Diff of the two buildlogs: -- --- b1/build.log 2024-05-19 22:14:23.183016017 +0000 +++ b2/build.log 2024-05-19 22:22:43.541728589 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 19 10:03:48 -12 2024 -I: pbuilder-time-stamp: 1716156228 +I: Current time: Mon May 20 12:14:58 +14 2024 +I: pbuilder-time-stamp: 1716156898 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying fixed-check-for-m64-flag.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22623/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13961/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 19 22:15 /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/13961/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13961/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='7a14d5065add4a569b239e79e47a638a' - 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='22623' - PS1='# ' - PS2='> ' + INVOCATION_ID=9e32291f0f174e298043e684020ac20d + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=13961 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.kAYjA240/pbuilderrc_8ml8 --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.kAYjA240/b1 --logfile b1/build.log fsa_1.15.9+dfsg-6.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kAYjA240/pbuilderrc_N4cC --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.kAYjA240/b2 --logfile b2/build.log fsa_1.15.9+dfsg-6.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff64a 6.1.0-21-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-armmp-lpae #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 18 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/22623/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 17 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/13961/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -157,7 +189,7 @@ Get: 37 http://deb.debian.org/debian trixie/main armhf exonerate armhf 2.4.0-5+b1 [1661 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf help2man armhf 1.49.3 [198 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf mummer armhf 3.23+dfsg-8 [627 kB] -Fetched 23.1 MB in 1s (32.5 MB/s) +Fetched 23.1 MB in 1s (40.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19447 files and directories currently installed.) @@ -334,7 +366,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/fsa-1.15.9+dfsg/ && 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 > ../fsa_1.15.9+dfsg-6_source.changes +I: user script /srv/workspace/pbuilder/13961/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/13961/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/fsa-1.15.9+dfsg/ && 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 > ../fsa_1.15.9+dfsg-6_source.changes dpkg-buildpackage: info: source package fsa dpkg-buildpackage: info: source version 1.15.9+dfsg-6 dpkg-buildpackage: info: source distribution unstable @@ -389,8 +425,8 @@ checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc @@ -495,7 +531,7 @@ Email with questions and bug reports. dh_auto_build - make -j5 + make -j4 make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' @@ -503,15 +539,13 @@ make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o dexception.o dexception.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o logfile.o logfile.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o memcheck.o memcheck.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o misc.o misc.cc -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o opts_list.o opts_list.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o regexp.o regexp.cc +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o opts_list.o opts_list.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ opts_list.cc:99:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 99 | SET_VERSION_INFO(*this); @@ -523,10 +557,6 @@ opts_list.cc:99:3: note: in expansion of macro 'SET_VERSION_INFO' 99 | SET_VERSION_INFO(*this); | ^~~~~~~~~~~~~~~~ -regexp.cc: In member function 'char* CRegCompilerBase::regatom(int*)': -regexp.cc:995:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 995 | register char ch; - | ^~ In file included from misc.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { @@ -607,6 +637,12 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o regexp.o regexp.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +regexp.cc: In member function 'char* CRegCompilerBase::regatom(int*)': +regexp.cc:995:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 995 | register char ch; + | ^~ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o sstring.o sstring.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/util/sstring.h:14, @@ -683,11 +719,9 @@ make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o alphabet.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o alignment.o alignment.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o gff.o gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o mercator.o mercator.cc -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o sequence.o sequence.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ @@ -739,23 +773,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/math/mathematics.h:23, - from sequence.cc:11: -../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 187 | struct Duple_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from ../../src/util/regexp.h:8, - from sequence.cc:10: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 203 | struct Map_value_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from ../../src/seq/alignment.h:16, from alignment.cc:13: @@ -773,20 +790,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/seq/interval.h:13, - from ../../src/seq/sequence.h:21: -../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 185 | struct GFF_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/math/mathematics.h:23, from gff.cc:14: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -808,16 +811,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/seq/interval.h:13, - from ../../src/seq/sequence.h:21, - from sequence.cc:12: +In file included from gff.cc:15: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from gff.cc:15: +In file included from ../../src/seq/interval.h:13, + from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ @@ -856,20 +858,16 @@ /usr/include/c++/13/bits/stl_function.h:1046:5: note: declared here 1046 | not1(const _Predicate& __pred) | ^~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o sequence.o sequence.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/math/mathematics.h:23, - from similarity_matrix.cc:11: + from sequence.