Sat Jan 18 07:15:07 UTC 2025 I: starting to build disulfinder/trixie/arm64 on jenkins on '2025-01-18 07:14'
Sat Jan 18 07:15:07 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/78773/console.log
Sat Jan 18 07:15:07 UTC 2025 I: Downloading source for trixie/disulfinder=1.2.11-12
--2025-01-18 07:15:08-- http://deb.debian.org/debian/pool/main/d/disulfinder/disulfinder_1.2.11-12.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2201 (2.1K) [text/prs.lines.tag]
Saving to: ‘disulfinder_1.2.11-12.dsc’
0K .. 100% 301M=0s
2025-01-18 07:15:08 (301 MB/s) - ‘disulfinder_1.2.11-12.dsc’ saved [2201/2201]
Sat Jan 18 07:15:08 UTC 2025 I: disulfinder_1.2.11-12.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: disulfinder
Binary: disulfinder, disulfinder-data
Architecture: any all
Version: 1.2.11-12
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Guy Yachdav <gyachdav@rostlab.org>, Laszlo Kajan <lkajan@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://disulfind.dsi.unifi.it/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/disulfinder
Vcs-Git: https://salsa.debian.org/med-team/disulfinder.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libboost-dev, libboost-graph-dev, libf2c2-dev, debhelper
Package-List:
disulfinder deb science optional arch=any
disulfinder-data deb science optional arch=all
Checksums-Sha1:
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407927fbe004d1c16487e4f787cd23d79ce80cdef4e4d17315b967109d5d33ca 8332 disulfinder_1.2.11-12.debian.tar.xz
Files:
a4f0ed137b56fc0674a207351b659eba 2480613 disulfinder_1.2.11.orig.tar.gz
53a5bfd7ad95f806bdee5a7888491ba0 8332 disulfinder_1.2.11-12.debian.tar.xz
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Sat Jan 18 07:15:08 UTC 2025 I: Checking whether the package is not for us
Sat Jan 18 07:15:08 UTC 2025 I: Starting 1st build on remote node codethink01-arm64.debian.net.
Sat Jan 18 07:15:08 UTC 2025 I: Preparing to do remote build '1' on codethink01-arm64.debian.net.
Sat Jan 18 07:18:51 UTC 2025 I: Deleting $TMPDIR on codethink01-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Feb 20 01:38:10 -12 2026
I: pbuilder-time-stamp: 1771594690
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [disulfinder_1.2.11-12.dsc]
I: copying [./disulfinder_1.2.11.orig.tar.gz]
I: copying [./disulfinder_1.2.11-12.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./disulfinder_1.2.11-12.dsc: unsupported subcommand
dpkg-source: info: extracting disulfinder in disulfinder-1.2.11
dpkg-source: info: unpacking disulfinder_1.2.11.orig.tar.gz
dpkg-source: info: unpacking disulfinder_1.2.11-12.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying variable_length_array
dpkg-source: info: applying unknown_escape
dpkg-source: info: applying gcc-6.patch
dpkg-source: info: applying gcc-7.patch
dpkg-source: info: applying cross.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/169441/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='2bde30bc0a314980872a6d3ec90299a3'
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='169441'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/pbuilderrc_ulkj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/b1 --logfile b1/build.log disulfinder_1.2.11-12.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink01-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/169441/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 <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), libboost-dev, libboost-graph-dev, libf2c2-dev, debhelper
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19967 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on libboost-dev; however:
Package libboost-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however:
Package libboost-graph-dev is not installed.
pbuilder-satisfydepends-dummy depends on libf2c2-dev; however:
Package libf2c2-dev is not installed.
