: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::SuperInterval&}; _Tp = mems::SuperInterval; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2896,11 +2809,134 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from ../libMems/AbstractMatch.h:18, + from ../libMems/GreedyBreakpointElimination.h:8: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:311:17: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:313:17: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::GenericInterval::GetColumnAndMatch(gnSeqI, std::vector&, std::vector&, size_t&, gnSeqI&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:315:17: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 \ + | ^~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::GenericInterval::GetAlignedSequences(mems::gnAlignedSequences&, const std::vector&) const [with GappedBaseImpl = mems::AbstractGappedAlignment >]' at ../libMems/Interval.h:934:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from ../libMems/AbstractMatch.h:17: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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 /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const' at ../libMems/PairwiseMatchAdapter.h:90:16: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'virtual void mems::PairwiseMatchAdapter::GetColumn(gnSeqI, std::vector&, std::vector&) const' at ../libMems/PairwiseMatchAdapter.h:91:16: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mems::LCB&}; _Tp = mems::LCB; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -2909,6 +2945,20 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o +In file included from dmSML/asyncio.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -2917,6 +2967,7 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1942:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1942 | __sort(_RandomAccessIterator __first, _RandomAccessIterator __last, @@ -2960,6 +3011,35 @@ /usr/include/c++/13/bits/stl_algo.h:4894:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4894 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o +In file included from ../libMems/dmSML/alinuxaio.h:8, + from dmSML/alinuxaio.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o +In file included from ../libMems/dmSML/aPOSIXaio.h:8, + from dmSML/aPOSIXaio.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +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); + | ^~~~~~~~~~~~~ + | | + | struct aiocb ** +In file included from /usr/include/features.h:490, + from /usr/include/arm-linux-gnueabihf/sys/types.h:25, + from ../libMems/dmSML/asyncio.h:24: +/usr/include/aio.h:197:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' + 197 | extern int __REDIRECT_NTH (aio_suspend, + | ^~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator]', inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector*>]' at ../libMems/GreedyBreakpointElimination.h:287:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -2983,6 +3063,33 @@ /usr/include/c++/13/bits/stl_algo.h:4894:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4894 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o +In file included from dmSML/alibc.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o +In file included from ../libMems/dmSML/awin32aio.h:8, + from dmSML/awin32aio.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o +In file included from ../libMems/dmSML/buffer.h:8, + from dmSML/buffer.c:7: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator]', inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = GenericMatchList >*>]' at ../libMems/GreedyBreakpointElimination.h:287:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3006,6 +3113,7 @@ /usr/include/c++/13/bits/stl_algo.h:4894:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 4894 | std::__sort(__first, __last, __gnu_cxx::__ops::__iter_comp_iter(__comp)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: @@ -3031,11 +3139,38 @@ /usr/include/c++/13/bits/stl_vector.h:1563:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1563 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:381:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +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 ); + | ^ +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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o +In file included from ../libMems/dmSML/buffer.h:8, + from ../libMems/dmSML/sorting.h:8, + from dmSML/sorting.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o +In file included from dmSML/dmsort.c:10: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = GenericMatchList >*>]' at ../libMems/GreedyBreakpointElimination.h:223:11: @@ -3061,6 +3196,15 @@ /usr/include/c++/13/bits/stl_vector.h:1563:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1563 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void mems::filterMatches_v2(std::vector&, std::vector&, std::vector&, MatchVector&) [with MatchVector = GenericMatchList >*>]' at ../libMems/GreedyBreakpointElimination.h:381:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3070,11 +3214,113 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, std::allocator > >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = mems::LCB; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mems::LCB; _Alloc = std::allocator]', + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:287:24: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBLeftComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:292:12: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = mems::LCBIDComparator]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'void mems::computeLCBAdjacencies_v3(const std::vector&, std::vector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:309:11: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long int; _Alloc = std::allocator]', inlined from 'void mems::ProgressiveAligner::pairwiseAnchorSearch(mems::MatchList&, mems::Match*, mems::Match*, const mems::AbstractMatch*, uint, uint)' at ProgressiveAligner.cpp:605:19: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:195:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:213:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:215:26: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:221:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, + inlined from 'void mems::IdentifyBreakpoints(MatchVector&, std::vector&) [with MatchVector = std::vector]' at ../libMems/GreedyBreakpointElimination.h:223:11: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void mems::ProgressiveAligner::recurseOnPairs(const std::vector&, const std::vector&, const GappedAlignmentType&, Matrix >*> >&, Matrix >*, mems::UngappedLocalAlignment >*> > >&, Matrix >*, mems::UngappedLocalAlignment >*> > >&, boost::multi_array >, 2>&) [with GappedAlignmentType = mems::CompactGappedAlignment<>]' at ProgressiveAligner.cpp:715:36: @@ -3139,6 +3385,18 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1 +/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o +In file included from ../libMems/dmSML/sml.h:8, + from dmSML/sml.c:5: +../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined + 18 | # define _LARGEFILE_SOURCE + | +: note: this is the location of the previous definition +libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1 In function 