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from similarity_matrix.cc:8: + from ../../src/util/regexp.h:8, + from sequence.cc:10: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -881,8 +879,7 @@ | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, - from ../../src/seq/similarity_matrix.h:13, - from similarity_matrix.cc:12: + from sequence.cc:12: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ @@ -907,6 +904,45 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ../../src/math/mathematics.h:23, + from similarity_matrix.cc:11: +../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 187 | struct Duple_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from similarity_matrix.cc:8: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 203 | struct Map_value_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from ../../src/seq/interval.h:13, + from ../../src/seq/sequence.h:21, + from ../../src/seq/similarity_matrix.h:13, + from similarity_matrix.cc:12: +../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 185 | struct GFF_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ rm -f libseq.a ar cru libseq.a alphabet.o alignment.o gff.o mercator.o sequence.o similarity_matrix.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -916,12 +952,12 @@ make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o manager.o manager.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o mw_adapter.o mw_adapter.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o db_adapter.o db_adapter.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o db_misc.o db_misc.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/manager/manager.h:12, from manager.cc:6: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': @@ -992,11 +1028,9 @@ make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o algebras.o algebras.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o aminoacid_indel2dp.o aminoacid_indel2dp.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o aminoaciddp.o aminoaciddp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o anchors.o anchors.cc -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o constraints.o constraints.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ @@ -1021,22 +1055,6 @@ algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o fsa.o fsa.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); - | ^ -In file included from ../../src/fsa/fsa.h:66, - from fsa.cc:11: -../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; - | ^~~~~~~~ -../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO' - 152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS); - | ^~~~~~~~~~~~~~~~ -fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST' - 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from aminoacid_indel2dp.h:28, from aminoacid_indel2dp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': @@ -1047,32 +1065,32 @@ algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ +algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 218 | register double mantisse = a.f*b; + | ^~~~~~~~ +algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 231 | register double mantisse = a.f*b; + | ^~~~~~~~ +algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 238 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ In file included from aminoaciddp.h:28, from aminoaciddp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ -algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 218 | register double mantisse = a.f*b; - | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ -algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 231 | register double mantisse = a.f*b; - | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ -algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 238 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; @@ -1081,6 +1099,8 @@ algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o constraints.o constraints.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ aminoaciddp.cc: In function 'Algebra Forward(AminoAcidAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:821:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 821 | register double iTempResult[1]; @@ -1092,12 +1112,12 @@ aminoacid_indel2dp.cc:821:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 821 | register double iTempResult[1]; | ^~~~~~~~~~~ -aminoacid_indel2dp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 823 | register bfloat iTempProb[1]; - | ^~~~~~~~~ aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ +aminoacid_indel2dp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 823 | register bfloat iTempProb[1]; + | ^~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBaumWelch(AminoAcidAlignBaumWelch&, AminoAcidAlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:1009:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1009 | register double iTempResult[1]; @@ -1105,6 +1125,13 @@ aminoaciddp.cc:1011:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1011 | register bfloat iTempProb[3]; | ^~~~~~~~~ +aminoaciddp.cc: In function 'Algebra Backward(AminoAcidAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +aminoaciddp.cc:1283:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1283 | register double iTempResult[1]; + | ^~~~~~~~~~~ +aminoaciddp.cc:1285:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1285 | register bfloat iTempProb[1]; + | ^~~~~~~~~ aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ @@ -1115,23 +1142,9 @@ aminoacid_indel2dp.cc:1041:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1041 | register bfloat iTempProb[3]; | ^~~~~~~~~ -aminoaciddp.cc: In function 'Algebra Backward(AminoAcidAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -aminoaciddp.cc:1283:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1283 | register double iTempResult[1]; - | ^~~~~~~~~~~ -aminoaciddp.cc:1285:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1285 | register bfloat iTempProb[1]; - | ^~~~~~~~~ aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1230 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -aminoacid_indel2dp.cc: In function 'Algebra Backward(AminoAcidIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -aminoacid_indel2dp.cc:1373:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1373 | register double iTempResult[1]; - | ^~~~~~~~~~~ -aminoacid_indel2dp.cc:1375:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1375 | register bfloat iTempProb[1]; - | ^~~~~~~~~ aminoaciddp.cc: In function 'Algebra ForwardBanding(AminoAcidAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:1502:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1502 | register double iTempResult[1]; @@ -1139,9 +1152,13 @@ aminoaciddp.cc:1504:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1504 | register bfloat iTempProb[1]; | ^~~~~~~~~ -aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1320 