Diff of the two buildlogs: -- --- b1/build.log 2023-04-23 01:33:56.540099946 +0000 +++ b2/build.log 2023-04-23 01:38:06.489024805 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 22 13:27:03 -12 2023 -I: pbuilder-time-stamp: 1682213223 +I: Current time: Sat May 25 21:57:10 +14 2024 +I: pbuilder-time-stamp: 1716623830 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./fsa_1.15.9+dfsg.orig.tar.xz] I: copying [./fsa_1.15.9+dfsg-6.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Nov 15 05:07:02 2020 -12 +gpgv: Signature made Mon Nov 16 07:07:02 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -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/19775/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14590/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-arm64. +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 25 21:57 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/14590/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14590/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='19775' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=14590 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.1SCIpWxH/pbuilderrc_rgls --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1SCIpWxH/b1 --logfile b1/build.log fsa_1.15.9+dfsg-6.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1SCIpWxH/pbuilderrc_6ju8 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1SCIpWxH/b2 --logfile b2/build.log --extrapackages usrmerge fsa_1.15.9+dfsg-6.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/19775/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 24 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/14590/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 bookworm/main arm64 exonerate arm64 2.4.0-5 [1439 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 help2man arm64 1.49.3 [198 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 mummer arm64 3.23+dfsg-8 [636 kB] -Fetched 22.8 MB in 1s (26.8 MB/s) +Fetched 22.8 MB in 0s (47.5 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 ... 19616 files and directories currently installed.) @@ -329,8 +361,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/14590/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/14590/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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 @@ -383,8 +424,8 @@ 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 @@ -536,14 +577,18 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/util/sstring.h:14, - from ../../src/util/dexception.h:6, - from dexception.cc:4: +In file included from ../../src/util/logfile.h:13, + from logfile.cc:1: ../../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++/12/string:48, - from ../../src/util/sstring.h:5: + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from ../../src/util/logfile.h:8: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -569,18 +614,14 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/util/logfile.h:13, - from logfile.cc:1: +In file included from ../../src/util/sstring.h:14, + from ../../src/util/dexception.h:6, + from dexception.cc:4: ../../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++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from ../../src/util/logfile.h:8: + from ../../src/util/sstring.h:5: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -672,32 +713,6 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mercator.o mercator.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence.o sequence.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc -In file included from ../../src/seq/sequence.h:19, - from ../../src/seq/alignment.h:16, - from ../../src/seq/mercator.h:13, - from mercator.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++/12/numeric:75, - from mercator.cc:9: -/usr/include/c++/12/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++/12/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++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/alphabet.h:20, from alphabet.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -714,24 +729,15 @@ /usr/include/c++/12/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++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -In file included from ../../src/math/mathematics.h:23, - from similarity_matrix.cc:11: +In file included from ../../src/seq/sequence.h:19, + from ../../src/seq/alignment.h:16, + from ../../src/seq/mercator.h:13, + from mercator.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++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from similarity_matrix.cc:8: +In file included from /usr/include/c++/12/numeric:75, + from mercator.cc:9: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -759,9 +765,7 @@ 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: + 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 { | ^~~~~~~~~~~~~~~ @@ -789,17 +793,13 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/math/mathematics.h:23, - from gff.cc:14: + 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++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from gff.cc:8: + from ../../src/util/regexp.h:8, + from sequence.cc:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -809,7 +809,9 @@ /usr/include/c++/12/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, + 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 { | ^~~~~~~~~~~~~~~ @@ -829,20 +831,9 @@ /usr/include/c++/12/bits/stl_function.h:1046:5: note: declared here 1046 | not1(const _Predicate& __pred) | ^~~~ -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++/12/string:48, - from ../../src/util/regexp.h:8, - from sequence.cc:10: -/usr/include/c++/12/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -859,9 +850,59 @@ /usr/include/c++/12/bits/stl_function.h:1046:5: note: declared here 1046 | not1(const _Predicate& __pred) | ^~~~ +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] + 187 | struct Duple_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from gff.cc:8: +/usr/include/c++/12/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++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +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++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from similarity_matrix.cc:8: +/usr/include/c++/12/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++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +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++/12/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: + 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 { | ^~~~~~~~~~~~~~~ @@ -900,9 +941,7 @@ | ^~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, - from ../../src/fsa/anchors.h:20, - from ../../src/fsa/fsa.h:71, - from manager.cc:8: + from ../../src/fsa/anchors.h:20: ../../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 ); @@ -925,7 +964,9 @@ | ^~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, - from ../../src/fsa/anchors.h:20: + from ../../src/fsa/anchors.h:20, + from ../../src/fsa/fsa.h:71, + from manager.