Sat May 4 05:14:12 UTC 2024 I: starting to build disulfinder/trixie/armhf on jenkins on '2024-05-04 05:13' Sat May 4 05:14:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_4/4699/console.log Sat May 4 05:14:12 UTC 2024 I: Downloading source for trixie/disulfinder=1.2.11-12 --2024-05-04 05:14:12-- http://deb.debian.org/debian/pool/main/d/disulfinder/disulfinder_1.2.11-12.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2201 (2.1K) [text/prs.lines.tag] Saving to: ‘disulfinder_1.2.11-12.dsc’ 0K .. 100% 267M=0s 2024-05-04 05:14:13 (267 MB/s) - ‘disulfinder_1.2.11-12.dsc’ saved [2201/2201] Sat May 4 05:14:13 UTC 2024 I: disulfinder_1.2.11-12.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: disulfinder Binary: disulfinder, disulfinder-data Architecture: any all Version: 1.2.11-12 Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan , Andreas Tille Homepage: https://disulfind.dsi.unifi.it/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/disulfinder Vcs-Git: https://salsa.debian.org/med-team/disulfinder.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libboost-dev, libboost-graph-dev, libf2c2-dev, debhelper Package-List: disulfinder deb science optional arch=any disulfinder-data deb science optional arch=all Checksums-Sha1: 275abbe8b4ac8e7f83d8a38c81c7f75c0ec7481e 2480613 disulfinder_1.2.11.orig.tar.gz 52738db0241d3d67646b28e2f265eadbcad5a33e 8332 disulfinder_1.2.11-12.debian.tar.xz Checksums-Sha256: d653aaac3ea26e9f6106a371de4f43d05b781a8b8b690c97820e4b27ea9d3495 2480613 disulfinder_1.2.11.orig.tar.gz 407927fbe004d1c16487e4f787cd23d79ce80cdef4e4d17315b967109d5d33ca 8332 disulfinder_1.2.11-12.debian.tar.xz Files: a4f0ed137b56fc0674a207351b659eba 2480613 disulfinder_1.2.11.orig.tar.gz 53a5bfd7ad95f806bdee5a7888491ba0 8332 disulfinder_1.2.11-12.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHpPFYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFsKg//d8XmEUEc8jwvfScAQTiNjpgBaHrtO6Jd Cl0bAsD/btgLF43f6tk/Tlxe6aCHWy+Qgyh+xKucTvX/5JjxYF8lHutZBgDHNqHF yDtFygJBtMfeZZe5DX/EozWefBSFn9Pwmd0gqLcQ8PU/mJKI9l6dDo7i7UqBNOou 6zmszsM7thzUdxwXT1h78drmvXO+8FqawpyLxHMZbQ6OYb3bEsU2PLE1D/B+pASY Q59rtJvG491VAA3/uB7lb4vGwpq1L0gNKkVC9l4XsjP9sWsZE1AZ7jBLZEaL/ICN OdbLjV5POK5XTcKpTvA2sV+eBnBVstON6SnU1D0yetF7EQ4uac7hNZmpOqygX0x2 nXkodDk/TEktlBlpZBDULBdNt2809gWY7rUFxrg1qhVOZdpq9omytH6i2azY03JC IJfClHaDzLFvaaN2hbTqstue4eAW8LwzY4AoZ6mcr/c4Yox5ecDwUK2Zd2TF8WYI KiilYQK8eVQ4OKuYXFuRQeRKgX0yBr35lseBRk+ErWXIviimYFWudlrd4w0QA3kI vHrCNzl42xPHoZjA4xIxqpP7rjDNIbpUJAQbz6a1oAJ1bCewQUe4JKWzHMYwKgzM exeUdHdSwWOZVQsj11jeftTUSwdQhoXPKtas9SbpoHHE+irQE/9giPoDOHncynwU xtsP1O2LT8s= =WaZA -----END PGP SIGNATURE----- Sat May 4 05:14:13 UTC 2024 I: Checking whether the package is not for us Sat May 4 05:14:13 UTC 2024 I: Starting 1st build on remote node virt64z-armhf-rb.debian.net. Sat May 4 05:14:13 UTC 2024 I: Preparing to do remote build '1' on virt64z-armhf-rb.debian.net. Sat May 4 05:19:01 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 3 17:14:20 -12 2024 I: pbuilder-time-stamp: 1714799660 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 [disulfinder_1.2.11-12.dsc] I: copying [./disulfinder_1.2.11.orig.tar.gz] I: copying [./disulfinder_1.2.11-12.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 20 10:41:26 2022 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 ./disulfinder_1.2.11-12.dsc: no acceptable signature found dpkg-source: info: extracting disulfinder in disulfinder-1.2.11 dpkg-source: info: unpacking disulfinder_1.2.11.orig.tar.gz dpkg-source: info: unpacking disulfinder_1.2.11-12.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying variable_length_array dpkg-source: info: applying unknown_escape dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying gcc-7.patch dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11225/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='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='93e352b7be704660becf29817da642a5' 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='11225' 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.8TLewLcy/pbuilderrc_H09M --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.8TLewLcy/b1 --logfile b1/build.log disulfinder_1.2.11-12.dsc' SUDO_GID='110' SUDO_UID='103' 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 virt64z 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 2 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/11225/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), libboost-dev, libboost-graph-dev, libf2c2-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19441 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. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however: Package libboost-graph-dev is not installed. pbuilder-satisfydepends-dummy depends on libf2c2-dev; however: Package libf2c2-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-graph-dev{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libf2c2{a} libf2c2-dev{a} libfile-stripnondeterminism-perl{a} libicu-dev{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, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 42.5 MB of archives. After unpacking 302 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-3 [1088 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40-8 [85.