Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 03:21:33.391223796 +0000 +++ b2/build.log 2024-05-13 03:22:00.118086437 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun May 12 15:20:56 -12 2024 -I: pbuilder-time-stamp: 1715570456 +I: Current time: Sun Jun 15 23:44:36 +14 2025 +I: pbuilder-time-stamp: 1749980676 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,54 +34,86 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/6250/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/65033/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-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 Jun 15 09:44 /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/65033/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/65033/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=11 ' - DISTRIBUTION='unstable' - 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=21 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='08f3c9a5e59d42cab9fc92ad3a6fc925' - 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='6250' - PS1='# ' - PS2='> ' + INVOCATION_ID=c09243ee40b940c78b1713e4afdb3139 + 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=65033 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.HCA5NV9d/pbuilderrc_iH42 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HCA5NV9d/b1 --logfile b1/build.log proda_1.0-14.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://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.HCA5NV9d/pbuilderrc_5930 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HCA5NV9d/b2 --logfile b2/build.log proda_1.0-14.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://213.165.73.152:3128 I: uname -a - Linux ionos12-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 11 07:43 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/6250/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 13 14:06 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/65033/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -147,7 +179,7 @@ Get: 28 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] -Fetched 19.3 MB in 0s (56.5 MB/s) +Fetched 19.3 MB in 0s (91.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19684 files and directories currently installed.) @@ -282,7 +314,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/proda-1.0/ && 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 > ../proda_1.0-14_source.changes +I: user script /srv/workspace/pbuilder/65033/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/65033/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/proda-1.0/ && 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 > ../proda_1.0-14_source.changes dpkg-buildpackage: info: source package proda dpkg-buildpackage: info: source version 1.0-14 dpkg-buildpackage: info: source distribution unstable @@ -292,7 +328,7 @@ debian/rules clean dh clean dh_auto_clean - make -j11 clean + make -j21 clean make[1]: Entering directory '/build/reproducible-path/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/reproducible-path/proda-1.0' @@ -303,7 +339,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j11 "INSTALL=install --strip-program=true" + make -j21 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proda-1.0' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o AlignedFragment.o AlignedFragment.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Assert.o Assert.cc @@ -317,6 +353,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o MultiSequence.o MultiSequence.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ProbModel.o ProbModel.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc In file included from Matrix.h:12, from GlobalAlign.h:11, from GlobalAlign.cc:7: @@ -361,11 +402,17 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc +In file included from Sequence.cc:8: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ In file included from Matrix.h:12, from Types.h:12, - from ProbModel.h:11, - from ProbModel.cc:8: + from Block.h:10, + from Block.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -378,10 +425,16 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ +Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 121 | const int Sequence::GetLength () const { + | ^~~~~ +Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 129 | const int Sequence::GetID () const { + | ^~~~~ In file included from Matrix.h:12, from Types.h:12, - from Block.h:10, - from Block.cc:6: + from ProbModel.h:11, + from ProbModel.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -395,7 +448,30 @@ 62 | const int GetNumCols() const; | ^~~~~ In file included from MultiSequence.h:12, - from Main.cc:12: + from MultiSequence.cc:10: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ +In file included from Matrix.h:12, + from Tree.h:9, + from Tree.cc:6: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 57 | const int GetRowSize (int layer, int row) const; + | ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; + | ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | const int GetNumRows() const; + | ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() const; + | ^~~~~ +In file included from PairAligner.h:10, + from PairAligner.cc:9: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -403,7 +479,7 @@ 52 | const int GetID () const; | ^~~~~ In file included from ScoreMatrix.h:12, - from Matrix.h:13: + from ScoreMatrix.cc:7: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -419,6 +495,32 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ +In file included from Matrix.h:12, + from Types.h:12, + from Block.h:10, + from MultiSequence.h:13: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 