Wed May 6 01:54:58 UTC 2020 I: starting to build disulfinder/buster/i386 on jenkins on '2020-05-06 01:54' Wed May 6 01:54:58 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_13/7399/console.log Wed May 6 01:54:58 UTC 2020 I: Downloading source for buster/disulfinder=1.2.11-8 --2020-05-06 01:54:58-- http://deb.debian.org/debian/pool/main/d/disulfinder/disulfinder_1.2.11-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2180 (2.1K) Saving to: ‘disulfinder_1.2.11-8.dsc’ 0K .. 100% 106M=0s 2020-05-06 01:54:58 (106 MB/s) - ‘disulfinder_1.2.11-8.dsc’ saved [2180/2180] Wed May 6 01:54:58 UTC 2020 I: disulfinder_1.2.11-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: disulfinder Binary: disulfinder, disulfinder-data Architecture: any all Version: 1.2.11-8 Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan , Andreas Tille Homepage: http://disulfind.dsi.unifi.it/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/disulfinder Vcs-Git: https://salsa.debian.org/med-team/disulfinder.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev 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 6f1b8adf28a7f68eb9ab1017d404cc8ff219000b 7588 disulfinder_1.2.11-8.debian.tar.xz Checksums-Sha256: d653aaac3ea26e9f6106a371de4f43d05b781a8b8b690c97820e4b27ea9d3495 2480613 disulfinder_1.2.11.orig.tar.gz 8a101f70997f8df0fcf75ae44be28548ffed2128ead3ad7cc9b60655f8b8630d 7588 disulfinder_1.2.11-8.debian.tar.xz Files: a4f0ed137b56fc0674a207351b659eba 2480613 disulfinder_1.2.11.orig.tar.gz c28edeb4b97d4c55fcc1e4b94796db9b 7588 disulfinder_1.2.11-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAluntPgRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGNlg//d8PAW3d5XTdQVkWgT3Z9Q6jOJ72yU8hn XPmnFWXI60NfpaBpfUi/JjxyY0FxpAJme5S0+A4Dbj/luqKetvQNMdglf5W53n6V DrEh3OQvVI92PBm/d2cvxk7PrLDUsQZiRFj4djGVMxltgH2HusCklHTR91svF2A2 GT91vG3Vf/1DKTMaSUoWCl9WqhCJorNkZ/n2vRMfsmqANkb1vFoVlLGYJAh0mxqI FU94cJPipfS5exfINcsjUJVxL6mUAwC0ea7s4cWEhX3K5+nIhVAhBayc/Vc+mGO1 xL9mHoHCbTotAVsGo8hD6enZNN05jHvVxkpF3VOXyniS3+U4SPCdIUqzhbfycDi8 jLC84az+dXL/x+ipygLe2Ikx0T+myP9N3zWHCviVR+GsYKnsQFijGDoJFO15KmDj Fsemx1UAo2x/JgScSc2vMJfavWyuB4evw2+hSu2I9p48cKQQiFNDROfTv3zJKICm A4AQ/a/RP2InZNlJzai//Ya94ebLhcExaf+FhfTLwYw4y64Je5gEc2YDeWP5LWVM nzkkeuXcyMD4M6/YewREOug95pzr60VVtmFW34h1diO/4muEOf4XAPAirHDSiehM fxE3xu1WncrnNn1+qPuEpMpgXTXuc6mP7OaMHCsd3bLDAkltU6kT5AJRcb6VSa/j +d9te5pex8U= =/H2a -----END PGP SIGNATURE----- Wed May 6 01:54:58 UTC 2020 I: Checking whether the package is not for us Wed May 6 01:54:58 UTC 2020 I: Starting 1st build on remote node profitbricks-build12-i386.debian.net. Wed May 6 01:54:58 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build12-i386.debian.net. Wed May 6 02:06:23 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. W: cgroups are not available on the host, not using them. unshare: unshare failed: Cannot allocate memory W: pbuilder: unshare CLONE_NEWNET not available I: pbuilder: network access is available during build! I: Current time: Tue May 5 13:55:02 -12 2020 I: pbuilder-time-stamp: 1588730102 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [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 '/root/.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 -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), 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 ... 19231 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. 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 31.3 MB of archives. After unpacking 229 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6 [8443 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libboost-chrono1.67.0 i386 1.67.0-13+deb10u1 [235 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libboost1.67-dev i386 1.67.0-13+deb10u1 [8388 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libboost-dev i386 1.67.0.1 [3864 B] Get: 37 http://deb.debian.org/debian buster/main i386 libboost-regex1.67.0 i386 1.67.0-13+deb10u1 [508 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libboost-graph1.67.0 i386 1.67.0-13+deb10u1 [324 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libboost-serialization1.67.0 i386 1.67.0-13+deb10u1 [325 kB] Get: 40 http://deb.debian.org/debian buster/main i386 libboost-serialization1.67-dev i386 1.67.0-13+deb10u1 [367 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libboost-timer1.67.0 i386 1.67.0-13+deb10u1 [232 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libboost-test1.67.0 i386 1.67.0-13+deb10u1 [471 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libboost-test1.67-dev i386 1.67.0-13+deb10u1 [525 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libboost-graph1.67-dev i386 1.67.0-13+deb10u1 [332 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libboost-graph-dev i386 1.67.0.1 [3752 B] Get: 46 http://deb.debian.org/debian buster/main i386 libf2c2 i386 20130926-3 [124 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libf2c2-dev i386 20130926-3 [134 kB] Fetched 31.3 MB in 5s (5930 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19231 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.