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf icu-devtools armhf 72.1-4+b1 [185 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-2+b2 [10.6 MB] Get: 33 http://deb.debian.org/debian trixie/main armhf libboost-dev armhf 1.83.0.2+b2 [3832 B] Get: 34 http://deb.debian.org/debian trixie/main armhf libboost-graph1.83.0 armhf 1.83.0-2+b2 [335 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83.0 armhf 1.83.0-2+b2 [307 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libicu-dev armhf 72.1-4+b1 [10.1 MB] Get: 37 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83-dev armhf 1.83.0-2+b2 [335 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libboost-serialization1.83.0 armhf 1.83.0-2+b2 [315 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libboost-serialization1.83-dev armhf 1.83.0-2+b2 [385 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libboost-test1.83.0 armhf 1.83.0-2+b2 [429 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libboost-test1.83-dev armhf 1.83.0-2+b2 [531 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libboost-graph1.83-dev armhf 1.83.0-2+b2 [379 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libboost-graph-dev armhf 1.83.0.2+b2 [3688 B] Get: 44 http://deb.debian.org/debian trixie/main armhf libf2c2 armhf 20140711-1+b1 [112 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libf2c2-dev armhf 20140711-1+b1 [119 kB] Fetched 42.5 MB in 0s (86.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19441 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_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-3_armhf.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_armhf.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_armhf.deb ... Unpacking man-db (2.12.1-1) ... 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_2.71-3_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:armhf. Preparing to unpack .../22-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../24-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/disulfinder-1.2.11/ && 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 > ../disulfinder_1.2.11-12_source.changes dpkg-buildpackage: info: source package disulfinder dpkg-buildpackage: info: source version 1.2.11-12 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j3 distclean make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src' make -C NN clean make -C Common clean make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common' make -C eig clean make -C SVM clean make[4]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM' make[4]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/NN' make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common' cd SVM && make clean make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Input' cd Output && make clean make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src' rm -f *.[12345678] *.[12345678].gz #if [ -d "disulfind" ]; then rm -rf disulfind; fi if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi rm -rf patch-stamp \ initial-clean-stamp \ "disulfinder-1.2.11.tar.gz" \ .pc make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars debian/files rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11' dh_auto_build --no-parallel make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/disulfinder-1.2.11' make -C disulfind/src disulfinder make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src' g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o In file included from Input/utils.h:2, from Input/GlobalDescriptor.cpp:3: Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o In file included from Input/utils.h:2, from Input/createBRNNDataset.h:1, from Input/createBRNNDataset.cpp:2: Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o In file included from Input/utils.h:2, from Input/createKernelDataset.h:1, from Input/createKernelDataset.cpp:2: Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from Input/../Common/Matrix.h:10, from Input/utils.h:1: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void createDataKernel(Protein&, std::ostream&, unsigned int, const GlobalDescriptorMaker&, const std::string&, bool)' at Input/createKernelDataset.cpp:39:35: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void createDataKernel(Protein&, std::ostream&, unsigned int, const GlobalDescriptorMaker&, const std::string&, bool)' at Input/createKernelDataset.cpp:42:38: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o In file included from /usr/include/c++/13/map:62, from Input/Protein.cpp:9: /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = char; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/13/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:323:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:338:26: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:341:18: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:342:18: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:345:18: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:346:18: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:350:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:364:36: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:366:55: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:366:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadProfile(std::istream&)' at Input/Protein.cpp:1071:34: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from Input/../Common/Util.h:7, from Input/Protein.