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ +aminoacid_indel2dp.cc: In function 'Algebra Backward(AminoAcidIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +aminoacid_indel2dp.cc:1373:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1373 | register double iTempResult[1]; + | ^~~~~~~~~~~ +aminoacid_indel2dp.cc:1375:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1375 | register bfloat iTempProb[1]; + | ^~~~~~~~~ aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1448 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ @@ -1152,13 +1169,9 @@ aminoaciddp.cc:1729:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1729 | register bfloat iTempProb[3]; | ^~~~~~~~~ -aminoacid_indel2dp.cc: In function 'Algebra ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -aminoacid_indel2dp.cc:1622:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1622 | register double iTempResult[1]; - | ^~~~~~~~~~~ -aminoacid_indel2dp.cc:1624:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1624 | register bfloat iTempProb[1]; - | ^~~~~~~~~ +aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1320 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBanding(AminoAcidAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:2033:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2033 | register double iTempResult[1]; @@ -1166,12 +1179,19 @@ aminoaciddp.cc:2035:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2035 | register bfloat iTempProb[1]; | ^~~~~~~~~ -aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1568 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ +aminoacid_indel2dp.cc: In function 'Algebra ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +aminoacid_indel2dp.cc:1622:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1622 | register double iTempResult[1]; + | ^~~~~~~~~~~ +aminoacid_indel2dp.cc:1624:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1624 | register bfloat iTempProb[1]; + | ^~~~~~~~~ aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1979 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ +aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1568 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBaumWelchBanding(AminoAcidIndel2AlignWithBandingBaumWelch&, AminoAcidIndel2AlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:1877:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1877 | register double iTempResult[1]; @@ -1218,8 +1238,51 @@ ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o model.o model.cc +anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const std::string&, const std::string&, int) const': +anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 863 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +anchors.cc:864:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 864 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const std::string&, const std::string&, size_t) const': +anchors.cc:1100:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1100 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +anchors.cc:1101:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1101 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o fsa.o fsa.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); + | ^ +In file included from ../../src/fsa/fsa.h:66, + from fsa.cc:11: +../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; + | ^~~~~~~~ +../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO' + 152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS); + | ^~~~~~~~~~~~~~~~ +fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST' + 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from ../../src/seq/sequence.h:16, + from ../../src/seq/alignment.h:16, + from anchors.cc:15: +/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = fsa::Anchor; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 315 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = fsa::Anchor; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 751 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': @@ -1249,76 +1312,77 @@ ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -In file included from ../../src/fsa/nucleotidedp.h:28, - from ../../src/fsa/model.h:25, - from model.cc:8: -../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': -../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 195 | register BFloat a( 0.0, 0 ); - | ^ -../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 211 | register BFloat sf(a.f*b.f,a.e+b.e); - | ^~ -../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 218 | register double mantisse = a.f*b; - | ^~~~~~~~ -../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 231 | register double mantisse = a.f*b; - | ^~~~~~~~ -../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 238 | register BFloat sf(a.f/b.f, a.e-b.e); - | ^~ -anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const std::string&, const std::string&, int) const': -anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 863 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -anchors.cc:864:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 864 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const std::string&, const std::string&, size_t) const': -anchors.cc:1100:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1100 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -anchors.cc:1101:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1101 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from ../../src/fsa/model.h:32: -../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': -../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] - 241 | int yprev = -1; // the previous y-coordinate - | ^~~~~ -In file included from /usr/include/c++/13/vector:72, - from ../../src/seq/sequence.h:16, - from ../../src/seq/alignment.h:16, - from anchors.cc:15: -/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = fsa::Anchor; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 315 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = fsa::Anchor; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 751 | vector<_Tp, _Alloc>:: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fsa::Anchor&}; _Tp = fsa::Anchor; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc +In file included from /usr/include/c++/13/vector:66: +/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]': +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'static fsa::Anchors fsa::Anchors::convert_constraints_to_anchors(const fsa::Constraints&, const fsa::Sequence&, const fsa::Sequence&, bool)' at anchors.cc:164:19: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'static fsa::Anchors fsa::Anchors::convert_constraints_to_anchors(const fsa::Constraints&, const fsa::Sequence&, const fsa::Sequence&, bool)' at anchors.cc:165:19: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const' at anchors.cc:762:17: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const' at anchors.cc:763:17: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const' at anchors.cc:764:17: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'void fsa::Anchors::enforce_immutable_unique()' at anchors.cc:425:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'void fsa::Anchors::enforce_immutable_unique()' at anchors.cc:443:15: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::enforce_immutable_unique()' at anchors.cc:450:20: +/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'void fsa::Anchors::remove_overlaps(size_t, unsigned int)' at anchors.cc:668:20: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::remove_overlaps(size_t, unsigned int)' at anchors.cc:672:20: +/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o model.o model.