57 | const int GetRowSize (int layer, int row) const; + | ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; + | ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | const int GetNumRows() const; + | ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() const; + | ^~~~~ +In file included from Matrix.h:13: +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 88 | const int GetNumLayers() const { + | ^~~~~ +ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 96 | const int GetNumRows() const { + | ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 104 | const int GetNumCols() const { + | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -428,7 +530,6 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -In file included from GlobalAlign.h:12: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ @@ -443,8 +544,8 @@ | ^~~~~ In file included from Matrix.h:12, from Types.h:12, - from Block.h:10, - from MultiSequence.h:13: + from ProbModel.h:11, + from ScoreMatrix.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -457,7 +558,35 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from Matrix.h:13: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 100 | const int GetNumLayers() const { + | ^~~~~ +MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 86 | const int MultiSequence::GetNumSequences() const { + | ^~~~~ +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 108 | const int GetNumRows() const { + | ^~~~~ +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 116 | const int GetNumCols() const { + | ^~~~~ +MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 94 | const int MultiSequence::GetLength() const { + | ^~~~~ +MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 130 | const int MultiSequence::AutoDetectFileFormat (const char *filename) const { + | ^~~~~ +MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 388 | const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { + | ^~~~~ +In file included from ScoreMatrix.h:12, + from Matrix.h:13: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -476,6 +605,7 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ +In file included from GlobalAlign.h:12: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ @@ -488,37 +618,23 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ -In file included from Main.cc:18: -Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 44 | const bool GetIsLeaf() const; - | ^~~~~ -Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 45 | const int GetNumSequences() const; - | ^~~~~ -In file included from PairAligner.h:10, - from PairAligner.cc:9: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -In file included from MultiSequence.h:12, - from MultiSequence.cc:10: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; +In file included from Matrix.h:12, + from Types.h:12, + from ProbModel.h:11, + from PairAligner.h:11: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; | ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | const int GetNumRows() const; | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() const; | ^~~~~ +In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -566,23 +682,6 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 88 | const int GetNumLayers() const { - | ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 96 | const int GetNumRows() const { - | ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 104 | const int GetNumCols() const { - | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -595,15 +694,6 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { - | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { - | ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 116 | const int GetNumCols() const { - | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -630,17 +720,19 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': -Matrix.cc:165:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] - 165 | int pos = 0; - | ^~~ -Matrix.cc:166:16: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] - 166 | float *ptr; - | ^~~ -Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': -Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] - 186 | int pos = 0; - | ^~~ +In file included from Block.cc:9: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 24 | const int AutoDetectFileFormat (const char *filename) const; + | ^~~~~ +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 28 | const char ComputeAnnotation (const char *data, const int size) const; + | ^~~~~ +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 48 | const int GetNumSequences() const; + | ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 49 | const int GetLength() const; + | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -667,10 +759,22 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ +Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': +Block.cc:58:43: warning: variable 'end' set but not used [-Wunused-but-set-variable] + 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + | ^~~ +In file included from MultiSequence.h:12, + from Main.cc:12: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; + | ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; + | ^~~~~ In file included from Matrix.h:12, from Types.h:12, - from ProbModel.h:11, - from PairAligner.h:11: + from Block.h:10, + from MultiSequence.h:13: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -702,7 +806,6 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -In file included from Block.cc:9: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ @@ -715,23 +818,21 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ -In file included from