I: pbuilder: network access will be disabled during build 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 I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [proda_1.0-12.dsc] I: copying [./proda_1.0.orig.tar.gz] I: copying [./proda_1.0-12.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error 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 dpkg-source: warning: failed to verify signature on ./proda_1.0-12.dsc dpkg-source: info: extracting proda in proda-1.0 dpkg-source: info: unpacking proda_1.0.orig.tar.gz dpkg-source: info: unpacking proda_1.0-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01-fix_gcc4.3_warnings.patch dpkg-source: info: applying 02-fix_CXXFLAGS.patch dpkg-source: info: applying 03-fix_FTBFS_gcc4.3_missing_includes.patch dpkg-source: info: applying 04-honour_CXX.patch dpkg-source: info: applying 05-fix_FTBFS_with_GCC6.patch 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 Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 70.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] 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 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.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... 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No schema files found: doing nothing. Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:i386 (63.1-6) ... Setting up autotools-dev (20180224.1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... 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:/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 dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_auto_clean make -j18 clean make[1]: Entering directory '/build/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/proda-1.0' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build 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 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 Block.o Block.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 Consistency.o Consistency.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 GlobalAlign.o GlobalAlign.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 LocalAlign.o LocalAlign.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 Main.o Main.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 PairAligner.o PairAligner.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 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 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; ^~~~~ 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 LocalAlign.h:12, from LocalAlign.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 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] 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; ^~~~~ 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 Types.h:12, from Block.h:10, from Block.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; ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from ProbModel.cc:8: 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 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 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 { ^~~~~ 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 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 { ^~~~~ 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 Matrix.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 Matrix.cc:7: 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 Matrix.cc:7: 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 { ^~~~~ 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 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 ScoreMatrix.cc:7: 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 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; ^~~~~ 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 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 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; ^~~~~ 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 MultiSequence.h:12, from MultiSequence.cc:10: 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 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: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; ^~~~~ 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 Types.h:12, from Block.h:10, from MultiSequence.h:13, from MultiSequence.cc:10: 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 Block.h:10, from MultiSequence.h:13, from MultiSequence.cc:10: 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 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; ^~~~~ 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 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 { ^~~~~ 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 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 { ^~~~~ 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 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; ^~~~~ 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 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; ^~~~~ 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 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 { ^~~~~ 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 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 { ^~~~~ 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 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 { ^~~~~ 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 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 { ^~~~~ 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 { ^~~~~ MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int MultiSequence::GetNumSequences() const { ^~~~~ MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int MultiSequence::GetLength() const { ^~~~~ MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] const int MultiSequence::AutoDetectFileFormat (const char *filename) 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: 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 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 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 { ^~~~~ 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 { ^~~~~ 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; ^~~~~ In file included from ScoreMatrix.h:12, 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 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 { ^~~~~ 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 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 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; ^~~~~ 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 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 { ^~~~~ 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 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 { ^~~~~ 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 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] 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.cc:6: 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 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 { ^~~~~ 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 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 create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb 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/57485 and its subdirectories I: Current time: Mon May 24 04:13:06 +14 2021 I: pbuilder-time-stamp: 1621779186