pbuilder-satisfydepends-dummy depends on debhelper; however:
Package debhelper is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-dev{a} libboost-graph-dev{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libdebhelper-perl{a} libelf1t64{a} libf2c2{a} libf2c2-dev{a} libfile-stripnondeterminism-perl{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 44.2 MB of archives. After unpacking 321 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB]
Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-13 [91.4 kB]
Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB]
Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB]
Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 21 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 22 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 24 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB]
Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB]
Get: 31 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB]
Get: 32 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4 [10.6 MB]
Get: 33 http://deb.debian.org/debian trixie/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B]
Get: 34 http://deb.debian.org/debian trixie/main arm64 libboost-graph1.83.0 arm64 1.83.0-4 [341 kB]
Get: 35 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83.0 arm64 1.83.0-4 [314 kB]
Get: 36 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB]
Get: 37 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83-dev arm64 1.83.0-4 [338 kB]
Get: 38 http://deb.debian.org/debian trixie/main arm64 libboost-serialization1.83.0 arm64 1.83.0-4 [325 kB]
Get: 39 http://deb.debian.org/debian trixie/main arm64 libboost-serialization1.83-dev arm64 1.83.0-4 [375 kB]
Get: 40 http://deb.debian.org/debian trixie/main arm64 libboost-test1.83.0 arm64 1.83.0-4 [438 kB]
Get: 41 http://deb.debian.org/debian trixie/main arm64 libboost-test1.83-dev arm64 1.83.0-4 [531 kB]
Get: 42 http://deb.debian.org/debian trixie/main arm64 libboost-graph1.83-dev arm64 1.83.0-4 [377 kB]
Get: 43 http://deb.debian.org/debian trixie/main arm64 libboost-graph-dev arm64 1.83.0.2+b2 [3688 B]
Get: 44 http://deb.debian.org/debian trixie/main arm64 libf2c2 arm64 20240504-1+b2 [115 kB]
Get: 45 http://deb.debian.org/debian trixie/main arm64 libf2c2-dev arm64 20240504-1+b2 [126 kB]
Fetched 44.2 MB in 1s (85.0 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
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(Reading database ... 19967 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
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Preparing to unpack .../04-gettext-base_0.22.5-4_arm64.deb ...
Unpacking gettext-base (0.22.5-4) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_arm64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.2-13_arm64.deb ...
Unpacking bsdextrautils (2.40.2-13) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-5_arm64.deb ...
Unpacking m4 (1.4.19-5) ...
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Unpacking autoconf (2.72-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
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Unpacking autopoint (0.22.5-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.23_all.deb ...
Unpacking libdebhelper-perl (13.23) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-2_all.deb ...
Unpacking libtool (2.5.4-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
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Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
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Unpacking dh-strip-nondeterminism (1.14.0-1) ...
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Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ...
Unpacking libelf1t64:arm64 (0.192-4) ...
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Unpacking dwz (0.15-1+b1) ...
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Unpacking libunistring5:arm64 (1.3-1) ...
Selecting previously unselected package libicu72:arm64.
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Unpacking libicu72:arm64 (72.1-6) ...
Selecting previously unselected package libxml2:arm64.
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Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
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Unpacking gettext (0.22.5-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
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Unpacking po-debconf (1.0.21+nmu1) ...
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Unpacking debhelper (13.23) ...
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Unpacking icu-devtools (72.1-6) ...
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I: Building the package
I: Running cd /build/reproducible-path/disulfinder-1.2.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../disulfinder_1.2.11-12_source.changes
dpkg-buildpackage: info: source package disulfinder
dpkg-buildpackage: info: source version 1.2.11-12
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
dh_auto_clean
make -j12 distclean
make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11'
if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi
make[2]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src'
make -C NN clean
make -C Common clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/NN'
rm -f *~ *.o brnn-train brnn-test
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/NN'
make -C SVM clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common'
make -C eig clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM'
rm *~ *.o *.a *.exe SVMClassifier -f
make[4]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common/eig'
rm *.o libeig.a *~ -f
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM'
make[4]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common/eig'
rm *.o libCommon.a Eig Norm *~ -f
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common'
cd SVM && make clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM'
rm *~ *.o *.a *.exe SVMClassifier -f
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/SVM'
cd Input && make clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Input'
rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Input'
cd Output && make clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Output'
