I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 15 16:13:11 -12 2024 I: pbuilder-time-stamp: 1734322391 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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: Copying source file I: copying [proda_1.0-14.dsc] I: copying [./proda_1.0.orig.tar.gz] I: copying [./proda_1.0-14.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 19 15:50:20 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./proda_1.0-14.dsc: no acceptable signature found dpkg-source: info: extracting proda in proda-1.0 dpkg-source: info: unpacking proda_1.0.orig.tar.gz dpkg-source: info: unpacking proda_1.0-14.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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4110/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='3346455a791b4137912520e734a60a62' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='4110' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.XAFWtDUQ/pbuilderrc_Ik3C --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.XAFWtDUQ/b1 --logfile b1/build.log proda_1.0-14.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32a 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4110/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf 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-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19680 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-compat (= 13); however: Package debhelper-compat 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} bsdextrautils{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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{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 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.1 MB of archives. After unpacking 71.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-3 [195 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-6 [1091 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-3 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-3 [1488 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Fetched 19.1 MB in 1s (35.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19680 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-3_armhf.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-6_armhf.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-12_armhf.deb ... Unpacking bsdextrautils (2.40.2-12) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../23-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-3_armhf.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:armhf (1.5.8-1) ... Setting up libicu72:armhf (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-12) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-3) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:armhf (0.0.8-1+b2) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-3) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-4) ... 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 I: Building the package I: Running cd /build/reproducible-path/proda-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../proda_1.0-14_source.changes dpkg-buildpackage: info: source package proda dpkg-buildpackage: info: source version 1.0-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/reproducible-path/proda-1.0' rm -f *.o make[1]: Leaving directory '/build/reproducible-path/proda-1.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/proda-1.0' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o AlignedFragment.o AlignedFragment.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Assert.o Assert.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Block.o Block.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Consistency.o Consistency.cc 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] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, from Consistency.h:10, from Consistency.cc:5: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from Block.cc:9: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:43: warning: variable 'end' set but not used [-Wunused-but-set-variable] 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o GlobalAlign.o GlobalAlign.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o LocalAlign.o LocalAlign.cc In file included from Matrix.h:12, from GlobalAlign.h:11, from GlobalAlign.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Sequence.h:11: In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: AlignedFragment.h:66:91: warning: 'best_id' may be used uninitialized [-Wmaybe-uninitialized] 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} | ~~~^~~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:18: note: 'best_id' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~~~ In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: AlignedFragment.h:66:24: warning: 'best_pos' may be used uninitialized [-Wmaybe-uninitialized] 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} | ~~~~~~^~~~~~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:27: note: 'best_pos' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~~~~ In member function 'Fragment& Fragment::operator=(Fragment)', inlined from 'Block::Block(std::vector&, MultiSequence*, bool, Block*)' at Block.cc:105:9: AlignedFragment.h:66:80: warning: 'best_end' may be used uninitialized [-Wmaybe-uninitialized] 66 | {begin = f.begin; length = f.length; multiply = f.multiply;end = f.end;id = f.id;return *this;} | ~~~~^~~~~~~ Block.cc: In constructor 'Block::Block(std::vector&, MultiSequence*, bool, Block*)': Block.cc:58:56: note: 'best_end' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~~~~ Block.cc:130:21: warning: 'bfrag' may be used uninitialized [-Wmaybe-uninitialized] 130 | bad[bfrag]=bk; | ^~~~~ Block.cc:58:47: note: 'bfrag' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~~~~ Block.cc:130:27: warning: 'bk' may be used uninitialized [-Wmaybe-uninitialized] 130 | bad[bfrag]=bk; | ~~~~~~~~~~^~~ Block.cc:58:53: note: 'bk' was declared here 58 | int best,best_id, best_pos, multi,end,bfrag,bk,best_end; | ^~ Block.cc:263:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 