'void std::make_heap(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = mems::MoveScoreHeapComparator]', inlined from 'int64 mems::greedyBreakpointElimination_v4(std::vector&, std::vector&, BreakpointScorerType&, std::ostream*, size_t, size_t) [with BreakpointScorerType = GreedyRemovalScorer]' at ../libMems/GreedyBreakpointElimination.h:695:16, inlined from 'void mems::ProgressiveAligner::CreatePairwiseBPDistance(boost::multi_array&)' at ProgressiveAligner.cpp:3433:52: @@ -3155,6 +3413,12 @@ 1484 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'mems::EvenFasterSumOfPairsBreakpointScorer::EvenFasterSumOfPairsBreakpointScorer(double, double, boost::multi_array, boost::multi_array, std::vector*>, mems::PairwiseLCBMatrix&, std::vector&, std::vector&, boost::multi_array&, boost::multi_array&, size_t, size_t, size_t, size_t)' at GreedyBreakpointElimination.cpp:368:18: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void mems::ProgressiveAligner::alignProfileToProfile(node_id_t, node_id_t, node_id_t)' at ProgressiveAligner.cpp:2477:14: @@ -3187,236 +3451,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o -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] - 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); - | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.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/homology.cc:24: -/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 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); - | ^~ -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]; - | ^~~~~~~~~~~ -HomologyHMM/homology.cc:321:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 321 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -HomologyHMM/homology.cc: In function 'Algebra Backward(HomologyBaumWelch&, HomologyDPTable*, HomologyDPTable**, Params, char*, int)': -HomologyHMM/homology.cc:417:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 417 | register double iTempResult[1]; - | ^~~~~~~~~~~ -HomologyHMM/homology.cc:419:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 419 | register bfloat iTempProb[3]; - | ^~~~~~~~~ -HomologyHMM/homology.cc: In function 'Algebra Viterbi_recurse(HomologyDPTable**, Params, char*, int)': -HomologyHMM/homology.cc:565:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 565 | register double iTempResult[1]; - | ^~~~~~~~~~~ -HomologyHMM/homology.cc:567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 567 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -HomologyHMM/homology.cc: In function 'Path& Viterbi_trace(HomologyDPTable*, Params, char*, int)': -HomologyHMM/homology.cc:673:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 673 | register double iTempResult[1]; - | ^~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/backward/hashtable.h:62, - from /usr/include/c++/13/ext/hash_map:64: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void SimplePath::addEdge(int, double, std::vector&, int, int)' at HomologyHMM/homology.cc:248:20: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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 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); - | ^~ -libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o -In file included from dmSML/asyncio.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o -In file included from ../libMems/dmSML/alinuxaio.h:8, - from dmSML/alinuxaio.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o -In file included from ../libMems/dmSML/aPOSIXaio.h:8, - from dmSML/aPOSIXaio.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -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); - | ^~~~~~~~~~~~~ - | | - | struct aiocb ** -In file included from /usr/include/features.h:490, - from /usr/include/arm-linux-gnueabihf/sys/types.h:25, - from ../libMems/dmSML/asyncio.h:24: -/usr/include/aio.h:197:12: note: expected 'const struct aiocb * const*' but argument is of type 'struct aiocb **' - 197 | extern int __REDIRECT_NTH (aio_suspend, - | ^~~~~~~~~~~~~~ -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o -In file included from dmSML/alibc.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o -In file included from ../libMems/dmSML/awin32aio.h:8, - from dmSML/awin32aio.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o -In file included from ../libMems/dmSML/buffer.h:8, - from dmSML/buffer.c:7: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c -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 ); - | ^ -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o -In file included from ../libMems/dmSML/buffer.h:8, - from ../libMems/dmSML/sorting.h:8, - from dmSML/sorting.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o -/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c -In file included from dmSML/dmsort.c:10: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -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.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o -In file included from ../libMems/dmSML/sml.h:8, - from dmSML/sml.c:5: -../libMems/dmSML/asyncio.h:18: warning: "_LARGEFILE_SOURCE" redefined - 18 | # define _LARGEFILE_SOURCE - | -: note: this is the location of the previous definition -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1 -libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.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 -fstack-clash-protection -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/arm-linux-gnueabihf 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 -fstack-clash-protection -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-z,relro -Wl,-z,now -o libMems.la -rpath /usr/lib/arm-linux-gnueabihf 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/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/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/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/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") @@ -3429,7 +3465,7 @@ 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 -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --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' @@ -3447,7 +3483,7 @@ 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/arm-linux-gnueabihf' - /bin/bash ../libtool --mode=install /usr/bin/install -c libMems.la '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf' + /bin/sh ../libtool --mode=install /usr/bin/install -c libMems.la '/build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libMems.so.1.0.0 /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf/libMems.so.1.0.0 libtool: install: (cd /build/reproducible-path/libmems-1.6.0+4725/debian/tmp/usr/lib/arm-linux-gnueabihf && { 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/arm-linux-gnueabihf && { ln -s -f libMems.so.1.0.0 libMems.so || { rm -f libMems.so && ln -s libMems.so.1.0.0 libMems.so; }; }) @@ -3534,12 +3570,14 @@ 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/2713/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2713/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/20637 and its subdirectories -I: Current time: Wed Apr 24 06:56:14 -12 2024 -I: pbuilder-time-stamp: 1713984974 +I: removing directory /srv/workspace/pbuilder/2713 and its subdirectories +I: Current time: Thu Apr 25 09:28:02 +14 2024 +I: pbuilder-time-stamp: 1713986882