rm *.o makeASCIIOutput makeHTMLOutput *~ -f
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Output'
cd FSA-Alignment && make clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/FSA-Alignment'
rm *.o fold_automata viterbi_aligner timed_transitions *~ -f
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/FSA-Alignment'
cd BRNN && make clean
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/BRNN'
rm -f *.o core
rm -f ./RNNs/*.o ./RNNs/core disulfind-conn
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/BRNN'
rm disulfinder disultrainer *.o *~ -f
make[2]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src'
rm -f *.[12345678] *.[12345678].gz
#if [ -d "disulfind" ]; then rm -rf disulfind; fi
if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi
rm -rf patch-stamp \
initial-clean-stamp \
"disulfinder-1.2.11.tar.gz" \
.pc
make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars debian/files
rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11'
dh_auto_build --no-parallel
make -j1 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/disulfinder-1.2.11'
make -C disulfind/src disulfinder
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o
In file included from Input/utils.h:2,
from Input/GlobalDescriptor.cpp:3:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files
| ^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o
In file included from Input/utils.h:2,
from Input/createBRNNDataset.h:1,
from Input/createBRNNDataset.cpp:2:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files
| ^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o
In file included from Input/utils.h:2,
from Input/createKernelDataset.h:1,
from Input/createKernelDataset.cpp:2:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o
Output/makeHTMLOutput.cpp: In function 'void makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)':
Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~~
Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o
Output/makeASCIIOutput.cpp: In function 'void makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)':
Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~~
Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -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/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DataSet.cpp -o BRNN/RNNs/DataSet.o
In file included from BRNN/RNNs/DataSet.cpp:1:
BRNN/RNNs/DataSet.h:19:1: warning: 'typedef' was ignored in this declaration
19 | typedef struct StructuredInstanceTemplate {
| ^~~~~~~
BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)':
BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
86 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()':
BRNN/RNNs/DataSet.h:116:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
116 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h:135:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
135 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.cpp: In constructor 'DataSet::DataSet(const char*, const char*)':
BRNN/RNNs/DataSet.cpp:69:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
69 | if(pos == string::npos)
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.cpp: In member function 'bool DataSet::loadInstances(const char*)':
BRNN/RNNs/DataSet.cpp:141:7: warning: unused variable 'ng' [-Wunused-variable]
141 | int ng = 1;
| ^~
BRNN/RNNs/DataSet.cpp: At global scope:
BRNN/RNNs/DataSet.cpp:14:12: warning: 'int one(const dirent*)' defined but not used [-Wunused-function]
14 | static int one(const struct dirent* unused) {
| ^~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DPAG.cpp -o BRNN/RNNs/DPAG.o
BRNN/RNNs/DPAG.cpp: In function 'float PRMeasure(const DPAG&, const DPAG&, std::vector<float>&)':
BRNN/RNNs/DPAG.cpp:48:7: warning: unused variable 'global_predicted_positives' [-Wunused-variable]
48 | int global_predicted_positives = boost::num_edges(g),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable 'global_actual_positives' [-Wunused-variable]
49 | global_actual_positives = boost::num_edges(gtarget),
| ^~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable 'graphNode' [-Wunused-variable]
52 | Vertex_d graphNode, targetNode;
| ^~~~~~~~~
BRNN/RNNs/DPAG.cpp: In function 'float PrecisionMeasure(const DPAG&, const DPAG&, std::vector<float>&)':
BRNN/RNNs/DPAG.cpp:302:12: warning: unused variable 'graphNode' [-Wunused-variable]
302 | Vertex_d graphNode, targetNode;
| ^~~~~~~~~
BRNN/RNNs/DPAG.cpp: In function 'std::pair<float, float> globalPRMeasure(const DPAG&, const DPAG&, int&, int&, int&, int&, int&, int&, float&)':
BRNN/RNNs/DPAG.cpp:361:12: warning: unused variable 'graphNode' [-Wunused-variable]
361 | Vertex_d graphNode, targetNode, targetNode1;
| ^~~~~~~~~
BRNN/RNNs/DPAG.cpp: In function 'ConfusionTable getPredictionIndexes(const DPAG&, const DPAG&, std::vector<float>&)':
BRNN/RNNs/DPAG.cpp:560:45: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int>, boost::no_property, boost::listS>::config::vertices_size_type' {aka 'long unsigned int'} [-Wsign-compare]
559 | require(true_positives + true_negatives +
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
560 | false_positives + false_negatives ==
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
561 | boost::num_vertices(gpred) * (boost::num_vertices(gpred)-1) / 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable 'weight' [-Wunused-variable]
471 | float weight = 1.0 / boost::num_vertices(gpred);
| ^~~~~~
BRNN/RNNs/DPAG.cpp: In function 'float RecallMeasure(const DPAG&, const DPAG&, std::vector<float>&)':
BRNN/RNNs/DPAG.cpp:573:12: warning: unused variable 'graphNode' [-Wunused-variable]
573 | Vertex_d graphNode, targetNode;
| ^~~~~~~~~
BRNN/RNNs/DPAG.cpp: In function 'bool equal(const DPAG&, const DPAG&)':
BRNN/RNNs/DPAG.cpp:746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
746 | for(int i=0; i<children_1.size(); i++) {
| ~^~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:692:12: warning: unused variable 'node' [-Wunused-variable]
692 | Vertex_d node;
| ^~~~
BRNN/RNNs/DPAG.cpp: In function 'std::pair<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > > 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<boost::property<boost::vertex_index_t, unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
