Diff of the two buildlogs: -- --- b1/build.log 2025-02-19 14:01:45.339009575 +0000 +++ b2/build.log 2025-02-19 14:05:40.924451874 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 19 01:53:55 -12 2025 -I: pbuilder-time-stamp: 1739973235 +I: Current time: Wed Mar 25 10:24:47 +14 2026 +I: pbuilder-time-stamp: 1774383887 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying fix_mpi.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1432645/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4153904/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 24 20:24 /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/4153904/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4153904/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='fe69982230954817a4eb1700cf7e63c4' - 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='1432645' - PS1='# ' - PS2='> ' + INVOCATION_ID=af79b1a3152a406690603b3889fc9373 + 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=4153904 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.3QnmDQyK/pbuilderrc_xOnq --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.3QnmDQyK/b1 --logfile b1/build.log murasaki_1.68.6-14.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.3QnmDQyK/pbuilderrc_IgB8 --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.3QnmDQyK/b2 --logfile b2/build.log murasaki_1.68.6-14.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1432645/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4153904/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 119 http://deb.debian.org/debian trixie/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libtext-wrapper-perl all 1.05-4 [10.3 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.18 [3372 B] -Fetched 135 MB in 5s (28.6 MB/s) +Fetched 135 MB in 2s (70.0 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 ... 19809 files and directories currently installed.) @@ -756,7 +788,11 @@ Building tag database... -> Finished parsing the build-deps 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_1.68.6-14_source.changes +I: user script /srv/workspace/pbuilder/4153904/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4153904/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_1.68.6-14_source.changes dpkg-buildpackage: info: source package murasaki dpkg-buildpackage: info: source version 1.68.6-14 dpkg-buildpackage: info: source distribution unstable @@ -766,7 +802,7 @@ debian/rules clean dh clean dh_auto_clean - make -j20 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' rm -rf *.o *~ .*~ core make -C src clean @@ -783,7 +819,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/murasaki-1.68.6' dh_auto_build -- USE_MPI=YES - make -j20 "INSTALL=install --strip-program=true" USE_MPI=YES + make -j42 "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' @@ -808,6 +844,15 @@ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc +mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.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; @@ -816,138 +861,11 @@ cgr.cc:288:7: warning: variable 'res' set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc 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; | ^~~~~~~~~ -In file included from murasaki.h:24, - from sequence.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++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/14/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' -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]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/bits/stl_tree.h:63: -/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here - 284 | struct pair - | ^~~~ -sequence.cc:1114:9: 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] - 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here - 284 | struct pair - | ^~~~ -sequence.cc: In destructor 'BitSequence::~BitSequence()': -sequence.cc:1394:9: warning: 'throw' will always call 'terminate' [-Wterminate] - 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' -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++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': -seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 264 | stitchPath=stitchfile.branch_path(); - | ~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from seqread.cc:35: -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -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]); - | ^~~~~~~~ -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++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from murasaki.cc:29: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -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; - | ^~~ -cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' - 330 | pix *alt=new pix[size]; - | ^ -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 - 162 | sbox=new SBoxT(hash_bits); - | ^ -hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 56 | random_shuffle(boxes[b],boxes[b]+boxsize); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/algorithm:61, - 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++/14/bits/stl_algo.h:4492:5: note: declared here - 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': -cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 354 | delete alt; - | ^~~ -cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' - 345 | pix *alt=new pix[size]; - | ^ -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++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -cgr.cc: In member function 'std::pair Cgr::findNiceRange()': -cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 395 | delete alt; - | ^~~ -In file included from ecolist.h:23, - from openhash.h:29, - from openhash.cc:26: +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 { | ^~~~~~~~~~~~~~~ @@ -958,9 +876,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' - 376 | pix *alt=new pix[size]; - | ^ 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] @@ -977,20 +892,6 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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]' - 282 | shmRealloc(c); - | ^~~~~~~~~~ -sequence.cc:1110:17: required from here - 1110 | subSeqs.resize(binseq.regionSizes[0]); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair' declared here - 284 | struct pair - | ^~~~ 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; @@ -1014,9 +915,8 @@ /usr/include/c++/14/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: +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 { | ^~~~~~~~~~~~~~~ @@ -1031,6 +931,18 @@ binseq.cc:70:28: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ +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++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ 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)); @@ -1060,41 +972,23 @@ /usr/include/c++/14/bits/stl_pair.h:284:12: note: '__gnu_cxx::__alloc_traits >, std::pair >::value_type' {aka 'struct std::pair'} declared here 284 | struct pair | ^~~~ -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_mpi.cc:89:29: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 89 | struct lt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +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 { + | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:95:29: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 95 | struct gt_mpi_worldMemory : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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++/14/algorithm:61, - 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++/14/bits/stl_algo.h:4492:5: note: declared here - 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -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++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from cmultiset.h:33, @@ -1102,9 +996,30 @@ /usr/include/c++/14/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 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++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from murasaki.cc:29: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from murasaki.h:24, + from sequence.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++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1112,12 +1027,38 @@ 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 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++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/14/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++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/14/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 options.h:28, - from options.cc:26: +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 { | ^~~~~~~~~~~~~~~ @@ -1128,8 +1069,19 @@ /usr/include/c++/14/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 -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc -In file included from msethash.cc:25: +ecolist.cc:467:26: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 467 | struct less_map : public binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/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' +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 { | ^~~~~~~~~~~~~~~ @@ -1140,8 +1092,117 @@ /usr/include/c++/14/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 -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 -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.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]); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/bits/stl_tree.h:63: +/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here + 284 | struct pair + | ^~~~ +sequence.cc:1114:9: 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] + 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here + 284 | struct pair + | ^~~~ +sequence.cc: In destructor 'BitSequence::~BitSequence()': +sequence.cc:1394:9: warning: 'throw' will always call 'terminate' [-Wterminate] + 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' +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){ + | ^ +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; + | ^~~~~~~ +seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': +seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 264 | stitchPath=stitchfile.branch_path(); + | ~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from seqread.cc:35: +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +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++/14/algorithm:61, + 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++/14/bits/stl_algo.h:4492:5: note: declared here + 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ +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 '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; + | ^~~ +cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' + 330 | pix *alt=new pix[size]; + | ^ +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 + 162 | sbox=new SBoxT(hash_bits); + | ^ +hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 56 | random_shuffle(boxes[b],boxes[b]+boxsize); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/algorithm:61, + 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++/14/bits/stl_algo.h:4492:5: note: declared here + 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ +cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': +cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 354 | delete alt; + | ^~~ +cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' + 345 | pix *alt=new pix[size]; + | ^ +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]' + 282 | shmRealloc(c); + | ^~~~~~~~~~ +sequence.cc:1110:17: required from here + 1110 | subSeqs.resize(binseq.regionSizes[0]); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair' declared here + 284 | struct pair + | ^~~~ +cgr.cc: In member function 'std::pair Cgr::findNiceRange()': +cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 395 | delete alt; + | ^~~ +cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' + 376 | pix *alt=new pix[size]; + | ^ cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) @@ -1155,20 +1216,6 @@ cgr.cc:493:13: note: 'height' was declared here 493 | int width,height; | ^~~~~~ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.