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Protein::AddDescriptors(std::vector&)' at Input/Protein.cpp:199:36: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Protein::AddDescriptors(std::vector&)' at Input/Protein.cpp:202:34: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Protein::AddDescriptors(std::vector&)' at Input/Protein.cpp:205:32: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'static void Protein::AddDescriptors(std::vector&)' at Input/Protein.cpp:225:39: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 533 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'static void Protein::AddDescriptors(std::vector&)' at Input/Protein.cpp:242:37: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:487:24: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:488:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:506:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:518:36: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:520:55: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:520:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1315:34: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1316:34: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1321:32: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1322:32: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1323:32: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1337:33: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1111:32: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1116:34: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1120:34: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1122:19: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1235:31: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1242:34: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1249:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1250:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1256:45: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1258:29: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 514 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1265:22: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1271:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o Output/makeHTMLOutput.cpp: In function 'void makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)': Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 162 | char * altname[2] = {"Second","Third"}; | ^~~~~~~~ Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 162 | char * altname[2] = {"Second","Third"}; | ^~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o Output/makeASCIIOutput.cpp: In function 'void makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)': Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 144 | char * altname[2] = {"SECOND","THIRD"}; | ^~~~~~~~ Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] 144 | char * altname[2] = {"SECOND","THIRD"}; | ^~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o In file included from /usr/include/c++/13/vector:72, from FSA-Alignment/fsa.h:3, from FSA-Alignment/fsa.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Transition}; _Tp = Transition; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Transition}; _Tp = Transition; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Transition; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1299:21, inlined from 'void FiniteStateAutomata::Read(std::istream&)' at FSA-Alignment/fsa.cpp:80:34: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o In file included from /usr/include/c++/13/vector:72, from FSA-Alignment/../Common/Matrix.h:8, from FSA-Alignment/../Common/CommonMethods.h:15, from FSA-Alignment/viterbi_aligner.h:2, from FSA-Alignment/viterbi_aligner.cpp:3: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Matrix::Read(std::istream&) [with DATATYPE = double]' at FSA-Alignment/../Common/Matrix.h:403:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o In file included from /usr/include/c++/13/vector:72, from NN/multi-array.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'REAL* ReadArray(std::istream&, int&)' at NN/multi-array.cpp:292:21: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/array.cpp -o NN/array.o In file included from /usr/include/c++/13/vector:72, from NN/array.cpp:2: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void VECTOR::Read(std::istream&)' at NN/array.cpp:172:19: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void COLLECTIONA::Read(std::istream&)' at NN/array.cpp:246:16: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DataSet.cpp -o BRNN/RNNs/DataSet.o In file included from BRNN/RNNs/DataSet.cpp:1: BRNN/RNNs/DataSet.h:19:1: warning: 'typedef' was ignored in this declaration 19 | typedef struct StructuredInstanceTemplate { | ^~~~~~~ BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)': BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 86 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()': BRNN/RNNs/DataSet.h:116:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 116 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 135 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.cpp: In constructor 'DataSet::DataSet(const char*, const char*)': BRNN/RNNs/DataSet.cpp:69:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 69 | if(pos == string::npos) | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.cpp: In member function 'bool DataSet::loadInstances(const char*)': BRNN/RNNs/DataSet.cpp:141:7: warning: unused variable 'ng' [-Wunused-variable] 141 | int ng = 1; | ^~ BRNN/RNNs/DataSet.cpp: At global scope: BRNN/RNNs/DataSet.cpp:14:12: warning: 'int one(const dirent*)' defined but not used [-Wunused-function] 14 | static int one(const struct dirent* unused) { | ^~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DPAG.cpp -o BRNN/RNNs/DPAG.o BRNN/RNNs/DPAG.cpp: In function 'float PRMeasure(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:48:7: warning: unused variable 'global_predicted_positives' [-Wunused-variable] 48 | int global_predicted_positives = boost::num_edges(g), | ^~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable 'global_actual_positives' [-Wunused-variable] 49 | global_actual_positives = boost::num_edges(gtarget), | ^~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable 'graphNode' [-Wunused-variable] 52 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function 'float PrecisionMeasure(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:302:12: warning: unused variable 'graphNode' [-Wunused-variable] 302 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function 'std::pair globalPRMeasure(const DPAG&, const DPAG&, int&, int&, int&, int&, int&, int&, float&)': BRNN/RNNs/DPAG.cpp:361:12: warning: unused variable 'graphNode' [-Wunused-variable] 361 | Vertex_d graphNode, targetNode, targetNode1; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function 'ConfusionTable getPredictionIndexes(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:560:45: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type' {aka 'unsigned int'} [-Wsign-compare] 559 | require(true_positives + true_negatives + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | false_positives + false_negatives == | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 561 | boost::num_vertices(gpred) * (boost::num_vertices(gpred)-1) / 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable 'weight' [-Wunused-variable] 471 | float weight = 1.0 / boost::num_vertices(gpred); | ^~~~~~ BRNN/RNNs/DPAG.cpp: In function 'float RecallMeasure(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:573:12: warning: unused variable 'graphNode' [-Wunused-variable] 573 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function 'bool equal(const DPAG&, const DPAG&)': BRNN/RNNs/DPAG.cpp:746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 746 | for(int i=0; i, boost::property >, boost::adjacency_list, boost::property > > dpag_to_rnndpag(const DPAG&)': BRNN/RNNs/DPAG.cpp:832:24: warning: comparison of integer expressions of different signedness: 'boost::vec_adj_list_vertex_id_map, unsigned int>::value_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 832 | if(vertex_id[*v_i] != n_vertices-1) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:839:29: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits, int>::value_type' {aka 'int'} and 'boost::vec_adj_list_vertex_id_map, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare] 839 | if(children.front() == vertex_id[*v_i]+1) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:844:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 844 | for(int i=0; i, int>::value_type' {aka 'int'} and 'boost::vec_adj_list_vertex_id_map, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare] 862 | if((*it).second.front() == vertex_id[*v_i]-1) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:867:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 867 | for(int i=0; i<(*it).second.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable 'node' [-Wunused-variable] 813 | Vertex_d node; | ^~~~ BRNN/RNNs/DPAG.cpp: In function 'DPAG rnndpag_to_dpag(const std::pair, boost::property >, boost::adjacency_list, boost::property > >&)': BRNN/RNNs/DPAG.cpp:878:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] 878 | VertexId vertex_id = boost::get(boost::vertex_index, g);; | ^~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Options.cpp -o BRNN/RNNs/Options.o BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_config(const std::string&)': BRNN/RNNs/Options.cpp:30:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 30 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:36:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 36 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:42:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 42 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:47:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 47 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:61:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 61 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:79:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 79 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 85 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:90:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 90 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:99:29: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 99 | if(_input_mask.size() != _input_dimension) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_args(int, char**)': BRNN/RNNs/Options.cpp:138:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 138 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:144:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 144 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:150:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 150 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:155:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 155 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:169:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 169 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:187:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 187 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:193:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 193 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:198:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string::size_type' {aka 'const unsigned int'} [-Wsign-compare] 198 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/Options.cpp:207:29: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 207 | if(_input_mask.size() != _input_dimension) | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/protein_util.cpp -o BRNN/protein_util.o In file included from BRNN/protein_util.cpp:1: BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)': BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)': BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] 211 | int _bp1, _bp2; // bridge partners | ^~~~ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] 206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner | ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)': BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder] 241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set | ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] 239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment | ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] 245 | SSegment(char symbol): | ^~~~~~~~ In file included from /usr/include/c++/13/cassert:44, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp: In member function 'void Chain::setSShydrophobicity()': BRNN/protein_util.cpp:365:31: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 365 | assert(resHydrScales.size() == numResidues()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:380:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 380 | if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:386:24: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare] 386 | assert(hAvg.size() == (*c_it).numResidues()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:391:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 391 | for(int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 401 | assert(seq_pos == resHydrScales.size()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/blast_util.cpp -o BRNN/blast_util.o BRNN/blast_util.cpp: In member function 'void PSSM::parsePsiBlastReport(const char*)': BRNN/blast_util.cpp:34:13: warning: unused variable 'prof' [-Wunused-variable] 34 | Profile prof; | ^~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/rnn_util.cpp -o BRNN/rnn_util.o In file included from BRNN/rnn_util.cpp:4: BRNN/RNNs/DataSet.h:19:1: warning: 'typedef' was ignored in this declaration 19 | typedef struct StructuredInstanceTemplate { | ^~~~~~~ BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)': BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 86 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()': BRNN/RNNs/DataSet.h:116:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 116 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 135 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from BRNN/rnn_util.cpp:7: BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)': BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge): | ^~~~~~~ BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)': BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder] 209 | Coordinate3D _coord; // residue representative coordinates | ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] 208 | float _hydr, _acc; // residue hydrophobicity and acc. values | ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] 207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator | ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] 211 | int _bp1, _bp2; // bridge partners | ^~~~ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] 206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner | ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 219 | Residue(const Residue& r): | ^~~~~~~ BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)': BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder] 241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set | ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] 239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment | ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] 245 | SSegment(char symbol): | ^~~~~~~~ BRNN/rnn_util.cpp: In function 'void create_connectivity_input_data(const std::string&, const std::string&, int, int, const std::string&)': BRNN/rnn_util.cpp:233:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 233 | for(int i=0; i::size_type' {aka 'unsigned int'} [-Wsign-compare] 277 | if(i >=0 && i < pssm.size()) | ~~^~~~~~~~~~~~~ BRNN/rnn_util.cpp: In function 'void rnn_predict_disulphides(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)': BRNN/rnn_util.cpp:359:19: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::edges_size_type' {aka 'unsigned int'} [-Wsign-compare] 359 | require(B == boost::num_edges(candidate) && | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:348:16: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] 348 | VertexId vertex_id = boost::get(boost::vertex_index, candidate); | ^~~~~~~~~ BRNN/rnn_util.cpp:405:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, boost::property > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 405 | for(int j=0; j, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::edges_size_type' {aka 'unsigned int'} [-Wsign-compare] 406 | require(B == boost::num_edges(bestPatterns[j]) && | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:407:15: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type' {aka 'unsigned int'} [-Wsign-compare] 407 | B == boost::num_vertices(bestPatterns[j]) / 2, | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:378:18: warning: unused variable 'nodes' [-Wunused-variable] 378 | vector *nodes = it.currenTONodes(); | ^~~~~ In file included from BRNN/rnn_util.cpp:5: BRNN/RNNs/RecursiveNN.h: In instantiation of 'RecursiveNN::RecursiveNN(const char*) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]': BRNN/rnn_util.cpp:88:73: required from here BRNN/RNNs/RecursiveNN.h:1018:13: warning: unused variable 'trasd' [-Wunused-variable] 1018 | TrasdType trasd = Options::instance()->getTrasductionType(); | ^~~~~ BRNN/RNNs/RecursiveNN.h:1026:23: warning: variable 'indexes' set but not used [-Wunused-but-set-variable] 1026 | std::pair indexes = Options::instance()->getLayersIndexes(); | ^~~~~~~ BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable 'default_precision' [-Wunused-variable] 1047 | int default_precision = is.precision(); | ^~~~~~~~~~~~~~~~~ In file included from BRNN/rnn_util.cpp:6: BRNN/RNNs/StructureSearch.h: In instantiation of 'std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]': BRNN/rnn_util.cpp:396:37: required from here BRNN/RNNs/StructureSearch.h:977:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'unsigned int'} [-Wsign-compare] 977 | for(int i=0; i<_nodesInputs.size(); ++i) | ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/StructureSearch.h:984:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector, boost::property > >::size_type' {aka 'unsigned int'} [-Wsign-compare] 984 | for(int i=0; i::fPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]': BRNN/RNNs/RecursiveNN.h:1356:3: required from 'void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]' BRNN/rnn_util.cpp:99:32: required from here BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1390 | require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!"); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1415:45: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] 1415 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1418:45: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 1418 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] 1384 | VertexId vertex_id = boost::get(boost::vertex_index, sdag); | ^~~~~~~~~ BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN::bPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]': BRNN/RNNs/RecursiveNN.h:1359:19: required from 'void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]' BRNN/rnn_util.cpp:99:32: required from here BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 1470 | for(int t=0; t::size_type' {aka 'unsigned int'} [-Wsign-compare] 1471 | require(_n == toNodes[t]->_encodedInput.size(), "Error!"); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1492:45: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] 1492 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1495:45: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 1495 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1465:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] 1465 | VertexId vertex_id = boost::get(boost::vertex_index, sdag); | ^~~~~~~~~ BRNN/RNNs/StructureSearch.h: In instantiation of 'float StructureSearch::RNNMeasure(const DPAG&, RNN*, std::vector&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN; DPAG = boost::adjacency_list, boost::property >]': BRNN/RNNs/StructureSearch.h:990:17: required from 'std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]' BRNN/rnn_util.cpp:396:37: required from here BRNN/RNNs/StructureSearch.h:186:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 186 | for(int i=0; i > Util::tokenize(const std::string&, const std::string&, bool)': Util.cpp:135:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 135 | delete str; | ^~~ Util.cpp:127:38: note: returned from 'void* operator new [](std::size_t)' 127 | char *str = new char[s.length()+1]; | ^ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c CommonMethods.cpp -o CommonMethods.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c ConfusionMatrix.cpp -o ConfusionMatrix.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Exception.cpp -o Exception.o g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Statistics.cpp -o Statistics.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balanc.o eig/balanc.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balbak.o eig/balbak.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/cdiv.o eig/cdiv.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/elmhes.o eig/elmhes.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/eltran.o eig/eltran.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr.o eig/hqr.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr2.o eig/hqr2.c cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/rg.o eig/rg.c g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c coords.cpp -o coords.o cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/d_sign.o eig/d_sign.c ar rvs libCommon.a Vector.o Util.o CommonMethods.o ConfusionMatrix.o Exception.o Statistics.o eig/balanc.o eig/balbak.o eig/cdiv.o eig/elmhes.o eig/eltran.o eig/hqr.o eig/hqr2.o eig/rg.o coords.o eig/d_sign.o ar: creating libCommon.a a - Vector.o a - Util.o a - CommonMethods.o a - ConfusionMatrix.o a - Exception.o a - Statistics.o a - eig/balanc.o a - eig/balbak.o a - eig/cdiv.o a - eig/elmhes.o a - eig/eltran.o a - eig/hqr.o a - eig/hqr2.o a - eig/rg.o a - coords.o a - eig/d_sign.o make[4]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common' g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c disulfinder.cpp -o disulfinder.o In file included from Input/utils.h:2, from disulfinder.cpp:8: Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ g++ -o disulfinder disulfinder.o Input/GlobalDescriptor.o Input/createBRNNDataset.o Input/createKernelDataset.o Input/makeWindow.o Input/makeSparseVector.o Input/Protein.o Input/buildXfolds.o SVM/SVMClassifier.o Output/makeHTMLOutput.o Output/utils.o Output/makeASCIIOutput.o FSA-Alignment/fsa.o FSA-Alignment/viterbi_aligner.o NN/multi-array.o NN/array.o NN/brnn-model.o NN/brnn-test.o BRNN/RNNs/Node.o BRNN/RNNs/StructureSearch.o BRNN/RNNs/DataSet.o BRNN/RNNs/DPAG.o BRNN/RNNs/Options.o BRNN/protein_util.o BRNN/blast_util.o BRNN/rnn_util.o -Wl,-z,relro -Wl,-z,now -LCommon/ -lCommon make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src' sed -e 's|__datadir__||g;s|__docdir__|/usr/share/doc/disulfinder|g;s|__pkgdatadir__||g;s|__PREFIX__|/usr|g;s|__sysconfdir__||g;s|__VERSION__|1.2.11|g;' "disulfinder.pod" | \ pod2man -c 'User Commands' -r '1.2.11' -name DISULFINDER > "disulfinder.1" make[2]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11' make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-odFVnJRm create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars rm -fr -- debian/.debhelper/generated/disulfinder/ debian/disulfinder/ debian/tmp/ debian/.debhelper/generated/disulfinder-data/ debian/disulfinder-data/ rm -f debian/disulfinder-data.debhelper.log debian/disulfinder.