Diff of the two buildlogs: -- --- b1/build.log 2025-11-21 20:10:26.458366795 +0000 +++ b2/build.log 2025-11-21 20:12:54.654524445 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 24 14:30:26 -12 2026 -I: pbuilder-time-stamp: 1798165826 +I: Current time: Sat Nov 22 10:10:28 +14 2025 +I: pbuilder-time-stamp: 1763755828 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying buildflags.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/448365/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1523902/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 21 20:10 /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/1523902/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1523902/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f1052e077e3545edb4cef874f0927938' - 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='448365' - PS1='# ' - PS2='> ' + INVOCATION_ID=e87d2fe13ac247b293b9209d57ae0366 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1523902 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.BtEgDZi3/pbuilderrc_ZlDy --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BtEgDZi3/b1 --logfile b1/build.log murasaki_1.68.6-16.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.BtEgDZi3/pbuilderrc_Va9S --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BtEgDZi3/b2 --logfile b2/build.log murasaki_1.68.6-16.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.12.57+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.57-1 (2025-11-05) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/448365/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1523902/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -256,7 +288,7 @@ Get: 121 http://deb.debian.org/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libtext-wrapper-perl all 1.05-4 [10.3 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.19 [3432 B] -Fetched 145 MB in 4s (38.2 MB/s) +Fetched 145 MB in 4s (40.8 MB/s) Preconfiguring packages ... 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 ... 19866 files and directories currently installed.) @@ -773,7 +805,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/murasaki-1.68.6/ && 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 > ../murasaki_1.68.6-16_source.changes +I: user script /srv/workspace/pbuilder/1523902/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1523902/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/murasaki-1.68.6/ && 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 > ../murasaki_1.68.6-16_source.changes dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-16 dpkg-buildpackage: info: source distribution unstable @@ -783,7 +819,7 @@ debian/rules clean dh clean dh_auto_clean - make -j16 clean + make -j12 clean make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean @@ -800,7 +836,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=YES - make -j16 INSTALL="install --strip-program=true" USE_MPI=YES + make -j12 INSTALL="install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src' @@ -817,70 +853,8 @@ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc -binseq.cc: In member function 'bool SequenceBinary::save(std::string)': -binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] - 70 | }catch(ofstream::failure e){ - | ^ -binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': -binseq.cc:158:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_algobase.h:64, - from /usr/include/c++/15/string:53, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/istream:42, - from /usr/include/c++/15/fstream:42, - from seqread.h:30, - from binseq.hh:31, - from binseq.cc:21: -/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here - 302 | struct pair - | ^~~~ -binseq.cc:160:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here - 302 | struct pair - | ^~~~ -binseq.cc:162:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here - 302 | struct pair - | ^~~~ -In file included from ecolist.h:23, - from openhash.h:29, - from openhash.cc:26: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from ecolist.h:23, - from ecolist.cc:20: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, - from dinkymath.cc:27: + from murasaki_mpi.cc:33: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -891,8 +865,7 @@ from /usr/include/c++/15/bits/ostream.h:43, from /usr/include/c++/15/ostream:42, from /usr/include/c++/15/iostream:43, - from dinkymath.h:24, - from dinkymath.cc:26: + from murasaki_mpi.cc:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -908,34 +881,14 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': -dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] - 40 | int last=0; - | ^~~~ -dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)': -dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] - 53 | int last=0; - | ^~~~ -ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 467 | struct less_map : public binary_function { - | ^~~~~~~~~~~~~~~ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from murasaki.h:24, - from murasaki_mpi.cc:33: +In file included from msethash.cc:25: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from murasaki_mpi.cc:30: +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -951,32 +904,20 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ecolist.h:23, - from ecohash.h:29, - from ecohash.cc:26: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)': -murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable] - 561 | int send_done; - | ^~~~~~~~~ In file included from murasaki.h:24, - from scoring.cc:27: + from dinkymath.