Thu May 9 10:19:55 UTC 2024 I: starting to build proda/trixie/amd64 on jenkins on '2024-05-09 10:19' Thu May 9 10:19:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_35/10082/console.log Thu May 9 10:19:55 UTC 2024 I: Downloading source for trixie/proda=1.0-14 --2024-05-09 10:19:56-- http://deb.debian.org/debian/pool/main/p/proda/proda_1.0-14.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1981 (1.9K) [text/prs.lines.tag] Saving to: ‘proda_1.0-14.dsc’ 0K . 100% 287M=0s 2024-05-09 10:19:56 (287 MB/s) - ‘proda_1.0-14.dsc’ saved [1981/1981] Thu May 9 10:19:56 UTC 2024 I: proda_1.0-14.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: proda Binary: proda Architecture: any Version: 1.0-14 Maintainer: Debian Med Packaging Team Uploaders: David Paleino , Charles Plessy , Andreas Tille Homepage: http://proda.stanford.edu/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/proda Vcs-Git: https://salsa.debian.org/med-team/proda.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: proda deb science optional arch=any Checksums-Sha1: 44303e1639b5c52278758d23d149ef1c434593a4 38868 proda_1.0.orig.tar.gz 6cd1d4de287448c46d734f8484fd5123636c81cc 10264 proda_1.0-14.debian.tar.xz Checksums-Sha256: 439a93bf35e1a29ac1d5dde51e61f2cb174618596afaaaaa27d33a8ea1868a08 38868 proda_1.0.orig.tar.gz dace1621a1eba55e32cfb9840b1119c945e4aa9ab6e3569558d02f91db945ed6 10264 proda_1.0-14.debian.tar.xz Files: 99a0c04983d043f70e74b33ba6f38018 38868 proda_1.0.orig.tar.gz 0b87d063dbc6f0b43341198dbfca017d 10264 proda_1.0-14.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWBu7wRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHl2g/7BtJhfSDGgLYziMzuf6bVyWY+pJvqxltB 4QBZYJS/lBqaH3EtaPieFlKBhgqNmweBxRp0Tfn+SNpU3Ysj0QP4jT9urkP9d/O/ DZkzVcE1Jv0TE/2yzbDkbZU3YQ7RCTts6V0IiZBYOdUO4GwEUyVC35UhD0pfgWr9 CFElAJa2oHDBxuJssslkdt1duPvvEfXIehgjiW1sNP5fRkskRuvSq2h14n8ZYuIe zUyIifjB2VfTLqLn2M1RKTTAODSyjVGavgjtZHzI7pvbwy9tqD2KmG9fU3JZ3I+3 lZFHnDrRbwbwcjy+i8V+TGwbJToUITICKJnulwx24PeDGRYl1RBGhwtbrZIJjjwg apM48cRNUJuG+wBo1PdomaSuGBX8WcU8w5h5jOHwwQIgnqZUMLDM6AOVuXRlX/QG 0P8NK9ag+xJx/v8lxfEd9LQW+7fl3hckyF2E4GJwlRrn3WhjKCUHkfC8/HJjoCHe nOK+oOk6txEketNDOI+glHFevZi1lUdG+b70tOyWp/IrYcbK6zRv7F7eKscUEZhR UF+D+0ujQKlKVWKBN0xLA6Q3VJ9JImZsIOw/gbUgOp5nyLQfwIRzBu+nh5VZ6bcF vhh4CuCGIv3i2szOWktvoe0GlxeHGxvDwOlqGlFldAHdTLky/KTE44otahxO+/NS eRe5d08T1SY= =UIeA -----END PGP SIGNATURE----- Thu May 9 10:19:56 UTC 2024 I: Checking whether the package is not for us Thu May 9 10:19:56 UTC 2024 I: Starting 1st build on remote node infom01-amd64.debian.net. Thu May 9 10:19:56 UTC 2024 I: Preparing to do remote build '1' on infom01-amd64.debian.net. Thu May 9 10:20:55 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 8 22:19:58 -12 2024 I: pbuilder-time-stamp: 1715249998 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/2255566/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ef4befba4b8048cbb91d48034bdc1e40' 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='2255566' 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.w4peH7Tz/pbuilderrc_D22Q --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.w4peH7Tz/b1 --logfile b1/build.log proda_1.0-14.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 8 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2255566/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: amd64 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 ... 19699 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} libsub-override-perl{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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.0 MB of archives. After unpacking 73.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Fetched 19.0 MB in 0s (62.6 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 ... 19699 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../24-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... 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 (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-7) ... 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 amd64 debian/rules clean dh clean dh_auto_clean make -j12 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 -j12 "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 -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Score.o Score.