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11' /usr/bin/make DESTDIR=/build/reproducible-path/disulfinder-1.2.11/debian/disulfinder prefix=/usr install make[2]: Entering directory '/build/reproducible-path/disulfinder-1.2.11' /usr/bin/make -C disulfind/src install make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src' mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/bin cp disulfinder /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/bin/ mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models cp -r ../Models /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ && find /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ -depth -ignore_readdir_race -name .svn -execdir rm -rf {} \; rm -rf /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models/conn/data/sequences_w5 rm -rf /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Predictions rm -rf /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/tmp make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src' mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1 && cp disulfinder.1 /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1/ mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples && cp examples/res_id_* /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples/ make[2]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11' make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11' dh_install mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder mv /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/* /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11' dh_installdocs install -m0755 -d debian/disulfinder/usr/share/doc/disulfinder cp --reflink=auto -a ./debian/upstream/metadata debian/disulfinder/usr/share/doc/disulfinder cp --reflink=auto -a ./debian/README.test debian/disulfinder/usr/share/doc/disulfinder cp --reflink=auto -a ./debian/tests/installation-test debian/disulfinder/usr/share/doc/disulfinder chmod -R u\+rw,go=rX debian/disulfinder/usr/share/doc install -p -m0644 debian/copyright debian/disulfinder/usr/share/doc/disulfinder/copyright install -m0755 -d debian/disulfinder-data/usr/share/doc/disulfinder-data install -p -m0644 debian/copyright debian/disulfinder-data/usr/share/doc/disulfinder-data/copyright dh_installchangelogs install -m0755 -d debian/disulfinder-data/usr/share/doc/disulfinder-data install -p -m0644 debian/.debhelper/generated/disulfinder-data/dh_installchangelogs.dch.trimmed debian/disulfinder-data/usr/share/doc/disulfinder-data/changelog.Debian install -p -m0644 ./ChangeLog debian/disulfinder-data/usr/share/doc/disulfinder-data/changelog install -m0755 -d debian/disulfinder/usr/share/doc/disulfinder install -p -m0644 debian/.debhelper/generated/disulfinder/dh_installchangelogs.dch.trimmed debian/disulfinder/usr/share/doc/disulfinder/changelog.Debian install -p -m0644 ./ChangeLog debian/disulfinder/usr/share/doc/disulfinder/changelog dh_installman man-recode --to-code UTF-8 --suffix .dh-new debian/disulfinder/usr/share/man/man1/disulfinder.1 mv debian/disulfinder/usr/share/man/man1/disulfinder.1.dh-new debian/disulfinder/usr/share/man/man1/disulfinder.1 chmod 0644 -- debian/disulfinder/usr/share/man/man1/disulfinder.1 dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/disulfinder cd debian/disulfinder-data chmod a-x usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/man/man1/disulfinder.1 gzip -9nf usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/man/man1/disulfinder.1 chmod a-x usr/share/doc/disulfinder-data/changelog usr/share/doc/disulfinder-data/changelog.Debian gzip -9nf usr/share/doc/disulfinder-data/changelog usr/share/doc/disulfinder-data/changelog.Debian cd '/build/reproducible-path/disulfinder-1.2.11' cd '/build/reproducible-path/disulfinder-1.2.11' dh_fixperms find debian/disulfinder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/disulfinder-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/disulfinder/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder-data/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/disulfinder-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/disulfinder/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/disulfinder/usr/bin/disulfinder dh_strip -a install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/9c objcopy --only-keep-debug --compress-debug-sections debian/disulfinder/usr/bin/disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/9c/56a956d4acf5c9173749c5ef6883a1193dc066.debug chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/9c/56a956d4acf5c9173749c5ef6883a1193dc066.debug strip --remove-section=.comment --remove-section=.note debian/disulfinder/usr/bin/disulfinder objcopy --add-gnu-debuglink debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/9c/56a956d4acf5c9173749c5ef6883a1193dc066.debug debian/disulfinder/usr/bin/disulfinder install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc ln -s disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc/disulfinder-dbgsym install -m0755 -d debian/.debhelper/disulfinder dh_makeshlibs -a rm -f debian/disulfinder/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/disulfinder/DEBIAN dpkg-shlibdeps -Tdebian/disulfinder.substvars debian/disulfinder/usr/bin/disulfinder dh_installdeb install -m0755 -d debian/disulfinder/DEBIAN install -m0755 -d debian/disulfinder-data/DEBIAN dh_gencontrol install -m0755 -d debian/disulfinder-data/DEBIAN echo misc:Depends= >> debian/disulfinder-data.substvars