Diff of the two buildlogs: -- --- b1/build.log 2024-04-03 14:50:35.970118388 +0000 +++ b2/build.log 2024-04-03 14:53:27.246775731 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 6 09:12:01 -12 2025 -I: pbuilder-time-stamp: 1746565921 +I: Current time: Thu Apr 4 04:50:38 +14 2024 +I: pbuilder-time-stamp: 1712155838 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,54 +32,86 @@ 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/29660/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13230/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 3 14:50 /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/13230/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13230/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="i686-pc-linux-gnu") + 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=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='94b7cc31ec6447ac884add3d7dd093be' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='29660' - PS1='# ' - PS2='> ' + INVOCATION_ID=c6e6fd380344499ea89a0af022fd0530 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=13230 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.ni6buZfe/pbuilderrc_LruP --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.ni6buZfe/b1 --logfile b1/build.log fsa_1.15.9+dfsg-6.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.ni6buZfe/pbuilderrc_nfxy --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.ni6buZfe/b2 --logfile b2/build.log fsa_1.15.9+dfsg-6.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 5 17:48 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/29660/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 1 11:25 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/13230/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -160,7 +192,7 @@ Get: 37 http://deb.debian.org/debian trixie/main i386 exonerate i386 2.4.0-5 [1749 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 mummer i386 3.23+dfsg-8 [669 kB] -Fetched 24.4 MB in 0s (91.4 MB/s) +Fetched 24.4 MB in 1s (33.0 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 ... 19876 files and directories currently installed.) @@ -333,7 +365,11 @@ 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/13230/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/13230/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 @@ -388,8 +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 @@ -493,7 +529,7 @@ Email with questions and bug reports. dh_auto_build - make -j22 + make -j10 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' @@ -540,14 +576,18 @@ /usr/include/c++/13/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++/13/string:49, - from ../../src/util/sstring.h:5: + 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 | ^~~~~~~~~~~~~~~ @@ -557,18 +597,13 @@ /usr/include/c++/13/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 sstring.cc:5: ../../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: + from ../../src/util/sstring.h:5: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -579,7 +614,8 @@ 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/util/sstring.h:14, - from sstring.cc:5: + 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 { | ^~~~~~~~~~~~~~~ @@ -724,31 +760,6 @@ /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: -../../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/numeric:75, - from alignment.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: -../../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/math/mathematics.h:23, from sequence.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -766,12 +777,6 @@ /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/math/mathematics.h:23, from gff.cc:14: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -793,6 +798,23 @@ /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: +../../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/numeric:75, + from alignment.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 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 { @@ -800,19 +822,14 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -alignment.cc: In member function 'void fsa::Alignment::read_mfa(const std::string&, bool, bool)': -alignment.cc:295:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = char; _Result = bool]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] - 295 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here - 1126 | ptr_fun(_Result (*__x)(_Arg)) - | ^~~~~~~ -alignment.cc:295:31: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] - 295 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_function.h:1046:5: note: declared here - 1046 | not1(const _Predicate& __pred) - | ^~~~ +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/interval.h:13, from ../../src/seq/sequence.h:21, from sequence.cc:12: @@ -828,16 +845,22 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -alignment.cc: In member function 'void fsa::Stockholm::read_stockholm(const std::string&, bool, bool)': -alignment.cc:732:40: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = char; _Result = bool]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] - 732 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +../../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 + | ^~~~~~~~~~~~~~~ +alignment.cc: In member function 'void fsa::Alignment::read_mfa(const std::string&, bool, bool)': +alignment.cc:295:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = char; _Result = bool]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] + 295 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here 1126 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ -alignment.cc:732:26: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] - 732 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +alignment.cc:295:31: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] + 295 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:1046:5: note: declared here 1046 | not1(const _Predicate& __pred) | ^~~~ @@ -862,6 +885,19 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +alignment.cc: In member function 'void fsa::Stockholm::read_stockholm(const std::string&, bool, bool)': +alignment.cc:732:40: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = char; _Result = bool]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] + 732 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:1126:5: note: declared here + 1126 | ptr_fun(_Result (*__x)(_Arg)) + | ^~~~~~~ +alignment.cc:732:26: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] + 732 