Matrix.h:12, - from Types.h:12, - from Block.h:10, - from MultiSequence.h:13: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 57 | const int GetRowSize (int layer, int row) const; - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; - | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; +In file included from Main.cc:18: +Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 44 | const bool GetIsLeaf() const; + | ^~~~~ +Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 45 | const int GetNumSequences() const; + | ^~~~~ +In file included from ScoreMatrix.h:12, + from Matrix.h:13: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; | ^~~~~ -In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -750,97 +851,33 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': -Block.cc:58:43: warning: variable 'end' set but not used [-Wunused-but-set-variable] - 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - | ^~~ -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 24 | const int AutoDetectFileFormat (const char *filename) const; - | ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 28 | const char ComputeAnnotation (const char *data, const int size) const; - | ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 48 | const int GetNumSequences() const; +In file included from ScoreMatrix.h:12, + from Matrix.h:13, + from SparseMatrix.h:12, + from SparseMatrix.cc:6: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 51 | const int GetLength () const; | ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 49 | const int GetLength() const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; | ^~~~~ -MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 86 | const int MultiSequence::GetNumSequences() const { - | ^~~~~ -MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 94 | const int MultiSequence::GetLength() const { - | ^~~~~ -MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 130 | const int MultiSequence::AutoDetectFileFormat (const char *filename) const { - | ^~~~~ -MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 388 | const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { - | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc -Main.cc: In function 'void RunLocalAligner(int, char**)': -Main.cc:339:57: warning: 'fasta' may be used uninitialized [-Wmaybe-uninitialized] - 339 | seqs->WriteFASTA(fasta,block,result,start,end); - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Main.cc:214:9: note: 'fasta' was declared here - 214 | FILE *fasta; - | ^~~~~ -Main.cc:291:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 291 | delete used; - | ^~~~ -Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)' - 284 | int *used = new int[m]; - | ^ -GlobalAlign.cc: In static member function 'static float GlobalAlign::ComputeAlignmentScore(const MultiSequence&, int, SparseMatrix**)': -GlobalAlign.cc:226:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 226 | delete scores; - | ^~~~~~ -GlobalAlign.cc:191:35: note: returned from 'void* operator new [](std::size_t)' - 191 | float *scores = new float[length]; - | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc -LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)': -LocalAlign.cc:68:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 68 | delete nullX; - | ^~~~~ -LocalAlign.cc:22:38: note: returned from 'void* operator new [](std::size_t)' - 22 | float *nullX = new float[rows]; - | ^ -LocalAlign.cc:69:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 69 | delete nullY; - | ^~~~~ -LocalAlign.cc:23:38: note: returned from 'void* operator new [](std::size_t)' - 23 | float *nullY = new float[cols]; - | ^ -LocalAlign.cc:73:25: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 73 | delete traceback; - | ^~~~~~~~~ -LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)' - 19 | TracebackType *traceback = new TracebackType[rows * cols]; - | ^ -LocalAlign.cc:121:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 121 | delete s2; - | ^~ -LocalAlign.cc:99:34: note: returned from 'void* operator new [](std::size_t)' - 99 | int *s2 = new int[besty - c + 1]; - | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc -Main.cc: In function 'int main(int, char**)': -Main.cc:111:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 111 | delete filenames; - | ^~~~~~~~~ -Main.cc:61:38: note: returned from 'void* operator new [](std::size_t)' - 61 | string *filenames = new string[argc]; - | ^ In file included from ScoreMatrix.h:12, - from ScoreMatrix.cc:7: + from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 88 | const int GetNumLayers() const { + | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ +ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 96 | const int GetNumRows() const { + | ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 104 | const int GetNumCols() const { + | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ @@ -850,22 +887,14 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc -In file included from Matrix.h:12, - from Types.h:12, - from ProbModel.h:11, - from ScoreMatrix.cc:8: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 57 | const int GetRowSize (int layer, int row) const; - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 100 | const int GetNumLayers() const { | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 108 | const int GetNumRows() const { | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() const; +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 116 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { @@ -876,42 +905,6 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)': -PairAligner.cc:178:64: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 