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from /usr/include/c++/13/vector:72, - from ../../src/util/misc.h:17, - from ../../src/math/mst.h:11, - from fsa.cc:9: -/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 315 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from nucleotide_indel2dp.h:28, from nucleotide_indel2dp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': @@ -1395,168 +1459,35 @@ nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2029 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -In file included from nucleotidedp.h:28, - from nucleotidedp.cc:24: -algebras.h: In function 'BFloat double2bfloat(double)': -algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', + inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, + inlined from 'fsa::Anchors fsa::Mummer_adapter::get_candidate_anchors(size_t) const' at anchors.cc:994:18: +/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1292 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from ../../src/fsa/nucleotidedp.h:28, + from ../../src/fsa/model.h:25, + from model.cc:8: +../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': +../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ -algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': -algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ -algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': -algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ -algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': -algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ -algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': -algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] +../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ -nucleotidedp.cc: In function 'Algebra Forward(NucleotideAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -nucleotidedp.cc:789:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 789 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotidedp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 791 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 768 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -nucleotidedp.cc: In function 'Algebra BackwardBaumWelch(NucleotideAlignBaumWelch&, NucleotideAlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -nucleotidedp.cc:945:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 945 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotidedp.cc:947:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 947 | register bfloat iTempProb[3]; - | ^~~~~~~~~ -nucleotidedp.cc: In function 'Algebra Backward(NucleotideAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -nucleotidedp.cc:1187:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1187 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotidedp.cc:1189:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1189 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1166 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -nucleotidedp.cc: In function 'Algebra ForwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -nucleotidedp.cc:1374:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1374 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotidedp.cc:1376:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1376 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1352 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -nucleotidedp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideAlignWithBandingBaumWelch&, NucleotideAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -nucleotidedp.cc:1567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1567 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotidedp.cc:1569:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1569 | register bfloat iTempProb[3]; - | ^~~~~~~~~ -nucleotidedp.cc: In function 'Algebra BackwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -nucleotidedp.cc:1841:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1841 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotidedp.cc:1843:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1843 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1819 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const fsa::Anchor&}; _Tp = fsa::Anchor; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -/usr/include/c++/13/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]': -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'static fsa::Anchors fsa::Anchors::convert_constraints_to_anchors(const fsa::Constraints&, const fsa::Sequence&, const fsa::Sequence&, bool)' at anchors.cc:164:19: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'static fsa::Anchors fsa::Anchors::convert_constraints_to_anchors(const fsa::Constraints&, const fsa::Sequence&, const fsa::Sequence&, bool)' at anchors.cc:165:19: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const' at anchors.cc:762:17: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const' at anchors.cc:763:17: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'fsa::Anchors fsa::Cabbage_adapter::get_candidate_anchors() const' at anchors.cc:764:17: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'void fsa::Anchors::enforce_immutable_unique()' at anchors.cc:425:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'void fsa::Anchors::enforce_immutable_unique()' at anchors.cc:443:15: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::enforce_immutable_unique()' at anchors.cc:450:20: -/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'void fsa::Anchors::remove_overlaps(size_t, unsigned int)' at anchors.cc:668:20: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::remove_overlaps(size_t, unsigned int)' at anchors.cc:672:20: -/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]', - inlined