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o ScoreMatrix.o ScoreMatrix.cc In file included from Matrix.h:12, from 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; | ^~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Sequence.o Sequence.cc In file included from Matrix.h:12, from 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; | ^~~~~ 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 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 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; | ^~~~~ 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 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 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 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 Block.cc:9: MultiSequence.h:24:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 24 | const int AutoDetectFileFormat (const char *filename) const; | ^~~~~ MultiSequence.h:28:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 28 | const char ComputeAnnotation (const char *data, const int size) const; | ^~~~~ MultiSequence.h:48:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 48 | const int GetNumSequences() const; | ^~~~~ MultiSequence.h:49:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 49 | const int GetLength() const; | ^~~~~ In file included from Matrix.h:12, from 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 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 { | ^~~~~ 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; | ^~~~~ 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; | ^~~ 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; | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() 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; | ^~~~~ 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 Main.cc:18: Tree.h:44:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 44 | const bool GetIsLeaf() const; | ^~~~~ Tree.h:45:5: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 45 | const int GetNumSequences() const; | ^~~~~ SparseMatrix.h: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 { | ^~~~~ Matrix.cc: In member function 'float Matrix::SumOfRow(int, int) const': Matrix.cc:165:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 165 | int pos = 0; | ^~~ Matrix.cc:166:16: warning: variable 'ptr' set but not used [-Wunused-but-set-variable] 166 | float *ptr; | ^~~ Matrix.cc: In member function 'float Matrix::SumOfColumn(int, int) const': Matrix.cc:186:13: warning: variable 'pos' set but not used [-Wunused-but-set-variable] 186 | int pos = 0; | ^~~ In file included from 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 { | ^~~~~ 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: 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 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; | ^~~~~ 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; | ^~~~~ Sequence.cc:121:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 121 | const int Sequence::GetLength () const { | ^~~~~ ScoreMatrix.h:88:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 88 | const int GetNumLayers() const { | ^~~~~ ScoreMatrix.h:96:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 96 | const int GetNumRows() const { | ^~~~~ ScoreMatrix.h:104:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 104 | const int GetNumCols() const { | ^~~~~ Sequence.cc:129:1: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 129 | const int Sequence::GetID () 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 { | ^~~~~ 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; | ^~~~~ 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)]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o SparseMatrix.o SparseMatrix.cc 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]; | ^ LocalAlign.cc:121:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 121 | delete s2; | ^~ LocalAlign.cc:99:34: note: returned from 'void* operator new [](std::size_t)' 99 | int *s2 = new int[besty - c + 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]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Tree.o Tree.cc g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -W -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -DVERSION="\"1.00\"" -c -o Utilities.o Utilities.cc PairAligner.cc: In member function 'void PairAligner::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]; | ^ 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]; | ^ 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]; | ^ 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]; | ^ 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:130:27: 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: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:131:24: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 131 | delete frs; | ^~~ Block.cc:108:35: note: returned from 'void* operator new [](std::size_t)' 108 | frs = new Fragment[multi+1]; | ^ Block.cc:182:16: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 182 | delete frs; | ^~~ Block.cc:108:35: note: returned from 'void* operator new [](std::size_t)' 108 | frs = new Fragment[multi+1]; | ^ 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 Tree.h:9, from Tree.cc:6: SparseMatrix.h:57:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 57 | const int GetRowSize (int layer, int