echo misc:Pre-Depends= >> debian/disulfinder-data.substvars dpkg-gencontrol -pdisulfinder-data -ldebian/changelog -Tdebian/disulfinder-data.substvars -cdebian/control -Pdebian/disulfinder-data install -m0755 -d debian/disulfinder/DEBIAN echo misc:Depends= >> debian/disulfinder.substvars echo misc:Pre-Depends= >> debian/disulfinder.substvars install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -cdebian/control -Pdebian/.debhelper/disulfinder/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=disulfinder-dbgsym "-DDepends=disulfinder (= \${binary:Version})" "-DDescription=debug symbols for disulfinder" -DBuild-Ids=9c56a956d4acf5c9173749c5ef6883a1193dc066 -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -cdebian/control -Pdebian/disulfinder chmod 0644 -- debian/disulfinder-data/DEBIAN/control chmod 0644 -- debian/disulfinder/DEBIAN/control dh_md5sums install -m0755 -d debian/disulfinder/DEBIAN install -m0755 -d debian/disulfinder-data/DEBIAN cd debian/disulfinder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/disulfinder-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/disulfinder/DEBIAN/md5sums install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN cd debian/.debhelper/disulfinder/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/disulfinder-data/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/disulfinder .. dpkg-deb --root-owner-group --build debian/.debhelper/disulfinder/dbgsym-root .. dpkg-deb: building package 'disulfinder' in '../disulfinder_1.2.11-12_armhf.deb'. dpkg-deb: building package 'disulfinder-dbgsym' in '../disulfinder-dbgsym_1.2.11-12_armhf.deb'. dpkg-deb --root-owner-group --build debian/disulfinder-data .. dpkg-deb: building package 'disulfinder-data' in '../disulfinder-data_1.2.11-12_all.deb'. dpkg-genbuildinfo --build=binary -O../disulfinder_1.2.11-12_armhf.buildinfo dpkg-genchanges --build=binary -O../disulfinder_1.2.11-12_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/11225 and its subdirectories I: Current time: Fri May 3 17:18:50 -12 2024 I: pbuilder-time-stamp: 1714799930 Sat May 4 05:19:04 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ff4a-armhf-rb.debian.net. Sat May 4 05:19:04 UTC 2024 I: Preparing to do remote build '2' on ff4a-armhf-rb.debian.net. Sat May 4 05:31:52 UTC 2024 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. Sat May 4 05:31:54 UTC 2024 I: disulfinder_1.2.11-12_armhf.changes: Format: 1.8 Date: Thu, 20 Jan 2022 11:36:56 +0100 Source: disulfinder Binary: disulfinder disulfinder-data disulfinder-dbgsym Architecture: all armhf Version: 1.2.11-12 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: disulfinder - cysteines disulfide bonding state and connectivity predictor disulfinder-data - data files for predictor of disulfide bonds in proteins Changes: disulfinder (1.2.11-12) unstable; urgency=medium . * Upstream download vanished * Standards-Version: 4.6.0 (routine-update) * Add missing build dependency on dh addon. * Apply multi-arch hints. + disulfinder-data: Add Multi-Arch: foreign. Checksums-Sha1: c0e3f8d8ba191891b6fa3e0c43936bfc7945ceaa 1125600 disulfinder-data_1.2.11-12_all.deb d3d32749290ab003f68e497bd2ee13dd24dbfd5a 3421320 disulfinder-dbgsym_1.2.11-12_armhf.deb 5c1c697e8c31b46b95db9c8a13aa0f06a662c753 5851 disulfinder_1.2.11-12_armhf.buildinfo f98bc28fdc48ed23ebba1cdb2c68e6e051d7e88d 201300 disulfinder_1.2.11-12_armhf.deb Checksums-Sha256: d9660f8b02ffd7c141d78ca63c2b801bf9330b800885ea60e7f0830d2f82aa92 1125600 disulfinder-data_1.2.11-12_all.deb 7da5667e73a594eef5caa90ad60d9f15d6be444a01d211e8bb746b1300047ff7 3421320 disulfinder-dbgsym_1.2.11-12_armhf.deb ff6d4a1f518653ac218ff91164ab906e1735077367ac7f4cc515eb8b8678841e 5851 disulfinder_1.2.11-12_armhf.buildinfo 9643e3ab528e2ade2dc97e71644c104cba50e945a306afcda169e2e5f3e70c4b 201300 disulfinder_1.2.11-12_armhf.deb Files: a63e8d964808d1fe0f57a27a95107fc7 1125600 science optional disulfinder-data_1.2.11-12_all.deb faed055a9f1237677b12c7cf587aeb43 3421320 debug optional disulfinder-dbgsym_1.2.11-12_armhf.deb 31b7a752786a02becb64bcddc2a22f60 5851 science optional disulfinder_1.2.11-12_armhf.buildinfo 71106dd974c940a04f5190072c23b847 201300 science optional disulfinder_1.2.11-12_armhf.deb Sat May 4 05:31:55 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_4-4699.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.8TLewLcy/disulfinder_1.2.11-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8TLewLcy/disulfinder_1.2.11-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8TLewLcy/disulfinder_1.2.11-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8TLewLcy/b1/disulfinder_1.2.11-12_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.8TLewLcy/b2/disulfinder_1.2.11-12_armhf.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: 0.425s) 0.425s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.067s) 0.067s 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: 772ms CPU time consumed: 772ms Sat May 4 05:31:56 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sat May 4 05:31:56 UTC 2024 I: disulfinder from trixie built successfully and reproducibly on armhf. Sat May 4 05:31:58 UTC 2024 I: Submitting .buildinfo files to external archives: Sat May 4 05:31:58 UTC 2024 I: Submitting 8.0K b1/disulfinder_1.2.11-12_armhf.buildinfo.asc Sat May 4 05:32:00 UTC 2024 I: Submitting 8.0K b2/disulfinder_1.2.11-12_armhf.buildinfo.asc Sat May 4 05:32:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 4 05:32:01 UTC 2024 I: Done submitting .buildinfo files. Sat May 4 05:32:01 UTC 2024 I: Removing signed disulfinder_1.2.11-12_armhf.buildinfo.asc files: removed './b1/disulfinder_1.2.11-12_armhf.buildinfo.asc' removed './b2/disulfinder_1.2.11-12_armhf.buildinfo.asc'