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from dinkymath.h:24, + from dinkymath.cc:26: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -992,6 +933,18 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +murasaki_mpi.cc: In function 'void mpi_hasher_client_mode(BitSequence*)': +murasaki_mpi.cc:561:9: warning: variable 'send_done' set but not used [-Wunused-but-set-variable] + 561 | int send_done; + | ^~~~~~~~~ +dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': +dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] + 40 | int last=0; + | ^~~~ +dinkymath.cc: In function 'std::string littleEndianPat(unsigned int, int)': +dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] + 53 | int last=0; + | ^~~~ In file included from options.h:28, from options.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1004,7 +957,8 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from msethash.cc:25: +In file included from ecolist.h:23, + from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1015,27 +969,17 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from murasaki.h:24, - from murasaki.cc:37: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from murasaki.cc:29: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ sequence.cc: In destructor 'Sequence::~Sequence()': sequence.cc:377:9: warning: 'throw' will always call 'terminate' [-Wterminate] 377 | throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:377:9: note: in C++11 destructors default to 'noexcept' +ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 467 | struct less_map : public binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); @@ -1056,41 +1000,38 @@ 1394 | throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:1394:9: note: in C++11 destructors default to 'noexcept' -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc +In file included from murasaki.h:24, + from scoring.cc:27: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ sequence.cc: In member function 'std::pair IntervalSet::entropy() const': sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ -cgr.cc: In member function 'void Cgr::merge(Cgr&)': -cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] - 140 | int redist=(unsigned long)(rez*rez)<=seedcount; - | ^~~~~~ -cgr.cc: In member function 'bool Cgr::savePNG(std::string)': -cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] - 288 | int res; - | ^~~ -murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': -murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] - 1008 | bool revZero=false; - | ^~~~~~~ -cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': -cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] - 435 | int wordwidth=1; - | ^~~~~~~~~ -murasaki.cc: In function 'bool convertPattern(std::string&)': -murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 1287 | random_shuffle(randomStr.begin(),randomStr.end()); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/algorithm:63, - from /usr/include/boost/regex/v5/regex_workaround.hpp:23, - from /usr/include/boost/regex/v5/regex.hpp:29, - from /usr/include/boost/regex.hpp:34, - from seqread.h:33, - from binseq.hh:31, - from sequence.h:32: -/usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here - 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ +In file included from murasaki.h:24, + from murasaki.cc:37: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from murasaki.cc:29: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from sequence.cc:41: hashing.h: In instantiation of 'SBox::SBox(int) [with T = short unsigned int]': sequence.cc:162:29: required from here @@ -1109,8 +1050,7 @@ /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc In file included from sequence.h:44: shmvector.hh: In instantiation of 'void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = long unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]' @@ -1125,12 +1065,118 @@ /usr/include/c++/15/bits/stl_pair.h:302:12: note: 'struct std::pair' declared here 302 | struct pair | ^~~~ +In file included from ecolist.h:23, + from ecohash.h:29, + from ecohash.cc:26: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': +murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] + 1008 | bool revZero=false; + | ^~~~~~~ +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc +murasaki.cc: In function 'bool convertPattern(std::string&)': +murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 1287 | random_shuffle(randomStr.begin(),randomStr.end()); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/algorithm:63, + from /usr/include/boost/regex/v5/regex_workaround.hpp:23, + from /usr/include/boost/regex/v5/regex.hpp:29, + from /usr/include/boost/regex.hpp:34, + from seqread.h:33, + from binseq.hh:31, + from sequence.h:32: +/usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here + 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc +In file included from ecolist.h:23, + from openhash.h:29, + from openhash.cc:26: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc +cgr.cc: In member function 'void Cgr::merge(Cgr&)': +cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] + 140 | int redist=(unsigned long)(rez*rez)<=seedcount; + | ^~~~~~ +cgr.cc: In member function 'bool Cgr::savePNG(std::string)': +cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] + 288 | int res; + | ^~~ +cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': +cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] + 435 | int wordwidth=1; + | ^~~~~~~~~ +binseq.cc: In member function 'bool SequenceBinary::save(std::string)': +binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] + 70 | }catch(ofstream::failure e){ + | ^ +binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': +binseq.cc:158:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_algobase.h:64, + from /usr/include/c++/15/string:53, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/istream:42, + from /usr/include/c++/15/fstream:42, + from seqread.h:30, + from binseq.hh:31, + from binseq.cc:21: +/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here + 302 | struct pair + | ^~~~ +binseq.cc:160:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here + 302 | struct pair + | ^~~~ +binseq.cc:162:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here + 302 | struct pair + | ^~~~ +murasaki_mpi.cc: In function 'void mpi_types_init()': +murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized] + 107 | MPI_Get_address(&msg.key,disp); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +In file included from murasaki_mpi.cc:29: +/usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:1677:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here + 1677 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address); + | ^~~~~~~~~~~~~~~ +murasaki_mpi.cc:102:19: note: 'msg' declared here + 102 | MPI_HashMessage msg; + | ^~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc +cgr-sample.cc: In function 'int main(int, char**)': +cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] + 54 | bool repeatmask=false,save=false; + | ^~~~~~~~~~ cgr.cc: In member function 'std::pair Cgr::sampleHighLow(double, double)': cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; @@ -1152,7 +1198,6 @@ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc In file included from ecolist.h:23, from testeco.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1165,45 +1210,36 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -murasaki_mpi.cc: In function 'void mpi_types_init()': -murasaki_mpi.cc:107:18: warning: 'msg' may be used uninitialized [-Wmaybe-uninitialized] - 107 | MPI_Get_address(&msg.key,disp); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -In file included from murasaki_mpi.cc:29: -/usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:1677:20: note: by argument 1 of type 'const void*' to 'int MPI_Get_address(const void*, MPI_Aint*)' declared here - 1677 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address); - | ^~~~~~~~~~~~~~~ -murasaki_mpi.cc:102:19: note: 'msg' declared here - 102 | MPI_HashMessage msg; - | ^~~ -cgr-sample.cc: In function 'int main(int, char**)': -cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] - 54 | bool repeatmask=false,save=false; - | ^~~~~~~~~~ +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc +getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': +getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] + 153 | }catch(bad_lexical_cast e){ + | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now align-coverage.cc: In function 'int main(int, char**)': align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ -getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': -getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] - 153 | }catch(bad_lexical_cast e){ - | ^ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ @@ -1218,7 +1254,7 @@ make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=NO - make -j16 INSTALL="install --strip-program=true" USE_MPI=NO + make -j12 INSTALL="install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/build/reproducible-path/murasaki-1.68.6' make -C src all make[3]: Entering directory '/build/reproducible-path/murasaki-1.68.6/src' @@ -1236,44 +1272,17 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c scoring.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c openhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c genopts.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c binseq.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-image.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-compare.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-random.cc -binseq.cc: In member function 'bool SequenceBinary::save(std::string)': -binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] - 70 | }catch(ofstream::failure e){ - | ^ -binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': -binseq.cc:158:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_algobase.h:64, - from /usr/include/c++/15/string:53, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/istream:42, - from /usr/include/c++/15/fstream:42, - from seqread.h:30, - from binseq.hh:31, - from binseq.cc:21: -/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here - 302 | struct pair - | ^~~~ -binseq.cc:160:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here - 302 | struct pair - | ^~~~ -binseq.cc:162:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here - 302 | struct pair - | ^~~~ +In file included from msethash.cc:25: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, from dinkymath.cc:27: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1291,6 +1300,34 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from murasaki.h:24, + from arrayhash.cc:28: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from murasaki.h:24, + from murasaki.cc:37: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/string:51, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/bits/ostream.h:43, + from /usr/include/c++/15/ostream:42, + from /usr/include/c++/15/iostream:43, + from murasaki.cc:29: +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ dinkymath.cc: In function 'std::string littleEndianStr(unsigned int, int)': dinkymath.cc:40:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 40 | int last=0; @@ -1299,8 +1336,8 @@ dinkymath.cc:53:7: warning: variable 'last' set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ -In file included from murasaki.h:24, - from sequence.cc:28: +In file included from options.h:28, + from options.