from 'void fsa::FSA::init_subst_params(fsa::Params&, const std::vector&, unsigned int, double)' at fsa.cc:668:33: -/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]', - inlined from 'void fsa::FSA::init_subst_params(fsa::Params&, const std::vector&, unsigned int, double)' at fsa.cc:747:33: -/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = fsa::Anchor; _Alloc = std::allocator]', - inlined from 'void fsa::Anchors::store(const fsa::Anchor&)' at ../../src/fsa/anchors.h:467:27, - inlined from 'fsa::Anchors fsa::Mummer_adapter::get_candidate_anchors(size_t) const' at anchors.cc:994:18: -/usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1292 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/algorithm:61, from anchors.cc:13: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': @@ -1579,6 +1510,20 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from ../../src/util/misc.h:17, + from ../../src/math/mst.h:11, + from fsa.cc:9: +/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 315 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:315:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from ../../src/fsa/model.h:32: +../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': +../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] + 241 | int yprev = -1; // the previous y-coordinate + | ^~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = fsa::Anchor; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1622,12 +1567,6 @@ /usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/queue:64, - from sequence_pair_selector.cc:8: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_val >]': -/usr/include/c++/13/bits/stl_heap.h:135:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 135 | __push_heap(_RandomAccessIterator __first, - | ^~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = bool (*)(const fsa::Anchor&, const fsa::Anchor&)]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void fsa::Anchors::remove_overlaps(size_t)' at anchors.cc:460:13: @@ -1710,6 +1649,103 @@ /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]', + inlined from 'void fsa::FSA::init_subst_params(fsa::Params&, const std::vector&, unsigned int, double)' at fsa.cc:668:33: +/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]', + inlined from 'void fsa::FSA::init_subst_params(fsa::Params&, const std::vector&, unsigned int, double)' at fsa.cc:747:33: +/usr/include/c++/13/bits/stl_vector.h:829:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 829 | { _M_assign_aux(__first, __last, std::__iterator_category(__first)); } + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from nucleotidedp.h:28, + from nucleotidedp.cc:24: +algebras.h: In function 'BFloat double2bfloat(double)': +algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 195 | register BFloat a( 0.0, 0 ); + | ^ +algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': +algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 211 | register BFloat sf(a.f*b.f,a.e+b.e); + | ^~ +algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': +algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 218 | register double mantisse = a.f*b; + | ^~~~~~~~ +algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': +algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 231 | register double mantisse = a.f*b; + | ^~~~~~~~ +algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': +algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 238 | register BFloat sf(a.f/b.f, a.e-b.e); + | ^~ +nucleotidedp.cc: In function 'Algebra Forward(NucleotideAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +nucleotidedp.cc:789:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 789 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotidedp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 791 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 768 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ +nucleotidedp.cc: In function 'Algebra BackwardBaumWelch(NucleotideAlignBaumWelch&, NucleotideAlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +nucleotidedp.cc:945:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 945 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotidedp.cc:947:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 947 | register bfloat iTempProb[3]; + | ^~~~~~~~~ +nucleotidedp.cc: In function 'Algebra Backward(NucleotideAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +nucleotidedp.cc:1187:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1187 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotidedp.cc:1189:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1189 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1166 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ +nucleotidedp.cc: In function 'Algebra ForwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +nucleotidedp.cc:1374:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1374 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotidedp.cc:1376:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1376 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1352 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ +nucleotidedp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideAlignWithBandingBaumWelch&, NucleotideAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +nucleotidedp.cc:1567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1567 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotidedp.cc:1569:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1569 | register bfloat iTempProb[3]; + | ^~~~~~~~~ +nucleotidedp.cc: In function 'Algebra BackwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +nucleotidedp.cc:1841:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1841 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotidedp.cc:1843:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1843 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1819 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/queue:64, + from sequence_pair_selector.cc:8: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_val >]': +/usr/include/c++/13/bits/stl_heap.h:135:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 135 | __push_heap(_RandomAccessIterator __first, + | ^~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/queue:63: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': @@ -1736,6 +1772,27 @@ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ../../src/util/logfile.h:13, + from tree_weights.cc:8: +../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 187 | struct Duple_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/istream:40, + from /usr/include/c++/13/fstream:40, + from ../../src/util/logfile.h:8: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 203 | struct Map_value_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from dotplot.h:13, from dotplot.