Diff of the two buildlogs: -- --- b1/build.log 2020-04-20 07:49:47.275413827 +0000 +++ b2/build.log 2020-04-20 07:50:09.730971654 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 19 19:45:57 -12 2020 -I: pbuilder-time-stamp: 1587368757 +I: Current time: Mon May 24 04:12:46 +14 2021 +I: pbuilder-time-stamp: 1621779166 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 18 05:09:36 2018 -12 +gpgv: Signature made Wed Sep 19 07:09:36 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -35,6 +35,18 @@ dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps +I: user script /srv/workspace/pbuilder/57485/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/57485/tmp/hooks/D01_modify_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -103,7 +115,7 @@ Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] -Fetched 19.4 MB in 4s (4318 kB/s) +Fetched 19.4 MB in 0s (86.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19231 files and directories currently installed.) @@ -258,7 +270,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/proda-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/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 dpkg-buildpackage: info: source package proda dpkg-buildpackage: info: source version 1.0-12 dpkg-buildpackage: info: source distribution unstable @@ -268,7 +280,7 @@ fakeroot debian/rules clean dh clean dh_auto_clean - make -j10 clean + make -j18 clean make[1]: Entering directory '/build/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/proda-1.0' @@ -279,7 +291,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j10 "INSTALL=install --strip-program=true" + make -j18 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/proda-1.0' g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o AlignedFragment.o AlignedFragment.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Assert.o Assert.cc @@ -292,9 +304,14 @@ g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Matrix.o Matrix.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o MultiSequence.o MultiSequence.cc g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ProbModel.o ProbModel.cc +g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc +g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc +g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc +g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc +g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc +g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc In file included from Matrix.h:12, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: + from Matrix.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetRowSize (int layer, int row) const; ^~~~~ @@ -323,7 +340,23 @@ 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] + const int GetRowSize (int layer, int row) const; + ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const; + ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const; + ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 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] const int GetRowSize (int layer, int row) const; ^~~~~ @@ -368,19 +401,49 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const; ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: +In file included from Sequence.cc:8: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength () 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] const int GetLength () const; ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetID () const; ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetID () const; + ^~~~~ +Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int Sequence::GetLength () const { + ^~~~~ +Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int Sequence::GetID () const { + ^~~~~ +In file included from Matrix.h:12, + from Types.h:12, + from ProbModel.h:11, + from PairAligner.h:11, + from PairAligner.cc:9: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetRowSize (int layer, int row) const; + ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const; + ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const; + ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumCols() const; + ^~~~~ In file included from Matrix.h:13, - from GlobalAlign.h:11, - from GlobalAlign.cc:7: + from Types.h:12, + from ProbModel.h:11, + from PairAligner.h:11, + from PairAligner.cc:9: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -390,8 +453,10 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from GlobalAlign.h:11, - from GlobalAlign.cc:7: +In file included from Types.h:12, + from ProbModel.h:11, + from PairAligner.h:11, + from PairAligner.cc:9: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -403,9 +468,7 @@ ^~~~~ 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.cc:7: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetLength () const; ^~~~~ @@ -413,9 +476,7 @@ const int GetID () const; ^~~~~ In file included from Matrix.h:13, - from SparseMatrix.h:12, - from Consistency.h:10, - from Consistency.cc:5: + from Matrix.cc:7: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -425,9 +486,7 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from SparseMatrix.h:12, - from Consistency.h:10, - from Consistency.cc:5: +In file included from Matrix.cc:7: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -437,21 +496,26 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ +Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': +Matrix.cc:165:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] + int pos = 0; + ^~~ +Matrix.cc:166:9: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] + float *ptr; + ^~~ +Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': +Matrix.cc:186:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] + int pos = 0; + ^~~ In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: + from ScoreMatrix.cc:7: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetLength () const; ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetID () const; ^~~~~ -In file included from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: +In file included from ScoreMatrix.cc:7: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -461,8 +525,10 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from Consistency.h:10, - from Consistency.cc:5: +In file included from Matrix.h:12, + from Types.h:12, + from ProbModel.h:11, + from ScoreMatrix.