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1312,7 +1349,8 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, - from ecolist.cc:20: + from openhash.h:29, + from openhash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1323,13 +1361,20 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 467 | struct less_map : public binary_function { - | ^~~~~~~~~~~~~~~ +In file included from murasaki.h:24, + from scoring.cc:27: +sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 444 | struct ltRegion : binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_tree.h:67, + from /usr/include/c++/15/set:64, + from cmultiset.h:33, + from sequence.h:30: /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from msethash.cc:25: +In file included from ecolist.h:23, + from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1341,7 +1386,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from murasaki.h:24, - from arrayhash.cc:28: + from sequence.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1353,8 +1398,8 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, - from openhash.h:29, - from openhash.cc:26: + from ecohash.h:29, + from ecohash.cc:26: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1365,18 +1410,32 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cgr.cc: In member function 'void Cgr::merge(Cgr&)': -cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] - 140 | int redist=(unsigned long)(rez*rez)<=seedcount; - | ^~~~~~ -cgr.cc: In member function 'bool Cgr::savePNG(std::string)': -cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] - 288 | int res; - | ^~~ -cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': -cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] - 435 | int wordwidth=1; - | ^~~~~~~~~ +ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 467 | struct less_map : public binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': +murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] + 1008 | bool revZero=false; + | ^~~~~~~ +murasaki.cc: In function 'bool convertPattern(std::string&)': +murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 1287 | random_shuffle(randomStr.begin(),randomStr.end()); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/algorithm:63, + from /usr/include/boost/regex/v5/regex_workaround.hpp:23, + from /usr/include/boost/regex/v5/regex.hpp:29, + from /usr/include/boost/regex.hpp:34, + from seqread.h:33, + from binseq.hh:31, + from sequence.h:32: +/usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here + 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c binseq.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-image.cc sequence.cc: In member function 'void BitSequence::loadBinary(const SequenceBinary&)': sequence.cc:1113:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'ShmVector >::val_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); @@ -1392,51 +1451,14 @@ /usr/include/c++/15/bits/stl_pair.h:302:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here 302 | struct pair | ^~~~ -In file included from murasaki.h:24, - from scoring.cc:27: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from murasaki.h:24, - from murasaki.cc:37: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/string:51, - from /usr/include/c++/15/bits/locale_classes.h:42, - from /usr/include/c++/15/bits/ios_base.h:43, - from /usr/include/c++/15/ios:46, - from /usr/include/c++/15/bits/ostream.h:43, - from /usr/include/c++/15/ostream:42, - from /usr/include/c++/15/iostream:43, - from murasaki.cc:29: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from ecolist.h:23, - from ecohash.h:29, - from ecohash.cc:26: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr.cc sequence.cc: In member function 'std::pair IntervalSet::entropy() const': sequence.cc:3332:10: warning: variable 'shortest' set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-compare.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-random.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-sample.cc In file included from sequence.cc:41: hashing.h: In instantiation of 'SBox::SBox(int) [with T = short unsigned int]': sequence.cc:162:29: required from here @@ -1455,7 +1477,6 @@ /usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c cgr-sample.cc In file included from sequence.h:44: shmvector.hh: In instantiation of 'void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = long unsigned int]': shmvector.hh:282:5: required from 'void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]' @@ -1470,8 +1491,59 @@ /usr/include/c++/15/bits/stl_pair.h:302:12: note: 'struct std::pair' declared here 302 | struct pair | ^~~~ -In file included from options.h:28, - from options.cc:26: +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c testeco.