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 ); @@ -996,8 +1037,14 @@ 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: +In file included from aminoacid_indel2dp.h:28, + from aminoacid_indel2dp.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 ); + | ^ +In file included from nucleotide_indel2dp.h:28, + from nucleotide_indel2dp.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 ); @@ -1006,6 +1053,14 @@ 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_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 '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; @@ -1014,12 +1069,20 @@ 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 '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 aminoacid_indel2dp.h:28, - from aminoacid_indel2dp.cc:24: +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 ); @@ -1040,61 +1103,13 @@ 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); | ^~ -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]; - | ^~~~~~~~~~~ -aminoaciddp.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; - | ^~~~~~~~~~~~~~ -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]; - | ^~~~~~~~~~~ -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]; - | ^~~~~~~~~ -aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1230 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -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]; - | ^~~~~~~~~~~ -aminoaciddp.cc:1504:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1504 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc -aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1448 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -aminoaciddp.cc: In function 'Algebra BackwardBaumWelchBanding(AminoAcidAlignWithBandingBaumWelch&, AminoAcidAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -aminoaciddp.cc:1727:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1727 | register double iTempResult[1]; - | ^~~~~~~~~~~ -aminoaciddp.cc:1729:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1729 | register bfloat iTempProb[3]; - | ^~~~~~~~~ -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]; +nucleotide_indel2dp.cc: In function 'Algebra Forward(NucleotideIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +nucleotide_indel2dp.cc:789:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 789 | register double iTempResult[1]; | ^~~~~~~~~~~ -aminoaciddp.cc:2035:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2035 | register bfloat iTempProb[1]; +nucleotide_indel2dp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 791 | 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: In function 'Algebra Forward(AminoAcidIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:821:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 821 | register double iTempResult[1]; @@ -1102,9 +1117,20 @@ aminoacid_indel2dp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 823 | register bfloat iTempProb[1]; | ^~~~~~~~~ +nucleotide_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 768 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc +nucleotide_indel2dp.cc: In function 'Algebra BackwardBaumWelch(NucleotideIndel2AlignBaumWelch&, NucleotideIndel2AlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +nucleotide_indel2dp.cc:975:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 975 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotide_indel2dp.cc:977:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 977 | register bfloat iTempProb[3]; + | ^~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBaumWelch(AminoAcidIndel2AlignBaumWelch&, AminoAcidIndel2AlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:1039:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1039 | register double iTempResult[1]; @@ -1112,6 +1138,13 @@ aminoacid_indel2dp.cc:1041:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1041 | register bfloat iTempProb[3]; | ^~~~~~~~~ +nucleotide_indel2dp.cc: In function 'Algebra Backward(NucleotideIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': +nucleotide_indel2dp.cc:1277:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1277 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotide_indel2dp.cc:1279:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1279 | register bfloat iTempProb[1]; + | ^~~~~~~~~ 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]; @@ -1119,9 +1152,19 @@ aminoacid_indel2dp.cc:1375:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1375 | register bfloat iTempProb[1]; | ^~~~~~~~~ +nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1256 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1320 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ +nucleotide_indel2dp.cc: In function 'Algebra ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +nucleotide_indel2dp.cc:1494:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1494 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotide_indel2dp.cc:1496:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1496 | register bfloat iTempProb[1]; + | ^~~~~~~~~ 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]; @@ -1129,9 +1172,19 @@ aminoacid_indel2dp.cc:1624:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1624 | register bfloat iTempProb[1]; | ^~~~~~~~~ +nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1472 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1568 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ +nucleotide_indel2dp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideIndel2AlignWithBandingBaumWelch&, NucleotideIndel2AlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +nucleotide_indel2dp.cc:1717:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1717 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotide_indel2dp.cc:1719:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1719 | register bfloat iTempProb[3]; + | ^~~~~~~~~ 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]; @@ -1139,6 +1192,20 @@ aminoacid_indel2dp.cc:1879:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1879 | register bfloat iTempProb[3]; | ^~~~~~~~~ +nucleotide_indel2dp.cc: In function 'Algebra BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +nucleotide_indel2dp.cc:2051:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2051 | register double iTempResult[1]; + | ^~~~~~~~~~~ +nucleotide_indel2dp.cc:2053:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2053 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +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]; + | ^~~~~~~~~~~ +aminoaciddp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 823 | register bfloat iTempProb[1]; + | ^~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:2243:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2243 | register double iTempResult[1]; @@ -1146,84 +1213,58 @@ aminoacid_indel2dp.cc:2245:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2245 | register bfloat iTempProb[1]; | ^~~~~~~~~ +nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 2029 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2189 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -In file included from nucleotide_indel2dp.h:28, - from nucleotide_indel2dp.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); - | ^~ -nucleotide_indel2dp.cc: In function 'Algebra Forward(NucleotideIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -nucleotide_indel2dp.cc:789:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 789 | register double iTempResult[1]; - | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 791 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -nucleotide_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] +aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -nucleotide_indel2dp.cc: In function 'Algebra BackwardBaumWelch(NucleotideIndel2AlignBaumWelch&, NucleotideIndel2AlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -nucleotide_indel2dp.cc:975:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 975 | register double iTempResult[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]; | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:977:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 977 | register bfloat iTempProb[3]; +aminoaciddp.cc:1011:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1011 | register bfloat iTempProb[3]; | ^~~~~~~~~ -nucleotide_indel2dp.cc: In function 'Algebra Backward(NucleotideIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': -nucleotide_indel2dp.cc:1277:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1277 | register double iTempResult[1]; +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]; | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:1279:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1279 | register bfloat iTempProb[1]; +aminoaciddp.cc:1285:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1285 | register bfloat iTempProb[1]; | ^~~~~~~~~ -nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1256 | int iPrevSlowCoord; +aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1230 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -nucleotide_indel2dp.cc: In function 'Algebra ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -nucleotide_indel2dp.cc:1494:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1494 | register double iTempResult[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]; | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:1496:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1496 | register bfloat iTempProb[1]; +aminoaciddp.cc:1504:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1504 | register bfloat iTempProb[1]; | ^~~~~~~~~ -nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1472 | int iPrevSlowCoord; +aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1448 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -nucleotide_indel2dp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideIndel2AlignWithBandingBaumWelch&, NucleotideIndel2AlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -nucleotide_indel2dp.cc:1717:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1717 | register double iTempResult[1]; +aminoaciddp.cc: In function 'Algebra BackwardBaumWelchBanding(AminoAcidAlignWithBandingBaumWelch&, AminoAcidAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': +aminoaciddp.cc:1727:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1727 | register double iTempResult[1]; | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:1719:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1719 | register bfloat iTempProb[3]; +aminoaciddp.cc:1729:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 1729 | register bfloat iTempProb[3]; | ^~~~~~~~~ -nucleotide_indel2dp.cc: In function 'Algebra BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': -nucleotide_indel2dp.cc:2051:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2051 | register double iTempResult[1]; +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]; | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:2053:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2053 | register bfloat iTempProb[1]; +aminoaciddp.cc:2035:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2035 | register bfloat iTempProb[1]; | ^~~~~~~~~ -nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 2029 | int iPrevSlowCoord; +aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1979 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, @@ -1260,6 +1301,11 @@ ../../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/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 nucleotidedp.h:28, from nucleotidedp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': @@ -1282,40 +1328,6 @@ 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); | ^~ -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]; - | ^~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: @@ -1339,16 +1351,6 @@ ../../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: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]; - | ^~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: @@ -1368,15 +1370,54 @@ ../../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; | ^~~~~~~~ -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 - | ^~~~~ ../../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]; @@ -1585,30 +1626,8 @@ /usr/include/c++/12/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -In file included from ../../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++/12/string:48, - from ../../src/seq/gff.h:12: -/usr/include/c++/12/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++/12/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++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, - from slice_fasta.cc:11: + from prot2codon.