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1757,6 +1814,22 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from ../../src/seq/interval.h:13, + from ../../src/seq/sequence.h:21, + from ../../src/annealing/tree_weights.h:18, + from tree_weights.cc:9: +../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 185 | struct GFF_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from ../../src/annealing/alignment_DAG.h:56, from alignment_DAG.cc:12: @@ -1799,27 +1872,6 @@ /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from ../../src/util/logfile.h:13, - from tree_weights.cc:8: -../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 187 | struct Duple_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/istream:40, - from /usr/include/c++/13/fstream:40, - from ../../src/util/logfile.h:8: -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 203 | struct Map_value_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from dotplot.h:15: @@ -1869,22 +1921,6 @@ alignment_DAG.cc:28:174: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 28 | std::pair Column::get_accuracy_normalized (std::vector >& sparse_matrices, const Tree_weights& tree_weights, const size_t num_seqs) const { | ^~~~~ -In file included from ../../src/seq/interval.h:13, - from ../../src/seq/sequence.h:21, - from ../../src/annealing/tree_weights.h:18, - from tree_weights.cc:9: -../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 185 | struct GFF_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ rm -f libannealing.a ar cru libannealing.a alignment_DAG.o dotplot.o tree_weights.o ar: `u' modifier ignored since `D' is the default (see `U') @@ -1894,11 +1930,9 @@ make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o main.o main.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o gapcleaner.o gapcleaner.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o isect_mercator_alignment_gff.o isect_mercator_alignment_gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o map_coords.o map_coords.cc -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ @@ -1939,25 +1973,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/seq/sequence.h:21, - from ../../src/seq/alignment.h:16, - from isect_mercator_alignment_gff.cc:13: -../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, - from ../../src/annealing/alignment_DAG.h:56, - from gapcleaner.cc:11: + from ../../src/seq/alignment.h:16, + from map_coords.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/refwrap.h:39, - from /usr/include/c++/13/deque:67, - from /usr/include/c++/13/stack:62, - from ../../src/annealing/alignment_DAG.h:39: +In file included from /usr/include/c++/13/bits/stl_tree.h:65, + from /usr/include/c++/13/set:62, + from ../../src/seq/alignment.h:13: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1967,21 +1991,17 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/seq/interval.h:13, - from ../../src/seq/sequence.h:21: -../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 185 | struct GFF_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from ../../src/seq/gff.h:17, - from map_gff_coords.cc:11: +In file included from ../../src/fsa/fsa.h:65: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, - from ../../src/seq/gff.h:12: + from /usr/include/c++/13/bits/locale_classes.h:40, + from /usr/include/c++/13/bits/ios_base.h:41, + from /usr/include/c++/13/ios:44, + from /usr/include/c++/13/ostream:40, + from /usr/include/c++/13/iostream:41, + from ../../src/fsa/fsa.h:61: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1991,27 +2011,39 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from ../../src/seq/interval.h:13, + from ../../src/seq/sequence.h:21: +../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 185 | struct GFF_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from ../../src/seq/sequence.h:21, + from ../../src/seq/alignment.h:16, + from isect_mercator_alignment_gff.cc:13: ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 185 | struct GFF_less : std::binary_function { - | ^~~~~~~~~~~~~~~ +../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, - from ../../src/seq/alignment.h:16, - from map_coords.cc:11: + from ../../src/annealing/alignment_DAG.h:56, + from gapcleaner.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_tree.h:65, - from /usr/include/c++/13/set:62, - from ../../src/seq/alignment.h:13: +In file included from /usr/include/c++/13/bits/refwrap.h:39, + from /usr/include/c++/13/deque:67, + from /usr/include/c++/13/stack:62, + from ../../src/annealing/alignment_DAG.h:39: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2029,46 +2061,48 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/seq/sequence.h:21, - from ../../src/seq/alignment.h:16, - from map_gff_coords.cc:12: ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from ../../src/fsa/fsa.h:65: -../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 187 | struct Duple_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from /usr/include/c++/13/bits/locale_classes.h:40, - from /usr/include/c++/13/bits/ios_base.h:41, - from /usr/include/c++/13/ios:44, - from /usr/include/c++/13/ostream:40, - from /usr/include/c++/13/iostream:41, - from ../../src/fsa/fsa.h:61: +In file included from ../../src/seq/interval.h:13, + from ../../src/seq/sequence.h:21, + from ../../src/fsa/fsa.h:68: +../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 185 | struct GFF_less : std::binary_function { + | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 203 | struct Map_value_less : std::binary_function { - | ^~~~~~~~~~~~~~~ +../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +In file included from ../../src/annealing/dotplot.h:14, + from ../../src/fsa/anchors.h:16: +../../src/util/array2d.h:159:38: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 159 | struct xy_iterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/13/string:47: +/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from ../../src/fsa/anchors.h:17: +../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': +../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] + 241 | int yprev = -1; // the previous y-coordinate + | ^~~~~ In file included from ../../src/annealing/alignment_DAG.h:58: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ +In file included from ../../src/fsa/anchors.h:18: ../../src/annealing/alignment_DAG.h: At global scope: ../../src/annealing/alignment_DAG.h:415:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 415 | class greater_index : std::binary_function { @@ -2094,39 +2128,6 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -In file included from ../../src/seq/interval.h:13, - from ../../src/seq/sequence.h:21, - from ../../src/fsa/fsa.h:68: -../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 185 | struct GFF_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from ../../src/annealing/dotplot.h:14, - from ../../src/fsa/anchors.h:16: -../../src/util/array2d.h:159:38: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 159 | struct xy_iterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/13/string:47: -/usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o percentid.o percentid.