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_function.h:1046:5: note: declared here + 1046 | not1(const _Predicate& __pred) + | ^~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from ../../src/seq/similarity_matrix.h:13, @@ -904,9 +940,7 @@ | ^~~~~ 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 ); @@ -929,7 +963,9 @@ | ^~ 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 ); @@ -981,7 +1017,8 @@ 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 algebras.cc:27: +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 ); @@ -1024,30 +1061,24 @@ 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 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); - | ^~ -In file included from nucleotidedp.h:28, - from nucleotidedp.cc:24: +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] + 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]; + | ^~~~~~~~~~~ +nucleotide_indel2dp.cc:977:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 977 | register bfloat iTempProb[3]; + | ^~~~~~~~~ +In file included from algebras.cc:27: 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 ); @@ -1068,6 +1099,16 @@ 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 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]; + | ^~~~~~~~~ +nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1256 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ 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]; @@ -1075,6 +1116,13 @@ aminoaciddp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 823 | register bfloat iTempProb[1]; | ^~~~~~~~~ +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]; + | ^~~~~~~~~ aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ @@ -1085,19 +1133,15 @@ 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 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]; - | ^~~~~~~~~ -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]; +nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 1472 | 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]; | ^~~~~~~~~~~ -nucleotidedp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 791 | register bfloat iTempProb[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: 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] @@ -1109,25 +1153,12 @@ aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1230 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -nucleotide_indel2dp.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]; - | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:977:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 977 | register bfloat iTempProb[3]; - | ^~~~~~~~~ -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]; +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]; | ^~~~~~~~~~~ -nucleotidedp.cc:947:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 947 | register bfloat iTempProb[3]; +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 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] @@ -1136,6 +1167,9 @@ aminoaciddp.cc:1504:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1504 | 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:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1448 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ @@ -1146,33 +1180,6 @@ aminoaciddp.cc:1729:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1729 | 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]; - | ^~~~~~~~~ -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]; - | ^~~~~~~~~ -nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1166 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ -nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1256 | 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]; - | ^~~~~~~~~ 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]; @@ -1180,62 +1187,61 @@ aminoaciddp.cc:2035:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2035 | register bfloat iTempProb[1]; | ^~~~~~~~~ -nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1352 | 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]; - | ^~~~~~~~~ aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1979 | 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]; - | ^~~~~~~~~ -nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1472 | 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]; - | ^~~~~~~~~ -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]; +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:1843:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1843 | register bfloat iTempProb[1]; +nucleotidedp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 791 | register bfloat iTempProb[1]; | ^~~~~~~~~ -nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 1819 | int iPrevSlowCoord; +nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ -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]; +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]; | ^~~~~~~~~~~ -nucleotide_indel2dp.cc:2053:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2053 | register bfloat iTempProb[1]; +nucleotidedp.cc:947:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 947 | register bfloat iTempProb[3]; | ^~~~~~~~~ -nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 2029 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ 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 ); | ^ +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]; + | ^~~~~~~~~ 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); @@ -1252,6 +1258,36 @@ 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: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; + | ^~~~~~~~~~~~~~ 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]; @@ -1296,6 +1332,16 @@ aminoacid_indel2dp.cc:1879:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1879 | register bfloat iTempProb[3]; | ^~~~~~~~~ +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]; + | ^~~~~~~~~~~ +aminoacid_indel2dp.cc:2245:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 2245 | register bfloat iTempProb[1]; + | ^~~~~~~~~ +aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] + 2189 | int iPrevSlowCoord; + | ^~~~~~~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from model.cc:8: @@ -1319,29 +1365,14 @@ ../../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); | ^~ -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]; - | ^~~~~~~~~~~ -aminoacid_indel2dp.cc:2245:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 2245 | register bfloat iTempProb[1]; - | ^~~~~~~~~ -aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] - 2189 | int iPrevSlowCoord; - | ^~~~~~~~~~~~~~ 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&)': -../../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: + from anchors.cc:16: ../../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, - from anchors.cc:16: + 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&)': ../../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 @@ -1392,6 +1423,11 @@ ../../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/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 + | ^~~~~ 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 @@ -1578,7 +1614,6 @@ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta.o slice_fasta.