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++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) @@ -1182,20 +1229,9 @@ cgr.cc:426:13: note: 'height' was declared here 426 | int width,height; | ^~~~~~ -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc -mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 -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 -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 -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 -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){ - | ^ -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; - | ^~~~~~~~ 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); @@ -1207,17 +1243,17 @@ 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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 \ @@ -1232,7 +1268,7 @@ 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 -j20 "INSTALL=install --strip-program=true" USE_MPI=NO + make -j42 "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' @@ -1258,8 +1294,17 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc -In file included from murasaki.h:24, - from scoring.cc:27: +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.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 { | ^~~~~~~~~~~~~~~ @@ -1282,6 +1327,54 @@ cgr.cc:435:7: warning: variable 'wordwidth' set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ +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++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +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 { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': +seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] + 264 | stitchPath=stitchfile.branch_path(); + | ~~~~~~~~~~~~~~~~~~~~~~^~ +In file included from seqread.cc:35: +/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here + 1129 | path branch_path() const { return parent_path(); } + | ^~~~~~~~~~~ +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){ + | ^ +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++/14/bits/stl_tree.h:65, + from /usr/include/c++/14/set:62, + from cmultiset.h:33, + from sequence.h:30: +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ 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){ @@ -1316,24 +1409,6 @@ 284 | struct pair | ^~~~ 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++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/14/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 { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/14/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] @@ -1346,22 +1421,24 @@ /usr/include/c++/14/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 -DLARGESEQ_SUPPORT -c alignments.cc -In file included from msethash.cc:25: +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] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: +In file included from /usr/include/c++/14/string:49, + from /usr/include/c++/14/bits/locale_classes.h:40, + from /usr/include/c++/14/bits/ios_base.h:41, + from /usr/include/c++/14/ios:44, + from /usr/include/c++/14/ostream:40, + from /usr/include/c++/14/iostream:41, + from dinkymath.h:24, + from dinkymath.cc:26: /usr/include/c++/14/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 -DLARGESEQ_SUPPORT -c align-or.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc In file included from murasaki.h:24, - from sequence.cc:28: + from arrayhash.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1373,8 +1450,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ecolist.h:23, - from openhash.h:29, - from openhash.cc:26: + from ecolist.cc:20: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1385,23 +1461,7 @@ /usr/include/c++/14/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]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/bits/stl_tree.h:63: -/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here - 284 | struct pair - | ^~~~ -sequence.cc:1114:9: 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] - 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here - 284 | struct pair - | ^~~~ -In file included from murasaki.h:24, - from arrayhash.cc:28: +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 { | ^~~~~~~~~~~~~~~ @@ -1412,66 +1472,6 @@ /usr/include/c++/14/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]); - | ^~~~~~~~ -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 - 162 | sbox=new SBoxT(hash_bits); - | ^ -hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] - 56 | random_shuffle(boxes[b],boxes[b]+boxsize); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/algorithm:61, - 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++/14/bits/stl_algo.h:4492:5: note: declared here - 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) - | ^~~~~~~~~~~~~~ -seqread.cc: In member function 'void SequenceByteReader::addRedirect(boost::cmatch)': -seqread.cc:264:38: warning: 'boost::filesystem::path boost::filesystem::path::branch_path() const' is deprecated: Use path::parent_path() instead [-Wdeprecated-declarations] - 264 | stitchPath=stitchfile.branch_path(); - | ~~~~~~~~~~~~~~~~~~~~~~^~ -In file included from seqread.cc:35: -/usr/include/boost/filesystem/path.hpp:1129:10: note: declared here - 1129 | path branch_path() const { return parent_path(); } - | ^~~~~~~~~~~ -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]' - 282 | shmRealloc(c); - | ^~~~~~~~~~ -sequence.cc:1110:17: required from here - 1110 | subSeqs.resize(binseq.regionSizes[0]); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] - 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair' declared here - 284 | struct pair - | ^~~~ -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] - 444 | struct ltRegion : binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/string:49, - from /usr/include/c++/14/bits/locale_classes.h:40, - from /usr/include/c++/14/bits/ios_base.h:41, - from /usr/include/c++/14/ios:44, - from /usr/include/c++/14/ostream:40, - from /usr/include/c++/14/iostream:41, - from dinkymath.h:24, - from dinkymath.cc:26: -/usr/include/c++/14/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; @@ -1480,6 +1480,16 @@ 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 { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +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 murasaki.h:24, from murasaki.cc:37: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1495,28 +1505,8 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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 -DLARGESEQ_SUPPORT -c align-and.