263 | delete frs; | ^~~ Block.cc:228:42: note: returned from 'void* operator new [](std::size_t)' 228 | frs = new Fragment[t_frags.size()]; | ^ Block.cc:264:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 264 | delete used; | ^~~~ Block.cc:59:42: note: returned from 'void* operator new [](std::size_t)' 59 | int *used = new int[afrags.size()]; //indicators of used fragmentsem | ^ Block.cc:265:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 265 | delete bad; | ^~~ Block.cc:60:41: note: returned from 'void* operator new [](std::size_t)' 60 | int *bad = new int[afrags.size()];//fragments that cannot be a seed | ^ In file included from 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] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, Matrix*, float)': Block.cc:369:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 369 | delete used; | ^~~~ Block.cc:331:34: note: returned from 'void* operator new [](std::size_t)' 331 | int *used = new int[asize]; | ^ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from GlobalAlign.h:12: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ Block.cc: In member function 'int Block::AdjustAFragmentList(AVECT&, int, Matrix*, float)': Block.cc:426:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 426 | delete used; | ^~~~ Block.cc:387:34: note: returned from 'void* operator new [](std::size_t)' 387 | int *used = new int[asize]; | ^ LocalAlign.cc: In static member function 'static AlignedFragment* LocalAlign::ComputeLocalAlignment(const Sequence&, const Sequence&, const Matrix&, float*)': LocalAlign.cc:68:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 68 | delete nullX; | ^~~~~ LocalAlign.cc:22:38: note: returned from 'void* operator new [](std::size_t)' 22 | float *nullX = new float[rows]; | ^ LocalAlign.cc:69:17: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 69 | delete nullY; | ^~~~~ LocalAlign.cc:23:38: note: returned from 'void* operator new [](std::size_t)' 23 | float *nullY = new float[cols]; | ^ LocalAlign.cc:73:25: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 73 | delete traceback; | ^~~~~~~~~ LocalAlign.cc:19:65: note: returned from 'void* operator new [](std::size_t)' 19 | TracebackType *traceback = new TracebackType[rows * cols]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Main.o Main.cc GlobalAlign.cc: In static member function 'static float GlobalAlign::ComputeAlignmentScore(const MultiSequence&, int, SparseMatrix**)': GlobalAlign.cc:226:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 226 | delete scores; | ^~~~~~ GlobalAlign.cc:191:35: note: returned from 'void* operator new [](std::size_t)' 191 | float *scores = new float[length]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o PairAligner.o PairAligner.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Matrix.o Matrix.cc In file included from Matrix.h:12, from Matrix.cc:7: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from MultiSequence.h:12, from Main.cc:12: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ In file included from PairAligner.h:10, from PairAligner.cc:9: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, from MultiSequence.h:13: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ In file included from Main.cc:18: Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 44 | const bool GetIsLeaf() const; | ^~~~~ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() const; | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from PairAligner.h:11: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': Matrix.cc:165:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 165 | int pos = 0; | ^~~ Matrix.cc:166:16: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] 166 | float *ptr; | ^~~ Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 186 | int pos = 0; | ^~~ Main.cc: In function 'void RunLocalAligner(int, char**)': Main.cc:339:57: warning: 'fasta' may be used uninitialized [-Wmaybe-uninitialized] 339 | seqs->WriteFASTA(fasta,block,result,start,end); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Main.cc:214:9: note: 'fasta' was declared here 214 | FILE *fasta; | ^~~~~ Main.cc:291:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 291 | delete used; | ^~~~ Main.cc:284:48: note: returned from 'void* operator new [](std::size_t)' 284 | int *used = new int[m]; | ^ PairAligner.cc: In member function 'void PairAligner::ConsistencyCheck(AVECT&)': PairAligner.cc:178:64: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 178 | delete l_map; | ^~~~~ PairAligner.cc:169:98: note: returned from 'void* operator new [](std::size_t)' 169 | int *l_map = new int[(xLen+1)* (yLen + 1)]; | ^ PairAligner.cc: In member function 'void PairAligner::FastPairAlign(AVECT&)': PairAligner.cc:206:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 206 | delete s1;delete s2; | ^~ PairAligner.cc:200:39: note: returned from 'void* operator new [](std::size_t)' 200 | int *s1 = new int[xLen]; | ^ PairAligner.cc:206:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 206 | delete s1;delete s2; | ^~ PairAligner.cc:201:39: note: returned from 'void* operator new [](std::size_t)' 201 | int *s2 = new int[xLen]; | ^ Main.cc: In function 'int main(int, char**)': Main.cc:111:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 111 | delete filenames; | ^~~~~~~~~ Main.cc:61:38: note: returned from 'void* operator new [](std::size_t)' 61 | string *filenames = new string[argc]; | ^ PairAligner.cc: In member function 'void PairAligner::PairAlign(AVECT&)': PairAligner.cc:281:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 281 | delete s1;delete s2; | ^~ PairAligner.cc:275:39: note: returned from 'void* operator new [](std::size_t)' 275 | int *s1 = new int[xLen]; | ^ PairAligner.cc:281:34: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 281 | delete s1;delete s2; | ^~ PairAligner.cc:276:39: note: returned from 'void* operator new [](std::size_t)' 276 | int *s2 = new int[xLen]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o MultiSequence.o MultiSequence.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ProbModel.o ProbModel.