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_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.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_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.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:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6_i386.deb ... Unpacking libicu63:i386 (63.1-6) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... Selecting previously unselected package libncurses6:i386. Preparing to unpack .../28-libncurses6_6.1+20181013-2+deb10u2_i386.deb ... Unpacking libncurses6:i386 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../29-gettext_0.19.8.1-9_i386.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:i386. Preparing to unpack .../33-libboost-chrono1.67.0_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-chrono1.67.0:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost1.67-dev:i386. Preparing to unpack .../34-libboost1.67-dev_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost1.67-dev:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-dev:i386. Preparing to unpack .../35-libboost-dev_1.67.0.1_i386.deb ... Unpacking libboost-dev:i386 (1.67.0.1) ... Selecting previously unselected package libboost-regex1.67.0:i386. Preparing to unpack .../36-libboost-regex1.67.0_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-regex1.67.0:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-graph1.67.0:i386. Preparing to unpack .../37-libboost-graph1.67.0_1.67.0-13+deb10u1_i386.deb ... Unpacking libboost-graph1.67.0:i386 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-serialization1.67.0:i386. Preparing to unpack .../38-libboost-serialization1.67.0_1.67.0-13+deb10u1_i386.deb ... 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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 i386 fakeroot debian/rules clean dh clean dh_auto_clean make -j10 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[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make -C SVM clean 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 '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 '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 '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 '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 '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 '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, unsigned int>::value_type' {aka '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, unsigned int>::value_type' {aka '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 'unsigned int'} [-Wsign-compare] 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] 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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] for(int i=0; i::size_type' {aka '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 '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 '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 '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 '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 '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 '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 '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 'unsigned int'} [-Wsign-compare] for(int t=0; t::size_type' {aka '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 '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 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 cd '/build/disulfinder-1.2.11' 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 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/disulfinder-data -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/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/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 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/disulfinder/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x 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-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 dh_missing dh_strip install -d debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c4 objcopy --only-keep-debug --compress-debug-sections debian/disulfinder/usr/bin/disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c4/52062c00dc7816b7b22cffd223eaeff17cbd9c.debug chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c4/52062c00dc7816b7b22cffd223eaeff17cbd9c.debug chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c4/52062c00dc7816b7b22cffd223eaeff17cbd9c.