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 { | ^~~~~~~~~~~~~~~ @@ -1624,7 +1643,7 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, - from prot2codon.cc:11: + from slice_fasta.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 { | ^~~~~~~~~~~~~~~ @@ -1639,19 +1658,11 @@ /usr/include/c++/12/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] - 187 | struct Duple_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from ../../src/seq/sequence.h:13: -/usr/include/c++/12/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 { - | ^~~~~~~~~~~~~~~ +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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1663,18 +1674,25 @@ /usr/include/c++/12/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++/12/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++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/gff.h:17, - from isect_mercator_alignment_gff.cc:12: + 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++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/istream:38, - from /usr/include/c++/12/fstream:38, - from isect_mercator_alignment_gff.cc:9: + from ../../src/seq/gff.h:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1684,17 +1702,19 @@ /usr/include/c++/12/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 { - | ^~~~~~~~~~~~~~~ +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] + 187 | struct Duple_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from ../../src/seq/sequence.h:13: /usr/include/c++/12/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 { - | ^~~~~~~~~~~~~~~ +../../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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1712,7 +1732,8 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -In file included from ../../src/fsa/fsa.h:65: +In file included from ../../src/seq/gff.h:17, + from isect_mercator_alignment_gff.cc:12: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ @@ -1720,9 +1741,9 @@ from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from ../../src/fsa/fsa.h:61: + from /usr/include/c++/12/istream:38, + from /usr/include/c++/12/fstream:38, + from isect_mercator_alignment_gff.cc:9: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1738,12 +1759,6 @@ /usr/include/c++/12/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++/12/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: @@ -1762,6 +1777,20 @@ /usr/include/c++/12/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++/12/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++/12/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: @@ -1771,26 +1800,29 @@ /usr/include/c++/12/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++/12/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 { - | ^~~~~~~~~~~~~~~ +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++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from ../../src/fsa/fsa.h:61: /usr/include/c++/12/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 { - | ^~~~~~~~~~~~~~~ +../../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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1813,6 +1845,15 @@ /usr/include/c++/12/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++/12/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] @@ -1842,6 +1883,13 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc +g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc +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/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] @@ -1851,17 +1899,6 @@ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -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: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 - | ^~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc ../../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 { @@ -1887,8 +1924,13 @@ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc +g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 +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] @@ -1915,7 +1957,6 @@ /usr/include/c++/12/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': @@ -1941,8 +1982,6 @@ g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 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] @@ -1959,20 +1998,13 @@ /usr/include/c++/12/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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 ../../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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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] - 112 | struct Genomic_interval_less : std::binary_function { - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/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 slice_mercator_alignment.cc:12: @@ -1995,6 +2027,29 @@ /usr/include/c++/12/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++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +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] + 112 | struct Genomic_interval_less : std::binary_function { + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/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++/12/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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 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] @@ -2019,20 +2074,6 @@ /usr/include/c++/12/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++/12/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++/12/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 { | ^~~~~~~~~~~~~~~ @@ -2040,8 +2081,8 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 -ffile-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -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 make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main' @@ -2195,12 +2236,14 @@ 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/14590/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14590/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/19775 and its subdirectories -I: Current time: Sat Apr 22 13:33:55 -12 2023 -I: pbuilder-time-stamp: 1682213635 +I: removing directory /srv/workspace/pbuilder/14590 and its subdirectories +I: Current time: Sat May 25 22:01:05 +14 2024 +I: pbuilder-time-stamp: 1716624065