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc In file included from MultiSequence.h:12, from MultiSequence.cc:10: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from Block.h:10, from MultiSequence.h:13: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from Matrix.h:13: ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ MultiSequence.cc:86:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 86 | const int MultiSequence::GetNumSequences() const { | ^~~~~ MultiSequence.cc:94:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 94 | const int MultiSequence::GetLength() const { | ^~~~~ MultiSequence.cc:130:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 130 | const int MultiSequence::AutoDetectFileFormat (const char *filename) const { | ^~~~~ MultiSequence.cc:388:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 388 | const char MultiSequence::ComputeAnnotation (const char *data, const int size) const { | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from ProbModel.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ MultiSequence.cc: In member function 'void MultiSequence::WriteFASTA(FILE*, Block*, MultiSequence*, int, int)': MultiSequence.cc:757:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 757 | delete map; | ^~~ MultiSequence.cc:702:40: note: returned from 'void* operator new [](std::size_t)' 702 | int *map = new int[numSequences]; | ^ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ MultiSequence.cc: In member function 'void MultiSequence::FindBlock(Block&, int&, int&, int)': MultiSequence.cc:633:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 633 | delete map; | ^~~ MultiSequence.cc:534:50: note: returned from 'void* operator new [](std::size_t)' 534 | int **map = new pint[numSequences]; | ^ MultiSequence.cc:634:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 634 | delete data; | ^~~~ MultiSequence.cc:513:51: note: returned from 'void* operator new [](std::size_t)' 513 | const char **data = new pchar[numSequences]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc 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] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ In file included from Matrix.h:12, from Types.h:12, from ProbModel.h:11, from ScoreMatrix.cc:8: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc In file included from Sequence.cc:8: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 121 | const int Sequence::GetLength () const { | ^~~~~ Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 129 | const int Sequence::GetID () const { | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc In file included from ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, from SparseMatrix.cc:6: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ SparseMatrix.cc:199:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 199 | const int SparseMatrix::GetRowSize (int layer, int row) const { | ^~~~~ SparseMatrix.cc:209:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 209 | const int SparseMatrix::GetNumLayers() const { | ^~~~~ SparseMatrix.cc:217:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 217 | const int SparseMatrix::GetNumRows() const { | ^~~~~ SparseMatrix.cc:225:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 225 | const int SparseMatrix::GetNumCols() const { | ^~~~~ In file included from Matrix.h:12, from Tree.h:9, from Tree.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc ProbModel.cc: In member function 'void ProbModel::ViterbiUpdate(ScoreMatrix*, Matrix*, const Sequence&, const Sequence&, int*, AlignedFragment*, int)': ProbModel.cc:1239:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 1239 | delete buf; | ^~~ ProbModel.cc:969:42: note: returned from 'void* operator new [](std::size_t)' 969 | SCORE *buf = new SCORE[NUM_STATES]; | ^ Utilities.cc: In function 'int GetData(FILE*, char*&, const char*, const char*)': Utilities.cc:55:30: warning: comparison is always true due to limited range of data type [-Wtype-limits] 55 | while ((ch = fgetc (file)) != EOF){ | ^ In file included from ScoreMatrix.h:12, from Matrix.h:13: Sequence.h:51:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 51 | const int GetLength () const; | ^~~~~ Sequence.h:52:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 52 | const int GetID () const; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Matrix.h:100:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 100 | const int GetNumLayers() const { | ^~~~~ Matrix.h:108:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 108 | const int GetNumRows() const { | ^~~~~ Matrix.h:116:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 116 | const int GetNumCols() const { | ^~~~~ In file included from Tree.h:10: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 44 | const bool GetIsLeaf() const; | ^~~~~ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() const; | ^~~~~ Tree.cc:34:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 34 | const bool Tree::TreeNode::GetIsLeaf() const { | ^~~~~ Tree.cc:42:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 42 | const int Tree::TreeNode::GetNumSequences() const { | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -W -Wall -pedantic -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -lm AlignedFragment.o Assert.o Block.o Consistency.o GlobalAlign.o LocalAlign.o Main.o PairAligner.o Matrix.o MultiSequence.o ProbModel.o Score.o ScoreMatrix.o Sequence.o SparseMatrix.o Tree.o Utilities.o -o proda -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/proda-1.0' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/proda/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proda' in '../proda_1.0-14_armhf.deb'. dpkg-deb: building package 'proda-dbgsym' in '../proda-dbgsym_1.0-14_armhf.deb'. dpkg-genbuildinfo --build=binary -O../proda_1.0-14_armhf.buildinfo dpkg-genchanges --build=binary -O../proda_1.0-14_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/4110 and its subdirectories I: Current time: Sun Dec 15 16:15:17 -12 2024 I: pbuilder-time-stamp: 1734322517