row) const; | ^~~~~ SparseMatrix.h:60:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 60 | const int GetNumLayers() const; | ^~~~~ SparseMatrix.h:61:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 61 | const int GetNumRows() const; | ^~~~~ SparseMatrix.h:62:3: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 62 | const int GetNumCols() const; | ^~~~~ In file included from ScoreMatrix.h:12, from Matrix.h:13, from SparseMatrix.h:12, 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 { | ^~~~~ 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]; | ^ 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]; | ^ 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 { | ^~~~~ ProbModel.cc: In member function 'AlignedFragment* ProbModel::Viterbi(const Sequence&, const Sequence&, int*)': ProbModel.cc:866:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 866 | delete s2; | ^~ ProbModel.cc:843:34: note: returned from 'void* operator new [](std::size_t)' 843 | int *s2 = new int[besty - c + 1]; | ^ 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]; | ^ ProbModel.cc: In member function 'AlignedFragment* ProbModel::OneAligment(const Sequence&, const Sequence&, Matrix&, ScoreMatrix&)': ProbModel.cc:1311:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 1311 | delete s2; | ^~ ProbModel.cc:1289:34: note: returned from 'void* operator new [](std::size_t)' 1289 | int *s2 = new int[besty - c + 1]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/proda-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'proda' in '../proda_1.0-14_amd64.deb'. dpkg-deb: building package 'proda-dbgsym' in '../proda-dbgsym_1.0-14_amd64.deb'. dpkg-genbuildinfo --build=binary -O../proda_1.0-14_amd64.buildinfo dpkg-genchanges --build=binary -O../proda_1.0-14_amd64.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/2255566 and its subdirectories I: Current time: Wed May 8 22:20:54 -12 2024 I: pbuilder-time-stamp: 1715250054 Thu May 9 10:20:56 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom02-amd64.debian.net. Thu May 9 10:20:56 UTC 2024 I: Preparing to do remote build '2' on infom02-amd64.debian.net. Thu May 9 10:21:39 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. Thu May 9 10:21:40 UTC 2024 I: proda_1.0-14_amd64.changes: Format: 1.8 Date: Mon, 18 Dec 2023 21:58:24 +0700 Source: proda Binary: proda proda-dbgsym Architecture: amd64 Version: 1.0-14 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Lance Lin Description: proda - multiple alignment of protein sequences Closes: 1048254 Changes: proda (1.0-14) unstable; urgency=medium . * Team upload. * Standards-Version: 4.6.2 (routine-update) * d/clean: Remove generated binary (Closes: #1048254) Checksums-Sha1: 464357fe6e148bdf8b015b75aa395092c5cd595f 279868 proda-dbgsym_1.0-14_amd64.deb 3657bd8e2e7464d95032892c30477879cfb2d349 5089 proda_1.0-14_amd64.buildinfo f389ffdc523c4521a0b96ee348332eb8d82e15cb 65432 proda_1.0-14_amd64.deb Checksums-Sha256: 0c6805bbbb37eba0481b5f9fa994b0f3f0ace39fb2b30b70cc754e3691473725 279868 proda-dbgsym_1.0-14_amd64.deb b79f1a42b36caabb83b73c0e23313247efc238dc347051797dbf8f5027691289 5089 proda_1.0-14_amd64.buildinfo d32861515166eb4634fce22e5339664d2a351b0f997344c5f96a7369cacb5c0e 65432 proda_1.0-14_amd64.deb Files: 4f799c13eb7f32ec31b22094067a9547 279868 debug optional proda-dbgsym_1.0-14_amd64.deb 56e56dc72b4b4812b816a61b0c86be3d 5089 science optional proda_1.0-14_amd64.buildinfo d2ea15fe501950dbc51da63e1fe01b23 65432 science optional proda_1.0-14_amd64.deb Thu May 9 10:21:41 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_35-10082.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.w4peH7Tz/proda_1.0-14.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.w4peH7Tz/proda_1.0-14.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.w4peH7Tz/proda_1.0-14.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.w4peH7Tz/b1/proda_1.0-14_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.w4peH7Tz/b2/proda_1.0-14_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.363s) 0.363s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 733ms CPU time consumed: 733ms Thu May 9 10:21:42 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 10:21:42 UTC 2024 I: proda from trixie built successfully and reproducibly on amd64. Thu May 9 10:21:44 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 10:21:44 UTC 2024 I: Submitting 8.0K b1/proda_1.0-14_amd64.buildinfo.asc Thu May 9 10:21:44 UTC 2024 I: Submitting 8.0K b2/proda_1.0-14_amd64.buildinfo.asc Thu May 9 10:21:45 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 10:21:45 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 10:21:45 UTC 2024 I: Removing signed proda_1.0-14_amd64.buildinfo.asc files: removed './b1/proda_1.0-14_amd64.buildinfo.asc' removed './b2/proda_1.0-14_amd64.buildinfo.asc'