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; - | ^~~ -cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' - 330 | pix *alt=new pix[size]; - | ^ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc -cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': -cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 354 | delete alt; - | ^~~ -cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' - 345 | pix *alt=new pix[size]; - | ^ -In file included from ecolist.h:23, - from testeco.cc:20: +In file included from murasaki.h:24, + from sequence.cc:28: sequence.h:444:19: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 444 | struct ltRegion : binary_function { | ^~~~~~~~~~~~~~~ @@ -1527,6 +1517,25 @@ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +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; + | ^~~~~~~~ +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]); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/bits/stl_tree.h:63: +/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here + 284 | struct pair + | ^~~~ +sequence.cc:1114:9: 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] + 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'ShmVector >::val_type' {aka 'struct std::pair'} declared here + 284 | struct pair + | ^~~~ 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; @@ -1545,7 +1554,24 @@ /usr/include/c++/14/bits/stl_algo.h:4492:5: note: declared here 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.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]); + | ^~~~~~~~ +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; + | ^~~ +cgr.cc:330:24: note: returned from 'void* operator new [](std::size_t)' + 330 | pix *alt=new pix[size]; + | ^ +cgr.cc: In member function 'std::pair Cgr::sampleHighLow(int, int)': +cgr.cc:354:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 354 | delete alt; + | ^~~ +cgr.cc:345:24: note: returned from 'void* operator new [](std::size_t)' + 345 | pix *alt=new pix[size]; + | ^ cgr.cc: In member function 'std::pair Cgr::findNiceRange()': cgr.cc:395:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 395 | delete alt; @@ -1553,20 +1579,38 @@ cgr.cc:376:24: note: returned from 'void* operator new [](std::size_t)' 376 | pix *alt=new pix[size]; | ^ -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 { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_tree.h:65, - from /usr/include/c++/14/set:62, - from cmultiset.h:33, - from sequence.h:30: -/usr/include/c++/14/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 -DLARGESEQ_SUPPORT -c getsegments.cc -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.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 + 162 | sbox=new SBoxT(hash_bits); + | ^ +hashing.h:56:21: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = short unsigned int*]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] + 56 | random_shuffle(boxes[b],boxes[b]+boxsize); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/14/algorithm:61, + 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++/14/bits/stl_algo.h:4492:5: note: declared here + 4492 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) + | ^~~~~~~~~~~~~~ +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]' + 282 | shmRealloc(c); + | ^~~~~~~~~~ +sequence.cc:1110:17: required from here + 1110 | subSeqs.resize(binseq.regionSizes[0]); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +shmvector.hh:225:13: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] + 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair' declared here + 284 | struct pair + | ^~~~ cgr.cc: In member function 'int PgmBuffer::loadBinaryPGM(std::string)': cgr.cc:557:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) @@ -1580,6 +1624,7 @@ cgr.cc:493:13: note: 'height' was declared here 493 | int width,height; | ^~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 cgr.cc: In member function 'int PgmBuffer::loadPGM(std::string)': cgr.cc:485:31: warning: 'width' may be used uninitialized [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) @@ -1593,17 +1638,8 @@ cgr.cc:426:13: note: 'height' was declared here 426 | int width,height; | ^~~~~~ -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 -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){ - | ^ -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; - | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -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 -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 -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 @@ -1682,17 +1718,17 @@ 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-mpi: substitution variable ${perl:Depends} unused, but is 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-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_amd64.deb'. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-14_amd64.deb'. +dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_amd64.deb'. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-14_amd64.deb'. dpkg-deb: building package 'murasaki-common' in '../murasaki-common_1.68.6-14_all.deb'. -dpkg-deb: building package 'murasaki-mpi-dbgsym' in '../murasaki-mpi-dbgsym_1.68.6-14_amd64.deb'. -dpkg-deb: building package 'murasaki-dbgsym' in '../murasaki-dbgsym_1.68.6-14_amd64.deb'. dpkg-genbuildinfo --build=binary -O../murasaki_1.68.6-14_amd64.buildinfo dpkg-genchanges --build=binary -O../murasaki_1.68.6-14_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1700,12 +1736,14 @@ 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/4153904/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4153904/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/1432645 and its subdirectories -I: Current time: Wed Feb 19 02:01:44 -12 2025 -I: pbuilder-time-stamp: 1739973704 +I: removing directory /srv/workspace/pbuilder/4153904 and its subdirectories +I: Current time: Wed Mar 25 10:28:39 +14 2026 +I: pbuilder-time-stamp: 1774384119