I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 16 14:50:20 -12 2021 I: pbuilder-time-stamp: 1631847020 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [disulfinder_1.2.11-8.dsc] I: copying [./disulfinder_1.2.11.orig.tar.gz] I: copying [./disulfinder_1.2.11-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Sep 23 03:44:56 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./disulfinder_1.2.11-8.dsc 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_1.2.11-8.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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/21812/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='21812' 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/tmp.UxRG4TOu5B/pbuilderrc_53q9 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UxRG4TOu5B/b1 --logfile b1/build.log disulfinder_1.2.11-8.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled13-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 15 02:48 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/21812/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. 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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libboost-chrono1.67.0{a} libboost-dev{a} libboost-graph-dev{a} libboost-graph1.67-dev{a} libboost-graph1.67.0{a} libboost-regex1.67.0{a} libboost-serialization1.67-dev{a} libboost-serialization1.67.0{a} libboost-test1.67-dev{a} libboost-test1.67.0{a} libboost-timer1.67.0{a} libboost1.67-dev{a} libbsd0{a} libcroco3{a} libelf1{a} libf2c2{a} libf2c2-dev{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 30.4 MB of archives. After unpacking 230 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libboost-chrono1.67.0 arm64 1.67.0-13+deb10u1 [233 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libboost1.67-dev arm64 1.67.0-13+deb10u1 [8388 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libboost-dev arm64 1.67.0.1 [3864 B] Get: 37 http://deb.debian.org/debian buster/main arm64 libboost-regex1.67.0 arm64 1.67.0-13+deb10u1 [458 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libboost-graph1.67.0 arm64 1.67.0-13+deb10u1 [310 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libboost-serialization1.67.0 arm64 1.67.0-13+deb10u1 [311 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libboost-serialization1.67-dev arm64 1.67.0-13+deb10u1 [358 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libboost-timer1.67.0 arm64 1.67.0-13+deb10u1 [231 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libboost-test1.67.0 arm64 1.67.0-13+deb10u1 [433 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libboost-test1.67-dev arm64 1.67.0-13+deb10u1 [503 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libboost-graph1.67-dev arm64 1.67.0-13+deb10u1 [323 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libboost-graph-dev arm64 1.67.0.1 [3752 B] Get: 46 http://deb.debian.org/debian buster/main arm64 libf2c2 arm64 20130926-3 [110 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libf2c2-dev arm64 20130926-3 [123 kB] Fetched 30.4 MB in 7s (4609 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_arm64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.176-1.1_arm64.deb ... Unpacking libelf1:arm64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_arm64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:arm64. Preparing to unpack .../27-libcroco3_0.6.12-3_arm64.deb ... Unpacking libcroco3:arm64 (0.6.12-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_arm64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../31-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../32-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package libboost-chrono1.67.0:arm64. 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/disulfinder-1.2.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package disulfinder dpkg-buildpackage: info: source version 1.2.11-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean dh_auto_clean make -j8 distclean make[1]: Entering directory '/build/disulfinder-1.2.11' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory '/build/disulfinder-1.2.11/disulfind/src' make -C NN clean make -C Common clean make -C SVM clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Common' make -C eig clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/NN' make[4]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/SVM' make[4]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Common' cd SVM && make clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Input' cd Output && make clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory '/build/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/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 \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/disulfinder-1.2.11' dh_auto_build --no-parallel make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/disulfinder-1.2.11' make -C disulfind/src disulfinder make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 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] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] 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] static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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] static const char *aa_three_codes[23] = { ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable] static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files ^~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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::__cxx11::string, const char*, int, std::__cxx11::string, std::ostream&)': Output/makeHTMLOutput.cpp:162:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char * altname[2] = {"Second","Third"}; ^ Output/makeHTMLOutput.cpp:162:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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::__cxx11::string, const char*, int, std::__cxx11::string, std::ostream&)': Output/makeASCIIOutput.cpp:144:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char * altname[2] = {"SECOND","THIRD"}; ^ Output/makeASCIIOutput.cpp:144:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/array.cpp -o NN/array.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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 typedef struct StructuredInstanceTemplate { ^~~~~~~ In file included from BRNN/RNNs/DataSet.cpp:1: 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 'long unsigned int'} [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()': BRNN/RNNs/DataSet.h:116:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] 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] static int one(const struct dirent* unused) { ^~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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] int global_predicted_positives = boost::num_edges(g), ^~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable 'global_actual_positives' [-Wunused-variable] global_actual_positives = boost::num_edges(gtarget), ^~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable 'graphNode' [-Wunused-variable] 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] 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] Vertex_d graphNode, targetNode, targetNode1; ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function 'ConfusionTable getPredictionIndexes(const DPAG&, const DPAG&, std::vector&)': BRNN/RNNs/DPAG.cpp:560:38: 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 'long unsigned int'} [-Wsign-compare] require(true_positives + true_negatives + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ false_positives + false_negatives == ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ boost::num_vertices(gpred) * (boost::num_vertices(gpred)-1) / 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable 'weight' [-Wunused-variable] 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] Vertex_d graphNode, targetNode; ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function 'bool equal(const DPAG&, const DPAG&)': BRNN/RNNs/DPAG.cpp:746:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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, long unsigned int>::value_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(vertex_id[*v_i] != n_vertices-1) { ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:839:22: 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, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare] if(children.front() == vertex_id[*v_i]+1) ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:844:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i, int>::value_type' {aka 'int'} and 'boost::vec_adj_list_vertex_id_map, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare] if((*it).second.front() == vertex_id[*v_i]-1) ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:867:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i<(*it).second.size(); i++) ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable 'node' [-Wunused-variable] 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] VertexId vertex_id = boost::get(boost::vertex_index, g);; ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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 string&)': BRNN/RNNs/Options.cpp:30:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:36:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:42:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:47:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:61:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:79:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:90:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:99:29: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 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 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:144:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:150:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:155:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:169:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:187:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:193:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:198:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(pos != string::npos) { ~~~~^~~~~~~~~ BRNN/RNNs/Options.cpp:207:29: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if(_input_mask.size() != _input_dimension) ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] int _bp1, _bp2; // bridge partners ^~~~ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _baricentre; // baricentrum of C_alpha atoms set ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] SSegment(char symbol): ^~~~~~~~ In file included from /usr/include/c++/8/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 'long unsigned int'} and 'int' [-Wsign-compare] 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 'long unsigned int'} [-Wsign-compare] if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1; ~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/cassert:44, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp:386:24: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 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 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] assert(seq_pos == resHydrScales.size()); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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] Profile prof; ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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 typedef struct StructuredInstanceTemplate { ^~~~~~~ In file included from BRNN/rnn_util.cpp:4: 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 'long unsigned int'} [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()': BRNN/RNNs/DataSet.h:116:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] require(num_nodes == (*_nodes_targets_iter).size(), ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _coord; // residue representative coordinates ^~~~~~ BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder] float _hydr, _acc; // residue hydrophobicity and acc. values ^~~~ BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder] char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator ^~~~~~~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] Residue(const Residue& r): ^~~~~~~ BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder] int _bp1, _bp2; // bridge partners ^~~~ BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder] int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner ^~~~ BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder] 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] Coordinate3D _baricentre; // baricentrum of C_alpha atoms set ^~~~~~~~~~~ BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder] Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment ^~~~~ BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder] SSegment(char symbol): ^~~~~~~~ BRNN/rnn_util.cpp: In function 'void create_connectivity_input_data(const string&, const string&, int, int, const string&)': BRNN/rnn_util.cpp:233:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(i >=0 && i < pssm.size()) ~~^~~~~~~~~~~~~ BRNN/rnn_util.cpp: In function 'void rnn_predict_disulphides(const string&, const string&, const string&, const string&, const string&, const string&, int)': BRNN/rnn_util.cpp:359:12: 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 'long unsigned int'} [-Wsign-compare] require(B == boost::num_edges(candidate) && ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:348:16: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable] 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 'long unsigned int'} [-Wsign-compare] 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 'long unsigned int'} [-Wsign-compare] require(B == boost::num_edges(bestPatterns[j]) && ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:407:8: 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 'long unsigned int'} [-Wsign-compare] B == boost::num_vertices(bestPatterns[j]) / 2, ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:378:18: warning: unused variable 'nodes' [-Wunused-variable] 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] TrasdType trasd = Options::instance()->getTrasductionType(); ^~~~~ In file included from BRNN/rnn_util.cpp:5: BRNN/RNNs/RecursiveNN.h:1026:23: warning: variable 'indexes' set but not used [-Wunused-but-set-variable] std::pair indexes = Options::instance()->getLayersIndexes(); ^~~~~~~ BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable 'default_precision' [-Wunused-variable] 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:396:65: required from here BRNN/RNNs/StructureSearch.h:977:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 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 'long unsigned int'} [-Wsign-compare] 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:99:47: required from here BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!"); ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1415:38: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1418:38: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 