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/c4/52062c00dc7816b7b22cffd223eaeff17cbd9c.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=c452062c00dc7816b7b22cffd223eaeff17cbd9c -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/DEBIAN/control chown 0:0 -- debian/disulfinder/DEBIAN/control chmod 0644 -- debian/disulfinder-data/DEBIAN/control chown 0:0 -- debian/disulfinder-data/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/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/disulfinder-data/DEBIAN/md5sums chown 0:0 -- debian/disulfinder-data/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/.debhelper/disulfinder/dbgsym-root .. dpkg-deb --build debian/disulfinder .. dpkg-deb --build debian/disulfinder-data .. 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_i386.deb'. dpkg-deb: building package 'disulfinder' in '../disulfinder_1.2.11-8_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../disulfinder_1.2.11-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: 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/24478 and its subdirectories I: Current time: Tue May 5 14:06:23 -12 2020 I: pbuilder-time-stamp: 1588730783 Wed May 6 02:06:24 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build6-i386.debian.net. Wed May 6 02:06:24 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build6-i386.debian.net. Wed May 6 02:08:06 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. Wed May 6 02:08:06 UTC 2020 I: disulfinder_1.2.11-8_i386.changes: Format: 1.8 Date: Sun, 23 Sep 2018 17:15:15 +0200 Source: disulfinder Binary: disulfinder disulfinder-data disulfinder-dbgsym Architecture: all i386 Version: 1.2.11-8 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 (1.2.11-8) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata: - yamllint cleanliness - added references to registries . [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Do not parse d/changelog Checksums-Sha1: b37ed067bd97ff10492f6d7f14a7418c9501c66f 1125984 disulfinder-data_1.2.11-8_all.deb e309fe83e4dd776c9a700fcc2fa99abffabdf6fe 4018996 disulfinder-dbgsym_1.2.11-8_i386.deb 6d0fcef7ae33f36001757d364cdd83bdda45ea5a 5534 disulfinder_1.2.11-8_i386.buildinfo 72362b28b6f1108e88f3b9a2423b05893f2f02b2 247628 disulfinder_1.2.11-8_i386.deb Checksums-Sha256: d100a2843bf32cb9473ee8b9edfe5a5e0b2029d55c1a93a333f7d646e177b236 1125984 disulfinder-data_1.2.11-8_all.deb cc432ae9cd4321a3738a9898171451c04cfa21699cd4a6b64211a7522d8e176b 4018996 disulfinder-dbgsym_1.2.11-8_i386.deb c6f9741f636f59b74344013adeb183cf463347d4ed6f6ad0d8b052514cbaba20 5534 disulfinder_1.2.11-8_i386.buildinfo ba2f62ac93a165b75491867274bd0212253f4440e680d2cb85635f22085f8f60 247628 disulfinder_1.2.11-8_i386.deb Files: 4b7e41f1ee9380d33dda4afd6a5dcdd4 1125984 science optional disulfinder-data_1.2.11-8_all.deb 386912191df88258de04603816d1e6a5 4018996 debug optional disulfinder-dbgsym_1.2.11-8_i386.deb 954c6f6e350a4c8832015e2fdaea75c1 5534 science optional disulfinder_1.2.11-8_i386.buildinfo 4f31a466908ae2aad56facd421d6cffe 247628 science optional disulfinder_1.2.11-8_i386.deb Wed May 6 02:08:08 UTC 2020 I: diffoscope 143 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.U9pkbAG567/disulfinder_1.2.11-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.U9pkbAG567/disulfinder_1.2.11-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.U9pkbAG567/disulfinder_1.2.11-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.U9pkbAG567/b1/disulfinder_1.2.11-8_i386.changes /srv/reproducible-results/rbuild-debian/tmp.U9pkbAG567/b2/disulfinder_1.2.11-8_i386.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: 0.304s) 0.304s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.066s) 0.066s 10 calls diffoscope.comparators.binary.FilesystemFile Wed May 6 02:08:11 UTC 2020 I: diffoscope 143 found no differences in the changes files, and a .buildinfo file also exists. Wed May 6 02:08:11 UTC 2020 I: disulfinder from buster built successfully and reproducibly on i386. Wed May 6 02:08:13 UTC 2020 I: Submitting .buildinfo files to external archives: Wed May 6 02:08:13 UTC 2020 I: Submitting 8.0K b1/disulfinder_1.2.11-8_i386.buildinfo.asc Wed May 6 02:08:13 UTC 2020 I: Submitting 8.0K b2/disulfinder_1.2.11-8_i386.buildinfo.asc Wed May 6 02:08:15 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 6 02:08:15 UTC 2020 I: Done submitting .buildinfo files. Wed May 6 02:08:15 UTC 2020 I: Removing signed disulfinder_1.2.11-8_i386.buildinfo.asc files: removed './b1/disulfinder_1.2.11-8_i386.buildinfo.asc' removed './b2/disulfinder_1.2.11-8_i386.buildinfo.asc'