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc In file included from /usr/include/c++/13/ext/hash_map:60, from ../../src/fsa/dptables.h:43, from ../../src/fsa/mybanding.h:25, @@ -1590,7 +1625,7 @@ 32 | #warning \ | ^~~~~~~ In file included from ../../src/seq/gff.h:17, - from slice_fasta_gff.cc:11: + 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 { | ^~~~~~~~~~~~~~~ @@ -1605,13 +1640,24 @@ /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/gff.h:17, - from map_gff_coords.cc:11: + 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 { | ^~~~~~~~~~~~~~~ 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/istream:40, + from /usr/include/c++/13/fstream:40, + from isect_mercator_alignment_gff.cc:9: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1627,19 +1673,19 @@ /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:19, - from translate.cc:11: + from ../../src/seq/alignment.h:16, + from slice_mercator_alignment.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 { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, - from ../../src/seq/sequence.h:13: + 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 slice_mercator_alignment.cc:9: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1649,34 +1695,45 @@ /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 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 { - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/string:49, - from ../../src/seq/sequence.h:13: +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/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/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: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/seq/gff.h:17, - from isect_mercator_alignment_gff.cc:12: + from slice_fasta_gff.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/istream:40, - from /usr/include/c++/13/fstream:40, - from isect_mercator_alignment_gff.cc:9: + from ../../src/seq/gff.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1703,7 +1760,7 @@ 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 { | ^~~~~~~~~~~~~~~ @@ -1724,27 +1781,19 @@ /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/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 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 { + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/string:49, + from ../../src/seq/sequence.h:13: /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 { - | ^~~~~~~~~~~~~~~ +../../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 | ^~~~~~~~~~~~~~~ @@ -1774,23 +1823,19 @@ /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 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++/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 { - | ^~~~~~~~~~~~~~~ +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 { - | ^~~~~~~~~~~~~~~ +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 | ^~~~~~~~~~~~~~~ @@ -1814,24 +1859,6 @@ /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: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/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 { @@ -1858,33 +1885,17 @@ /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 slice_mercator_alignment.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 { - | ^~~~~~~~~~~~~~~ -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 slice_mercator_alignment.cc:9: -/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 { - | ^~~~~~~~~~~~~~~ +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++/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 { - | ^~~~~~~~~~~~~~~ +../../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 | ^~~~~~~~~~~~~~~ @@ -1907,12 +1918,6 @@ /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] @@ -1942,7 +1947,8 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc +g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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/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] @@ -1958,6 +1964,12 @@ ../../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++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 ../../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 { @@ -1983,14 +1995,7 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ -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++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 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] @@ -2017,8 +2022,9 @@ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ +g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 +g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': @@ -2041,10 +2047,40 @@ ../../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++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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/sequence.h:19, + from translate.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/sequence.h:13: +/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: +../../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 + | ^~~~~~~~~~~~~~~ g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/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 make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' Making all in perl @@ -2077,7 +2113,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fsa/ - make -j22 install DESTDIR=/build/reproducible-path/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no + make -j10 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' @@ -2197,12 +2233,14 @@ 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/13230/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13230/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/29660 and its subdirectories -I: Current time: Tue May 6 09:13:35 -12 2025 -I: pbuilder-time-stamp: 1746566015 +I: removing directory /srv/workspace/pbuilder/13230 and its subdirectories +I: Current time: Thu Apr 4 04:53:26 +14 2024 +I: pbuilder-time-stamp: 1712156006