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetRowSize (int layer, int row) const; ^~~~~ @@ -476,8 +542,8 @@ const int GetNumCols() const; ^~~~~ In file included from Types.h:12, - from Block.h:10, - from Block.cc:6: + from ProbModel.h:11, + from ScoreMatrix.cc:8: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -487,36 +553,11 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 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] - const int AutoDetectFileFormat (const char *filename) const; - ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const char ComputeAnnotation (const char *data, const int size) const; - ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumSequences() const; - ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetLength() const; - ^~~~~ -In file included from GlobalAlign.h:12, - from GlobalAlign.cc:7: -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int AutoDetectFileFormat (const char *filename) const; - ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const char ComputeAnnotation (const char *data, const int size) const; - ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumSequences() const; - ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetLength() const; - ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, - from Matrix.cc:7: + from Types.h:12, + from ProbModel.h:11, + from ProbModel.cc:8: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetLength () const; ^~~~~ @@ -524,7 +565,9 @@ const int GetID () const; ^~~~~ In file included from Matrix.h:13, - from Matrix.cc:7: + from Types.h:12, + from ProbModel.h:11, + from ProbModel.cc:8: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -534,7 +577,9 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from Matrix.cc:7: +In file included from Types.h:12, + from ProbModel.h:11, + from ProbModel.cc:8: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -544,29 +589,6 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': -Matrix.cc:165:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] - int pos = 0; - ^~~ -Matrix.cc:166:9: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] - float *ptr; - ^~~ -Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': -Matrix.cc:186:6: warning: variable 'pos' set but not used [-Wunused-but-set-variable] - int pos = 0; - ^~~ -Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': -Block.cc:58:36: warning: variable 'end' set but not used [-Wunused-but-set-variable] - int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - ^~~ -In file included from MultiSequence.h:12, - from Main.cc:12: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetLength () const; - ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetID () const; - ^~~~~ In file included from MultiSequence.h:12, from MultiSequence.cc:10: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -575,55 +597,19 @@ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 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] - const int GetLength () const; - ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetID () const; - ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from ProbModel.h:11, - from ProbModel.cc:8: +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] const int GetLength () const; ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetID () const; ^~~~~ -In file included from Matrix.h:13, - from Types.h:12, - from ProbModel.h:11, - from ProbModel.cc:8: -ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const { - ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const { - ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const { - ^~~~~ -In file included from Types.h:12, - from ProbModel.h:11, - from ProbModel.cc:8: -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const { - ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const { - ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const { - ^~~~~ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, from MultiSequence.h:13, - from Main.cc:12: + from MultiSequence.cc:10: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetRowSize (int layer, int row) const; ^~~~~ @@ -640,7 +626,7 @@ from Types.h:12, from Block.h:10, from MultiSequence.h:13, - from Main.cc:12: + from MultiSequence.cc:10: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -653,7 +639,7 @@ In file included from Types.h:12, from Block.h:10, from MultiSequence.h:13, - from Main.cc:12: + from MultiSequence.cc:10: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -665,8 +651,9 @@ ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, - from LocalAlign.h:12, - from LocalAlign.cc:5: + 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] const int GetLength () const; ^~~~~ @@ -674,8 +661,9 @@ const int GetID () const; ^~~~~ In file included from Matrix.h:13, - from LocalAlign.h:12, - from LocalAlign.cc:5: + from SparseMatrix.h:12, + from Consistency.h:10, + from Consistency.cc:5: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -685,8 +673,9 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from LocalAlign.h:12, - from LocalAlign.cc:5: +In file included from SparseMatrix.h:12, + from Consistency.h:10, + from Consistency.cc:5: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -696,7 +685,31 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from Main.cc:12: +In file included from Consistency.h:10, + from Consistency.cc:5: +SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetRowSize (int layer, int row) const; + ^~~~~ +SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const; + ^~~~~ +SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const; + ^~~~~ +SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumCols() const; + ^~~~~ +In file included from ScoreMatrix.h:12, + from Matrix.h:13, + from LocalAlign.h:12, + from LocalAlign.cc:5: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength () const; + ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetID () const; + ^~~~~ +In file included from MultiSequence.cc:10: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int AutoDetectFileFormat (const char *filename) const; ^~~~~ @@ -709,35 +722,31 @@ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetLength() const; ^~~~~ -In file included from Main.cc:18: -Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const bool GetIsLeaf() const; - ^~~~~ -Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumSequences() const; - ^~~~~ -In file included from Matrix.h:12, - from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from MultiSequence.cc:10: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetRowSize (int layer, int row) const; +In file included from ScoreMatrix.h:12, + from Matrix.h:13, + from GlobalAlign.h:11, + from GlobalAlign.cc:7: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength () const; ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetID () const; ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const; +In file included from Matrix.h:13, + from LocalAlign.h:12, + from LocalAlign.cc:5: +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const { ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const; +ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const { + ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumCols() const { ^~~~~ In file included from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from MultiSequence.cc:10: + from GlobalAlign.h:11, + from GlobalAlign.cc:7: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -747,10 +756,8 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from Types.h:12, - from Block.h:10, - from MultiSequence.h:13, - from MultiSequence.cc:10: +In file included from LocalAlign.h:12, + from LocalAlign.cc:5: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -760,18 +767,16 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from MultiSequence.cc:10: -MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int AutoDetectFileFormat (const char *filename) const; - ^~~~~ -MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const char ComputeAnnotation (const char *data, const int size) const; +In file included from GlobalAlign.h:11, + from GlobalAlign.cc:7: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const { ^~~~~ -MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumSequences() const; +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const { ^~~~~ -MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetLength() const; +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumCols() const { ^~~~~ MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int MultiSequence::GetNumSequences() const { @@ -782,31 +787,52 @@ MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int MultiSequence::AutoDetectFileFormat (const char *filename) const { ^~~~~ -MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { - ^~~~~ -In file included from Matrix.h:12, - from Types.h:12, - from ProbModel.h:11, - from PairAligner.h:11, - from PairAligner.cc:9: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetRowSize (int layer, int row) const; +In file included from ScoreMatrix.h:12, + from Matrix.h:13, + from Tree.h:9, + from Tree.cc:6: +Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength () const; ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const; +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetID () const; ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const; +In file included from Matrix.h:13, + from Tree.h:9, + from Tree.cc:6: +ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const { ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const; +ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const { + ^~~~~ +ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumCols() const { + ^~~~~ +In file included from Tree.h:9, + from Tree.cc:6: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const { + ^~~~~ +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const { + ^~~~~ +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + 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] + const int GetLength () const; + ^~~~~ +Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetID () const; ^~~~~ In file included from Matrix.h:13, - from Types.h:12, - from ProbModel.h:11, - from PairAligner.h:11, - from PairAligner.cc:9: + from SparseMatrix.h:12, + from SparseMatrix.cc:6: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -816,10 +842,11 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from Types.h:12, - from ProbModel.h:11, - from PairAligner.h:11, - from PairAligner.cc:9: +MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { + ^~~~~ +In file included from SparseMatrix.h:12, + from SparseMatrix.cc:6: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -829,62 +856,7 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc -Main.cc: In function 'void RunLocalAligner(int, char**)': -Main.cc:339:22: warning: 'fasta' may be used uninitialized in this function [-Wmaybe-uninitialized] - seqs->WriteFASTA(fasta,block,result,start,end); - ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc -g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc -g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc -g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc -g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc -In file included from Sequence.h:11, - from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: -AlignedFragment.h: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': -AlignedFragment.h:66:66: warning: 'best_end' may be used uninitialized in this function [-Wmaybe-uninitialized] - {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} - ~~~~^~~~~~~ -Block.cc:58:49: note: 'best_end' was declared here - int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - ^~~~~~~~ -Block.cc:130:13: warning: 'bk' may be used uninitialized in this function [-Wmaybe-uninitialized] - bad[bfrag]=bk; - ~~~~~~~~~~^~~ -Block.cc:130:12: warning: 'bfrag' may be used uninitialized in this function [-Wmaybe-uninitialized] - bad[bfrag]=bk; - ^ -In file included from Sequence.h:11, - from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: -AlignedFragment.h:61:68: warning: 'best_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] - { begin = start; end = e; multiply = mul; id = sid; length = end - begin + 1;} - ~~~~^~~~~~~ -Block.cc:58:20: note: 'best_pos' was declared here - int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - ^~~~~~~~ -In file included from Sequence.h:11, - from ScoreMatrix.h:12, - from Matrix.h:13, - from Types.h:12, - from Block.h:10, - from Block.cc:6: -AlignedFragment.h:66:77: warning: 'best_id' may be used uninitialized in this function [-Wmaybe-uninitialized] - {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} - ~~~^~~~~~ -Block.cc:58:11: note: 'best_id' was declared here - int best,best_id, best_pos, multi,end,bfrag,bk,best_end; - ^~~~~~~ -In file included from Matrix.h:12, - from Tree.h:9, - from Tree.cc:6: +In file included from SparseMatrix.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetRowSize (int layer, int row) const; ^~~~~ @@ -897,28 +869,21 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const; ^~~~~ -In file included from Sequence.cc:8: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetLength () const; - ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetID () const; - ^~~~~ -Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int Sequence::GetLength () const { - ^~~~~ -Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int Sequence::GetID () const { - ^~~~~ In file included from ScoreMatrix.h:12, - from ScoreMatrix.cc:7: + from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetLength () const; ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetID () const; ^~~~~ -In file included from ScoreMatrix.cc:7: +In file included from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -928,10 +893,35 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ +In file included from Types.h:12, + from Block.h:10, + from Block.cc:6: +Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumLayers() const { + ^~~~~ +Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumRows() const { + ^~~~~ +Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumCols() const { + ^~~~~ +SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int SparseMatrix::GetRowSize (int layer, int row) const { + ^~~~~ +SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int SparseMatrix::GetNumLayers() const { + ^~~~~ +SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int SparseMatrix::GetNumRows() const { + ^~~~~ +SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int SparseMatrix::GetNumCols() const { + ^~~~~ In file included from Matrix.h:12, from Types.h:12, - from ProbModel.h:11, - from ScoreMatrix.cc:8: + from Block.h:10, + from MultiSequence.h:13, + from Main.cc:12: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetRowSize (int layer, int row) const; ^~~~~ @@ -944,31 +934,11 @@ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const; ^~~~~ -In file included from Types.h:12, - from ProbModel.h:11, - from ScoreMatrix.cc:8: -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const { - ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const { - ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const { - ^~~~~ -In file included from ScoreMatrix.h:12, - from Matrix.h:13, - from Tree.h:9, - from Tree.cc:6: -Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetLength () const; - ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetID () const; - ^~~~~ In file included from Matrix.h:13, - from Tree.h:9, - from Tree.cc:6: + from Types.h:12, + from Block.h:10, + from MultiSequence.h:13, + from Main.cc:12: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -978,8 +948,10 @@ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumCols() const { ^~~~~ -In file included from Tree.h:9, - from Tree.cc:6: +In file included from Types.h:12, + from Block.h:10, + from MultiSequence.h:13, + from Main.cc:12: Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumLayers() const { ^~~~~ @@ -989,6 +961,46 @@ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 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] + const int AutoDetectFileFormat (const char *filename) const; + ^~~~~ +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const char ComputeAnnotation (const char *data, const int size) const; + ^~~~~ +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumSequences() const; + ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength() const; + ^~~~~ +In file included from GlobalAlign.h:12, + from GlobalAlign.cc:7: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int AutoDetectFileFormat (const char *filename) const; + ^~~~~ +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const char ComputeAnnotation (const char *data, const int size) const; + ^~~~~ +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumSequences() const; + ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength() const; + ^~~~~ +In file included from Main.cc:12: +MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int AutoDetectFileFormat (const char *filename) const; + ^~~~~ +MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const char ComputeAnnotation (const char *data, const int size) const; + ^~~~~ +MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumSequences() const; + ^~~~~ +MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetLength() const; + ^~~~~ In file included from Tree.h:10, from Tree.cc:6: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] @@ -1010,70 +1022,70 @@ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int GetNumSequences() const; ^~~~~ +In file included from Main.cc:18: +Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const bool GetIsLeaf() const; + ^~~~~ +Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] + const int GetNumSequences() const; + ^~~~~ Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const bool Tree::TreeNode::GetIsLeaf() const { ^~~~~ Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int Tree::TreeNode::GetNumSequences() const { ^~~~~ -In file included from ScoreMatrix.h:12, +Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': +Block.cc:58:36: warning: variable 'end' set but not used [-Wunused-but-set-variable] + int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + ^~~ +Main.cc: In function 'void RunLocalAligner(int, char**)': +Main.cc:339:22: warning: 'fasta' may be used uninitialized in this function [-Wmaybe-uninitialized] + seqs->WriteFASTA(fasta,block,result,start,end); + ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from Sequence.h:11, + 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] - const int GetLength () const; - ^~~~~ -Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetID () const; - ^~~~~ -In file included from Matrix.h:13, - from SparseMatrix.h:12, - from SparseMatrix.cc:6: -ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const { - ^~~~~ -ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const { - ^~~~~ -ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const { - ^~~~~ -In file included from SparseMatrix.h:12, - from SparseMatrix.cc:6: -Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const { - ^~~~~ -Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const { - ^~~~~ -Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const { - ^~~~~ -In file included from SparseMatrix.cc:6: -SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetRowSize (int layer, int row) const; - ^~~~~ -SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumLayers() const; - ^~~~~ -SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumRows() const; - ^~~~~ -SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int GetNumCols() const; - ^~~~~ -SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int SparseMatrix::GetRowSize (int layer, int row) const { - ^~~~~ -SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int SparseMatrix::GetNumLayers() const { - ^~~~~ -SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int SparseMatrix::GetNumRows() const { - ^~~~~ -SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] - const int SparseMatrix::GetNumCols() const { - ^~~~~ + from Types.h:12, + from Block.h:10, + from Block.cc:6: +AlignedFragment.h: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': +AlignedFragment.h:66:66: warning: 'best_end' may be used uninitialized in this function [-Wmaybe-uninitialized] + {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} + ~~~~^~~~~~~ +Block.cc:58:49: note: 'best_end' was declared here + int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + ^~~~~~~~ +Block.cc:130:13: warning: 'bk' may be used uninitialized in this function [-Wmaybe-uninitialized] + bad[bfrag]=bk; + ~~~~~~~~~~^~~ +Block.cc:130:12: warning: 'bfrag' may be used uninitialized in this function [-Wmaybe-uninitialized] + bad[bfrag]=bk; + ^ +In file included from Sequence.h:11, + from ScoreMatrix.h:12, + from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: +AlignedFragment.h:61:68: warning: 'best_pos' may be used uninitialized in this function [-Wmaybe-uninitialized] + { begin = start; end = e; multiply = mul; id = sid; length = end - begin + 1;} + ~~~~^~~~~~~ +Block.cc:58:20: note: 'best_pos' was declared here + int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + ^~~~~~~~ +In file included from Sequence.h:11, + from ScoreMatrix.h:12, + from Matrix.h:13, + from Types.h:12, + from Block.h:10, + from Block.cc:6: +AlignedFragment.h:66:77: warning: 'best_id' may be used uninitialized in this function [-Wmaybe-uninitialized] + {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} + ~~~^~~~~~ +Block.cc:58:11: note: 'best_id' was declared here + int best,best_id, best_pos, multi,end,bfrag,bk,best_end; + ^~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/proda-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -W -Wall -pedantic -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/proda-1.0' dh_auto_test @@ -1100,20 +1112,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'proda-dbgsym' in '../proda-dbgsym_1.0-12_i386.deb'. dpkg-deb: building package 'proda' in '../proda_1.0-12_i386.deb'. +dpkg-deb: building package 'proda-dbgsym' in '../proda-dbgsym_1.0-12_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../proda_1.0-12_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/57485/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/57485/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/17446 and its subdirectories -I: Current time: Sun Apr 19 19:49:46 -12 2020 -I: pbuilder-time-stamp: 1587368986 +I: removing directory /srv/workspace/pbuilder/57485 and its subdirectories +I: Current time: Mon May 24 04:13:06 +14 2021 +I: pbuilder-time-stamp: 1621779186