178 | delete l_map; - | ^~~~~ -PairAligner.cc:169:98: note: returned from 'void* operator new [](std::size_t)' - 169 | int *l_map = new int[(xLen+1)* (yLen + 1)]; - | ^ -PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)': -PairAligner.cc:206:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 206 | delete s1;delete s2; - | ^~ -PairAligner.cc:200:39: note: returned from 'void* operator new [](std::size_t)' - 200 | int *s1 = new int[xLen]; - | ^ -PairAligner.cc:206:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 206 | delete s1;delete s2; - | ^~ -PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)' - 201 | int *s2 = new int[xLen]; - | ^ -PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)': -PairAligner.cc:281:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 281 | delete s1;delete s2; - | ^~ -PairAligner.cc:275:39: note: returned from 'void* operator new [](std::size_t)' - 275 | int *s1 = new int[xLen]; - | ^ -PairAligner.cc:281:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 281 | delete s1;delete s2; - | ^~ -PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)' - 276 | int *s2 = new int[xLen]; - | ^ -In file included from Matrix.h:12, - from Tree.h:9, - from Tree.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -924,30 +917,56 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -MultiSequence.cc: In member function 'void MultiSequence::WriteFASTA(FILE*, Block*, MultiSequence*, int, int)': -MultiSequence.cc:757:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 757 | delete map; +Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': +Matrix.cc:165:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] + 165 | int pos = 0; + | ^~~ +Matrix.cc:166:16: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] + 166 | float *ptr; | ^~~ -MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' - 702 | int *map = new int[numSequences]; - | ^ -In file included from Sequence.cc:8: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; +Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': +Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] + 186 | int pos = 0; + | ^~~ +SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 199 | const int SparseMatrix::GetRowSize (int layer, int row) const { + | ^~~~~ +SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 209 | const int SparseMatrix::GetNumLayers() const { + | ^~~~~ +SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 217 | const int SparseMatrix::GetNumRows() const { + | ^~~~~ +SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 225 | const int SparseMatrix::GetNumCols() const { + | ^~~~~ +In file included from Tree.h:10: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ -Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 121 | const int Sequence::GetLength () const { +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 48 | const int GetNumSequences() const; + | ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 49 | const int GetLength() const; + | ^~~~~ +Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 44 | const bool GetIsLeaf() const; + | ^~~~~ +Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 45 | const int GetNumSequences() const; + | ^~~~~ +Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 34 | const bool Tree::TreeNode::GetIsLeaf() const { | ^~~~~ -Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 129 | const int Sequence::GetID () const { +Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 42 | const int Tree::TreeNode::GetNumSequences() const { | ^~~~~ In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from SparseMatrix.h:12, - from SparseMatrix.cc:6: + from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -963,6 +982,13 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ +PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)': +PairAligner.cc:178:64: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 178 | delete l_map; + | ^~~~~ +PairAligner.cc:169:98: note: returned from 'void* operator new [](std::size_t)' + 169 | int *l_map = new int[(xLen+1)* (yLen + 1)]; + | ^ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ @@ -972,30 +998,46 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 57 | const int GetRowSize (int layer, int row) const; - | ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; - | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; - | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() const; - | ^~~~~ -SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 199 | const int SparseMatrix::GetRowSize (int layer, int row) const { - | ^~~~~ -SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 209 | const int SparseMatrix::GetNumLayers() const { - | ^~~~~ -SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 217 | const int SparseMatrix::GetNumRows() const { - | ^~~~~ -SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 225 | const int SparseMatrix::GetNumCols() const { - | ^~~~~ +GlobalAlign.cc: In static member function 'static float GlobalAlign::ComputeAlignmentScore(const MultiSequence&, int, SparseMatrix**)': +GlobalAlign.cc:226:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 226 | delete scores; + | ^~~~~~ +GlobalAlign.cc:191:35: note: returned from 'void* operator new [](std::size_t)' + 191 | float *scores = new float[length]; + | ^ +PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)': +PairAligner.cc:206:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 206 | delete s1;delete s2; + | ^~ +PairAligner.cc:200:39: note: returned from 'void* operator new [](std::size_t)' + 200 | int *s1 = new int[xLen]; + | ^ +PairAligner.cc:206:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 206 | delete s1;delete s2; + | ^~ +PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)' + 201 | int *s2 = new int[xLen]; + | ^ +MultiSequence.cc: In member function 'void MultiSequence::WriteFASTA(FILE*, Block*, MultiSequence*, int, int)': +MultiSequence.cc:757:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 757 | delete map; + | ^~~ +MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' + 702 | int *map = new int[numSequences]; + | ^ +PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)': +PairAligner.cc:281:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 281 | delete s1;delete s2; + | ^~ +PairAligner.cc:275:39: note: returned from 'void* operator new [](std::size_t)' + 275 | int *s1 = new int[xLen]; + | ^ +PairAligner.cc:281:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 281 | delete s1;delete s2; + | ^~ +PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)' + 276 | int *s2 = new int[xLen]; + | ^ MultiSequence.cc: In member function 'void MultiSequence::FindBlock(Block&, int&, int&, int)': MultiSequence.cc:633:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 633 | delete map; @@ -1009,6 +1051,51 @@ MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' 513 | const char **data = new pchar[numSequences]; | ^ +LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)': +LocalAlign.cc:68:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 68 | delete nullX; + | ^~~~~ +LocalAlign.cc:22:38: note: returned from 'void* operator new [](std::size_t)' + 22 | float *nullX = new float[rows]; + | ^ +LocalAlign.cc:69:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 69 | delete nullY; + | ^~~~~ +LocalAlign.cc:23:38: note: returned from 'void* operator new [](std::size_t)' + 23 | float *nullY = new float[cols]; + | ^ +LocalAlign.cc:73:25: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 73 | delete traceback; + | ^~~~~~~~~ +LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)' + 19 | TracebackType *traceback = new TracebackType[rows * cols]; + | ^ +LocalAlign.cc:121:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 121 | delete s2; + | ^~ +LocalAlign.cc:99:34: note: returned from 'void* operator new [](std::size_t)' + 99 | int *s2 = new int[besty - c + 1]; + | ^ +Main.cc: In function 'void RunLocalAligner(int, char**)': +Main.cc:339:57: warning: 'fasta' may be used uninitialized [-Wmaybe-uninitialized] + 339 | seqs->WriteFASTA(fasta,block,result,start,end); + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Main.cc:214:9: note: 'fasta' was declared here + 214 | FILE *fasta; + | ^~~~~ +Main.cc:291:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 291 | delete used; + | ^~~~ +Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)' + 284 | int *used = new int[m]; + | ^ +Main.cc: In function 'int main(int, char**)': +Main.cc:111:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 111 | delete filenames; + | ^~~~~~~~~ +Main.cc:61:38: note: returned from 'void* operator new [](std::size_t)' + 61 | string *filenames = new string[argc]; + | ^ In file included from Sequence.h:11: In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: @@ -1079,57 +1166,6 @@ Block.cc:60:41: note: returned from 'void* operator new [](std::size_t)' 60 | int *bad = new int[afrags.size()];//fragments that cannot be a seed | ^ -In file included from ScoreMatrix.h:12, - from Matrix.h:13: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 51 | const int GetLength () const; - | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () const; - | ^~~~~ -ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 88 | const int GetNumLayers() const { - | ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 96 | const int GetNumRows() const { - | ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 104 | const int GetNumCols() const { - | ^~~~~ -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { - | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { - | ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 116 | const int GetNumCols() const { - | ^~~~~ -In file included from Tree.h:10: -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 24 | const int AutoDetectFileFormat (const char *filename) const; - | ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 28 | const char ComputeAnnotation (const char *data, const int size) const; - | ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 48 | const int GetNumSequences() const; - | ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 49 | const int GetLength() const; - | ^~~~~ -Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 44 | const bool GetIsLeaf() const; - | ^~~~~ -Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 45 | const int GetNumSequences() const; - | ^~~~~ -Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 34 | const bool Tree::TreeNode::GetIsLeaf() const { - | ^~~~~ -Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 42 | const int Tree::TreeNode::GetNumSequences() const { - | ^~~~~ Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, Matrix*, float)': Block.cc:369:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 369 | delete used; @@ -1198,12 +1234,14 @@ 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/65033/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/65033/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/6250 and its subdirectories -I: Current time: Sun May 12 15:21:32 -12 2024 -I: pbuilder-time-stamp: 1715570492 +I: removing directory /srv/workspace/pbuilder/65033 and its subdirectories +I: Current time: Sun Jun 15 23:44:58 +14 2025 +I: pbuilder-time-stamp: 1749980698