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -In file included from ../../src/fsa/anchors.h:17: -../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': -../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] - 241 | int yprev = -1; // the previous y-coordinate - | ^~~~~ -In file included from ../../src/fsa/anchors.h:18: ../../src/annealing/alignment_DAG.h: At global scope: ../../src/annealing/alignment_DAG.h:415:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 415 | class greater_index : std::binary_function { @@ -2152,10 +2153,6 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o prot2codon.o prot2codon.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta.o slice_fasta.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': @@ -2178,6 +2175,45 @@ ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o percentid.o percentid.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o prot2codon.o prot2codon.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta.o slice_fasta.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +In file included from ../../src/seq/gff.h:17, + from map_gff_coords.cc:11: +../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 187 | struct Duple_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from ../../src/seq/gff.h:12: +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 203 | struct Map_value_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 185 | struct GFF_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +In file included from ../../src/seq/sequence.h:21, + from ../../src/seq/alignment.h:16, + from map_gff_coords.cc:12: +../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from percentid.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2208,8 +2244,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/seq/sequence.h:19, from prot2codon.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2270,8 +2304,13 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a In file included from ../../src/seq/gff.h:17, from slice_fasta_gff.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2294,8 +2333,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/seq/sequence.h:21, from slice_fasta_gff.cc:12: ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2304,8 +2341,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a -g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a In file included from ../../src/seq/sequence.h:19, from ../../src/seq/alignment.h:16, from slice_mercator_alignment.cc:12: @@ -2328,7 +2363,7 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o isect_mercator_alignment_gff isect_mercator_alignment_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a +g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2337,6 +2372,12 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from translate.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2353,12 +2394,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -2373,14 +2408,15 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o isect_mercator_alignment_gff isect_mercator_alignment_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_coords map_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_gff_coords map_gff_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o percentid percentid.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o prot2codon prot2codon.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta slice_fasta.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a -g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o translate translate.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta_gff slice_fasta_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_mercator_alignment slice_mercator_alignment.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a +g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o translate translate.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' Making all in perl make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' @@ -2412,7 +2448,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fsa/ - make -j5 install DESTDIR=/build/reproducible-path/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/reproducible-path/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' Making install in src/util make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' @@ -2518,17 +2554,17 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/fsa/usr/bin/map_gff_coords contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_fasta_gff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fsa/usr/bin/percentid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fsa/usr/bin/prot2codon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fsa/usr/bin/fsa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fsa/usr/bin/isect_mercator_alignment_gff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/fsa-translate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fsa/usr/bin/map_coords contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_mercator_alignment contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fsa/usr/bin/fsa-translate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin -dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/percentid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/prot2codon contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/fsa/usr/bin/gapcleaner contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/fsa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/slice_fasta_gff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/fsa/usr/bin/map_gff_coords contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums @@ -2543,12 +2579,14 @@ 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/13961/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13961/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/22623 and its subdirectories -I: Current time: Sun May 19 10:14:18 -12 2024 -I: pbuilder-time-stamp: 1716156858 +I: removing directory /srv/workspace/pbuilder/13961 and its subdirectories +I: Current time: Mon May 20 12:22:39 +14 2024 +I: pbuilder-time-stamp: 1716157359