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] 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:99:47: required from here BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int t=0; t::size_type' {aka 'long unsigned int'} [-Wsign-compare] require(_n == toNodes[t]->_encodedInput.size(), "Error!"); ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1492:38: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1495:38: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 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] VertexId vertex_id = boost::get(boost::vertex_index, sdag); ^~~~~~~~~ In file included from BRNN/rnn_util.cpp:6: 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:989:11: 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:396:65: required from here BRNN/RNNs/StructureSearch.h:186:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i=0; i "disulfinder.1" make[2]: Leaving directory '/build/disulfinder-1.2.11' make[1]: Leaving directory '/build/disulfinder-1.2.11' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot 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/ dh_installdirs install -d debian/disulfinder-data/usr/share/disulfinder rm -f debian/disulfinder-data.debhelper.log debian/disulfinder.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/disulfinder-1.2.11' /usr/bin/make DESTDIR=/build/disulfinder-1.2.11/debian/disulfinder prefix=/usr install make[2]: Entering directory '/build/disulfinder-1.2.11' /usr/bin/make -C disulfind/src install make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src' mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/bin cp disulfinder /build/disulfinder-1.2.11/debian/disulfinder/usr/bin/ mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models cp -r ../Models /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ && find /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ -depth -ignore_readdir_race -name .svn -execdir rm -rf {} \; rm -rf /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models/conn/data/sequences_w5 rm -rf /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Predictions rm -rf /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/tmp make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src' mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1 && cp disulfinder.1 /build/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1/ mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples && cp examples/res_id_* /build/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples/ make[2]: Leaving directory '/build/disulfinder-1.2.11' make[1]: Leaving directory '/build/disulfinder-1.2.11' debian/rules override_dh_install make[1]: Entering directory '/build/disulfinder-1.2.11' dh_install install -d debian/.debhelper/generated/disulfinder install -d debian/.debhelper/generated/disulfinder-data mkdir -p /build/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder mv /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/* /build/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder make[1]: Leaving directory '/build/disulfinder-1.2.11' dh_installdocs 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 chown -R 0:0 debian/disulfinder/usr/share/doc chmod -R u\+rw,go=rX debian/disulfinder/usr/share/doc install -p -m0644 debian/copyright debian/disulfinder/usr/share/doc/disulfinder/copyright install -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 -p -m0644 debian/changelog debian/disulfinder-data/usr/share/doc/disulfinder-data/changelog.Debian install -p -m0644 ./ChangeLog debian/disulfinder-data/usr/share/doc/disulfinder-data/changelog install -p -m0644 debian/changelog debian/disulfinder/usr/share/doc/disulfinder/changelog.Debian install -p -m0644 ./ChangeLog debian/disulfinder/usr/share/doc/disulfinder/changelog dh_installman man -l --recode UTF-8 ./debian/disulfinder/usr/share/man/man1/disulfinder.1 > debian/disulfinder/usr/share/man/man1/disulfinder.1.dh-new 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-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/disulfinder-1.2.11' chmod a-x usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb usr/share/man/man1/disulfinder.1 gzip -9nf usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb usr/share/man/man1/disulfinder.1 cd '/build/disulfinder-1.2.11' dh_fixperms find debian/disulfinder-data -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/disulfinder -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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/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 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/man -type f -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-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_strip install -d debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/04 objcopy --only-keep-debug --compress-debug-sections debian/disulfinder/usr/bin/disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/04/49e6bd38aa9583f270074045e6fffb004b6c1d.debug chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/04/49e6bd38aa9583f270074045e6fffb004b6c1d.debug chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/04/49e6bd38aa9583f270074045e6fffb004b6c1d.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/04/49e6bd38aa9583f270074045e6fffb004b6c1d.debug debian/disulfinder/usr/bin/disulfinder install -d debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc ln -s disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc/disulfinder-dbgsym dh_makeshlibs rm -f debian/disulfinder/DEBIAN/shlibs rm -f debian/disulfinder-data/DEBIAN/shlibs dh_shlibdeps install -d debian/disulfinder/DEBIAN dpkg-shlibdeps -Tdebian/disulfinder.substvars debian/disulfinder/usr/bin/disulfinder dh_installdeb install -d debian/disulfinder-data/DEBIAN dh_gencontrol 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 -Pdebian/disulfinder-data -UMulti-Arch echo misc:Depends= >> debian/disulfinder.substvars echo misc:Pre-Depends= >> debian/disulfinder.substvars install -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -Pdebian/.debhelper/disulfinder/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -DPackage=disulfinder-dbgsym "-DDepends=disulfinder (= \${binary:Version})" "-DDescription=debug symbols for disulfinder" -DBuild-Ids=0449e6bd38aa9583f270074045e6fffb004b6c1d -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -Pdebian/disulfinder -UMulti-Arch chmod 0644 -- debian/disulfinder-data/DEBIAN/control chown 0:0 -- debian/disulfinder-data/DEBIAN/control chmod 0644 -- debian/disulfinder/DEBIAN/control chown 0:0 -- debian/disulfinder/DEBIAN/control dh_md5sums 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 chown 0:0 -- debian/disulfinder/DEBIAN/md5sums cd debian/.debhelper/disulfinder/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/disulfinder-data/DEBIAN/md5sums chown 0:0 -- debian/disulfinder-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/disulfinder .. dpkg-deb --build debian/.debhelper/disulfinder/dbgsym-root .. dpkg-deb --build debian/disulfinder-data .. dpkg-deb: building package 'disulfinder' in '../disulfinder_1.2.11-8_arm64.deb'. dpkg-deb: building package 'disulfinder-data' in '../disulfinder-data_1.2.11-8_all.deb'. dpkg-deb: building package 'disulfinder-dbgsym' in '../disulfinder-dbgsym_1.2.11-8_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../disulfinder_1.2.11-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: 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/21812 and its subdirectories I: Current time: Thu Sep 16 14:55:41 -12 2021 I: pbuilder-time-stamp: 1631847341