Diff of the two buildlogs: -- --- b1/build.log 2024-12-16 04:15:21.935770213 +0000 +++ b2/build.log 2024-12-16 04:16:34.796460188 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Dec 15 16:13:11 -12 2024 -I: pbuilder-time-stamp: 1734322391 +I: Current time: Mon Dec 16 18:15:32 +14 2024 +I: pbuilder-time-stamp: 1734322532 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/4110/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13962/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 Dec 16 04:15 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/13962/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13962/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='3346455a791b4137912520e734a60a62' - 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='4110' - PS1='# ' - PS2='> ' + INVOCATION_ID=82cbc80077aa4faa83f8a388b66e62bf + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=13962 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.XAFWtDUQ/pbuilderrc_Ik3C --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.XAFWtDUQ/b1 --logfile b1/build.log proda_1.0-14.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XAFWtDUQ/pbuilderrc_kpIu --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.XAFWtDUQ/b2 --logfile b2/build.log proda_1.0-14.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32a 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4110/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/13962/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -143,7 +175,7 @@ Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] -Fetched 19.1 MB in 1s (35.8 MB/s) +Fetched 19.1 MB in 0s (91.4 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 ... 19680 files and directories currently installed.) @@ -274,7 +306,11 @@ 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/13962/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/13962/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 @@ -284,7 +320,7 @@ debian/rules clean dh clean dh_auto_clean - make -j3 clean + make -j4 clean make[1]: Entering directory '/build/reproducible-path/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/reproducible-path/proda-1.0' @@ -295,12 +331,13 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "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 -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Assert.o Assert.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Block.o Block.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Consistency.o Consistency.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o GlobalAlign.o GlobalAlign.cc In file included from Matrix.h:12, from Types.h:12, from Block.h:10, @@ -343,6 +380,38 @@ 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 Matrix.h:12, + 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; + | ^~~~~ +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; + | ^~~~~ +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 ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, @@ -372,19 +441,6 @@ 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; - | ^~~~~ -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; - | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ @@ -397,27 +453,46 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | 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; - | ^~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o GlobalAlign.o GlobalAlign.cc -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o LocalAlign.o LocalAlign.cc -In file included from Matrix.h:12, - 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; +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:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 60 | const int GetNumLayers() const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 52 | const int GetID () const; | ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 61 | const int GetNumRows() const; +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 88 | const int GetNumLayers() const { | ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 62 | const int GetNumCols() 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 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; + | ^~~~~ +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; | ^~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o LocalAlign.o LocalAlign.cc 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: @@ -476,6 +551,21 @@ 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 | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Main.o Main.cc +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; + | ^~~~ +Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)' + 331 | int *used = new int[asize]; + | ^ +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 Matrix.h:12, from LocalAlign.h:12, from LocalAlign.cc:5: @@ -491,13 +581,15 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() 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; +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:331:34: note: returned from 'void* operator new [](std::size_t)' - 331 | int *used = new int[asize]; +Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)' + 387 | int *used = new int[asize]; | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o PairAligner.o PairAligner.cc +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Matrix.o Matrix.cc 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] @@ -524,52 +616,28 @@ 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; - | ^~~~~ -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: +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; | ^~~~~ -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 { +In file included from Matrix.h:12, + 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; | ^~~~~ -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 100 | const int GetNumLayers() const { +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 60 | const int GetNumLayers() const; | ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - 108 | const int GetNumRows() const { +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 61 | 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:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 62 | const int GetNumCols() 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]; - | ^ 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; @@ -589,38 +657,6 @@ LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)' 19 | TracebackType *traceback = new TracebackType[rows * cols]; | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Main.o Main.cc -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 -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o PairAligner.o PairAligner.cc -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Matrix.o Matrix.cc -In file included from Matrix.h:12, - 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; - | ^~~~~ -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 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 PairAligner.h:10, from PairAligner.cc:9: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -718,6 +754,7 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | 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 -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o MultiSequence.o MultiSequence.cc 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] @@ -755,19 +792,6 @@ Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 186 | int pos = 0; | ^~~ -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]; - | ^ 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; @@ -788,13 +812,19 @@ PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)' 201 | int *s2 = new int[xLen]; | ^ -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]; - | ^ +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]; + | ^ 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; @@ -808,9 +838,15 @@ PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)' 276 | int *s2 = new int[xLen]; | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.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 MultiSequence.h:12, from MultiSequence.cc:10: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -819,6 +855,7 @@ 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 -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc In file included from Matrix.h:12, from Types.h:12, from Block.h:10, @@ -878,7 +915,6 @@ 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 -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, @@ -895,13 +931,7 @@ 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; - | ^~~ -MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' - 702 | int *map = new int[numSequences]; - | ^ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc 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] @@ -928,20 +958,13 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ -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; +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:534:50: note: returned from 'void* operator new [](std::size_t)' - 534 | int **map = new pint[numSequences]; - | ^ -MultiSequence.cc:634:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 634 | delete data; - | ^~~~ -MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' - 513 | const char **data = new pchar[numSequences]; - | ^ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc +MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' + 702 | int *map = new int[numSequences]; + | ^ 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] @@ -984,6 +1007,19 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ +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; + | ^~~ +MultiSequence.cc:534:50: note: returned from 'void* operator new [](std::size_t)' + 534 | int **map = new pint[numSequences]; + | ^ +MultiSequence.cc:634:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 634 | delete data; + | ^~~~ +MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' + 513 | const char **data = new pchar[numSequences]; + | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc In file included from Sequence.cc:8: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -999,6 +1035,26 @@ 129 | const int Sequence::GetID () const { | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc +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 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 ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, @@ -1051,33 +1107,6 @@ SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 225 | const int SparseMatrix::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; - | ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc -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; - | ^~~ -ProbModel.cc:969:42: note: returned from 'void* operator new [](std::size_t)' - 969 | SCORE *buf = new SCORE[NUM_STATES]; - | ^ -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: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -1129,6 +1158,13 @@ Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 42 | const int Tree::TreeNode::GetNumSequences() const { | ^~~~~ +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; + | ^~~ +ProbModel.cc:969:42: note: returned from 'void* operator new [](std::size_t)' + 969 | SCORE *buf = new SCORE[NUM_STATES]; + | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -lm AlignedFragment.o Assert.o Block.o Consistency.o GlobalAlign.o LocalAlign.o Main.o PairAligner.o Matrix.o MultiSequence.o ProbModel.o Score.o ScoreMatrix.o Sequence.o SparseMatrix.o Tree.o Utilities.o -o proda -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/proda-1.0' dh_auto_test @@ -1166,12 +1202,14 @@ 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/13962/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13962/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/4110 and its subdirectories -I: Current time: Sun Dec 15 16:15:17 -12 2024 -I: pbuilder-time-stamp: 1734322517 +I: removing directory /srv/workspace/pbuilder/13962 and its subdirectories +I: Current time: Mon Dec 16 18:16:31 +14 2024 +I: pbuilder-time-stamp: 1734322591