Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 07:57:18.821818164 +0000 +++ b2/build.log 2024-05-07 07:58:13.211503144 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 19:56:54 -12 2024 -I: pbuilder-time-stamp: 1715068614 +I: Current time: Tue Jun 10 04:20:21 +14 2025 +I: pbuilder-time-stamp: 1749478821 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4002336/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1319663/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 9 14:20 /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/1319663/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1319663/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='c6a2bb6012c44b97a22402c38cfbb3dc' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='4002336' - PS1='# ' - PS2='> ' + INVOCATION_ID=91022e97dff64afab2e1cd270e32817c + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1319663 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.qnKJGcod/pbuilderrc_XnBx --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.qnKJGcod/b1 --logfile b1/build.log proda_1.0-14.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.qnKJGcod/pbuilderrc_dg2o --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.qnKJGcod/b2 --logfile b2/build.log proda_1.0-14.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 7 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4002336/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 9 14:06 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1319663/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -144,7 +176,7 @@ Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] -Fetched 18.7 MB in 0s (128 MB/s) +Fetched 18.7 MB in 0s (84.2 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 ... 19744 files and directories currently installed.) @@ -279,7 +311,11 @@ 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/1319663/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1319663/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 @@ -316,8 +352,7 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc In file included from Matrix.h:12, - from LocalAlign.h:12, - from LocalAlign.cc:5: + from Matrix.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -331,7 +366,8 @@ 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, - from Matrix.cc:7: + from GlobalAlign.h:11, + from GlobalAlign.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -345,8 +381,8 @@ 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:12, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: + from LocalAlign.h:12, + from LocalAlign.cc:5: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -359,10 +395,52 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc 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; + | ^~~~~ +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 ScoreMatrix.h:12, + from Matrix.h:13, + from SparseMatrix.h:12, + from Consistency.h:10, + from Consistency.cc:5: +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 { + | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -375,11 +453,10 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc 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; | ^~~~~ @@ -392,22 +469,52 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ -In file included from MultiSequence.h:12, - from MultiSequence.cc:10: +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 { + | ^~~~~ +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 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; | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc 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] @@ -451,26 +558,9 @@ 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; - | ^~~~~ MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) 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 { - | ^~~~~ 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; | ^~~~~ @@ -480,15 +570,6 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() 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 { - | ^~~~~ MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 86 | const int MultiSequence::GetNumSequences() const { | ^~~~~ @@ -501,14 +582,32 @@ 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: +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; | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc +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; + | ^~~~~ +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 { | ^~~~~ @@ -535,23 +634,41 @@ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () 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; - | ^~~~~ 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 { | ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 52 | const int GetID () 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 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 { | ^~~~~ @@ -567,31 +684,9 @@ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { - | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() 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 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] @@ -618,18 +713,11 @@ 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 GlobalAlign.h:12: +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; + | ^~~~~ MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ @@ -642,27 +730,16 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() 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 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 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; + | ^~~~~ +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 { | ^~~~~ @@ -681,6 +758,11 @@ 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; + | ^~~~~ +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; | ^~~~~ @@ -693,53 +775,17 @@ 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 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; - | ^~~~~ -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; - | ^~~~~ -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 { +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; | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 48 | const int GetNumSequences() const; | ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 116 | const int GetNumCols() 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, - from SparseMatrix.h:12, - from Consistency.h:10, - from Consistency.cc:5: + from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ @@ -749,6 +795,10 @@ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() 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; + | ^~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ @@ -764,18 +814,6 @@ 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; - | ^~~~~ In file included from ScoreMatrix.h:12, from ScoreMatrix.cc:7: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -818,6 +856,21 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() 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; + | ^~~~~ 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; @@ -843,8 +896,71 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.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; + | ^~~~~ +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 { + | ^~~~~ +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)]; + | ^ +Utilities.cc: In function 'int GetData(FILE*, char*&, const char*, const char*)': +Utilities.cc:55:30: warning: comparison is always true due to limited range of data type [-Wtype-limits] + 55 | while ((ch = fgetc (file)) != EOF){ + | ^ +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; + | ^~~~~ +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 { + | ^~~~~ +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; + | ^~~~~ 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); @@ -852,38 +968,24 @@ Main.cc:214:9: note: 'fasta' was declared here 214 | FILE *fasta; | ^~~~~ -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]; - | ^ +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 { + | ^~~~~ 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]; | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc -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)]; - | ^ -Utilities.cc: In function 'int GetData(FILE*, char*&, const char*, const char*)': -Utilities.cc:55:30: warning: comparison is always true due to limited range of data type [-Wtype-limits] - 55 | while ((ch = fgetc (file)) != EOF){ - | ^ -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::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; @@ -897,26 +999,64 @@ PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)' 201 | int *s2 = new int[xLen]; | ^ -In file included from Sequence.cc:8: +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]; + | ^ +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; | ^~~~~ -Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 121 | const int Sequence::GetLength () 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 { | ^~~~~ -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 { | ^~~~~ -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]; - | ^ 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; @@ -930,6 +1070,20 @@ 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::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]; + | ^ +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]; + | ^ 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; @@ -943,21 +1097,6 @@ MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' 513 | const char **data = new pchar[numSequences]; | ^ -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 Sequence.h:11: In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: @@ -1035,116 +1174,6 @@ Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)' 331 | int *used = new int[asize]; | ^ -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 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; - | ^~~~~ -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 { - | ^~~~~ -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 { - | ^~~~~ -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&, int, Matrix*, float)': -Block.cc:426:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 426 | delete used; - | ^~~~ -Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)' - 387 | int *used = new int[asize]; - | ^ ProbModel.cc: In member function 'AlignedFragment* ProbModel::Viterbi(const Sequence&, const Sequence&, int*)': ProbModel.cc:866:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 866 | delete s2; @@ -1152,6 +1181,13 @@ ProbModel.cc:843:34: note: returned from 'void* operator new [](std::size_t)' 843 | int *s2 = new int[besty - c + 1]; | ^ +Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, int, Matrix*, float)': +Block.cc:426:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 426 | delete used; + | ^~~~ +Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)' + 387 | int *used = new int[asize]; + | ^ ProbModel.cc: In member function 'void ProbModel::ViterbiUpdate(ScoreMatrix*, Matrix*, const Sequence&, const Sequence&, int*, AlignedFragment*, int)': ProbModel.cc:1239:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 1239 | delete buf; @@ -1199,12 +1235,14 @@ 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/1319663/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1319663/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/4002336 and its subdirectories -I: Current time: Mon May 6 19:57:17 -12 2024 -I: pbuilder-time-stamp: 1715068637 +I: removing directory /srv/workspace/pbuilder/1319663 and its subdirectories +I: Current time: Tue Jun 10 04:21:11 +14 2025 +I: pbuilder-time-stamp: 1749478871