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-compare.cc +cgr.cc: In member function 'void Cgr::merge(Cgr&)': +cgr.cc:140:7: warning: variable 'redist' set but not used [-Wunused-but-set-variable] + 140 | int redist=(unsigned long)(rez*rez)<=seedcount; + | ^~~~~~ +cgr.cc: In member function 'bool Cgr::savePNG(std::string)': +cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] + 288 | int res; + | ^~~ +cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': +cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] + 435 | int wordwidth=1; + | ^~~~~~~~~ +binseq.cc: In member function 'bool SequenceBinary::save(std::string)': +binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] + 70 | }catch(ofstream::failure e){ + | ^ +binseq.cc: In member function 'void SequenceBinary::fillCopyVectors()': +binseq.cc:158:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_algobase.h:64, + from /usr/include/c++/15/string:53, + from /usr/include/c++/15/bits/locale_classes.h:42, + from /usr/include/c++/15/bits/ios_base.h:43, + from /usr/include/c++/15/ios:46, + from /usr/include/c++/15/istream:42, + from /usr/include/c++/15/fstream:42, + from seqread.h:30, + from binseq.hh:31, + from binseq.cc:21: +/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here + 302 | struct pair + | ^~~~ +binseq.cc:160:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here + 302 | struct pair + | ^~~~ +binseq.cc:162:9: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/15/bits/stl_pair.h:302:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here + 302 | struct pair + | ^~~~ +cgr-sample.cc: In function 'int main(int, char**)': +cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] + 54 | bool repeatmask=false,save=false; + | ^~~~~~~~~~ +In file included from ecolist.h:23, + from testeco.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1482,32 +1554,6 @@ /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c testeco.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-compare.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c alignments.cc -murasaki.cc: In function 'void procLocs(LocList&, std::__cxx11::list&, int, int)': -murasaki.cc:1008:8: warning: variable 'revZero' set but not used [-Wunused-but-set-variable] - 1008 | bool revZero=false; - | ^~~~~~~ -murasaki.cc: In function 'bool convertPattern(std::string&)': -murasaki.cc:1287:17: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 1287 | random_shuffle(randomStr.begin(),randomStr.end()); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-or.cc -In file included from /usr/include/c++/15/algorithm:63, - from /usr/include/boost/regex/v5/regex_workaround.hpp:23, - from /usr/include/boost/regex/v5/regex.hpp:29, - from /usr/include/boost/regex.hpp:34, - from seqread.h:33, - from binseq.hh:31, - from sequence.h:32: -/usr/include/c++/15/bits/stl_algo.h:4537:5: note: declared here - 4537 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c geneparse.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-and.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-best.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-coverage.cc cgr.cc: In member function 'std::pair Cgr::sampleHighLow(double, double)': cgr.cc:339:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 339 | delete alt; @@ -1529,50 +1575,40 @@ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c alignments.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-or.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c geneparse.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-and.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-best.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c align-coverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c getsegments.cc -In file included from ecolist.h:23, - from testeco.cc:20: -sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_tree.h:67, - from /usr/include/c++/15/set:64, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -c mbfa.cc +getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': +getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] + 153 | }catch(bad_lexical_cast e){ + | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -cgr-sample.cc: In function 'int main(int, char**)': -cgr-sample.cc:54:8: warning: variable 'repeatmask' set but not used [-Wunused-but-set-variable] - 54 | bool repeatmask=false,save=false; - | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now align-coverage.cc: In function 'int main(int, char**)': align-coverage.cc:148:10: warning: variable 'seqStats' set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ -getsegments.cc: In function 'size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)': -getsegments.cc:153:29: warning: catching polymorphic type 'class boost::bad_lexical_cast' by value [-Wcatch-value=] - 153 | }catch(bad_lexical_cast e){ - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/murasaki-1.68.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/build/reproducible-path/murasaki-1.68.6/src' make[2]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' make[1]: Leaving directory '/build/reproducible-path/murasaki-1.68.6' - dh_auto_test +dh: command-omitted: The call to "dh_auto_test" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install @@ -1636,15 +1672,15 @@ dh_shlibdeps -a dh_installdeb dh_gencontrol -dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package murasaki-common: substitution variable ${misc:perl} used, but is not defined dpkg-gencontrol: warning: package murasaki-common: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined +dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-16_amd64.deb'. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-16_amd64.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-16_amd64.deb'. +dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-16_amd64.deb'. dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-16_amd64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-16_all.deb'. dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-16_amd64.buildinfo @@ -1654,12 +1690,14 @@ 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/1523902/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1523902/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/448365 and its subdirectories -I: Current time: Thu Dec 24 14:33:26 -12 2026 -I: pbuilder-time-stamp: 1798166006 +I: removing directory /srv/workspace/pbuilder/1523902 and its subdirectories +I: Current time: Sat Nov 22 10:12:54 +14 2025 +I: pbuilder-time-stamp: 1763755974