832 | if(vertex_id[*v_i] != n_vertices-1) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:839:29: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare]
839 | if(children.front() == vertex_id[*v_i]+1)
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:844:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
844 | for(int i=0; i<children.size(); i++)
| ~^~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:862:33: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, unsigned int>, long unsigned int>::value_type' {aka 'long unsigned int'} [-Wsign-compare]
862 | if((*it).second.front() == vertex_id[*v_i]-1)
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:867:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
867 | for(int i=0; i<(*it).second.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable 'node' [-Wunused-variable]
813 | Vertex_d node;
| ^~~~
BRNN/RNNs/DPAG.cpp: In function 'DPAG rnndpag_to_dpag(const std::pair<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&)':
BRNN/RNNs/DPAG.cpp:878:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
878 | VertexId vertex_id = boost::get(boost::vertex_index, g);;
| ^~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Options.cpp -o BRNN/RNNs/Options.o
BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_config(const std::string&)':
BRNN/RNNs/Options.cpp:30:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
30 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:36:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
36 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:42:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
42 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:47:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
47 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:61:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
61 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:79:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
79 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
85 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:90:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
90 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:99:29: warning: comparison of integer expressions of different signedness: 'std::vector<bool>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
99 | if(_input_mask.size() != _input_dimension)
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_args(int, char**)':
BRNN/RNNs/Options.cpp:138:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
138 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:144:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
144 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:150:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
150 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:155:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
155 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:169:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
169 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:187:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
187 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:193:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
193 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:198:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
198 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:207:29: warning: comparison of integer expressions of different signedness: 'std::vector<bool>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
207 | if(_input_mask.size() != _input_dimension)
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/protein_util.cpp -o BRNN/protein_util.o
In file included from BRNN/protein_util.cpp:1:
BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder]
211 | int _bp1, _bp2; // bridge partners
| ^~~~
BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder]
206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner
| ^~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)':
BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder]
241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set
| ^~~~~~~~~~~
BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder]
239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment
| ^~~~~
BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder]
245 | SSegment(char symbol):
| ^~~~~~~~
In file included from /usr/include/c++/14/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<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
365 | assert(resHydrScales.size() == numResidues());
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
BRNN/protein_util.cpp:380:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
380 | if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1;
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
BRNN/protein_util.cpp:386:24: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
386 | assert(hAvg.size() == (*c_it).numResidues());
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
BRNN/protein_util.cpp:391:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
391 | for(int i=0; i<hAvg.size(); ++i) {
| ~^~~~~~~~~~~~
BRNN/protein_util.cpp:401:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
401 | assert(seq_pos == resHydrScales.size());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/blast_util.cpp -o BRNN/blast_util.o
BRNN/blast_util.cpp: In member function 'void PSSM::parsePsiBlastReport(const char*)':
BRNN/blast_util.cpp:34:13: warning: unused variable 'prof' [-Wunused-variable]
34 | Profile prof;
| ^~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/rnn_util.cpp -o BRNN/rnn_util.o
In file included from BRNN/rnn_util.cpp:4:
BRNN/RNNs/DataSet.h:19:1: warning: 'typedef' was ignored in this declaration
19 | typedef struct StructuredInstanceTemplate {
| ^~~~~~~
BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)':
BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
86 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()':
BRNN/RNNs/DataSet.h:116:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
116 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h:135:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
135 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from BRNN/rnn_util.cpp:7:
BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder]
211 | int _bp1, _bp2; // bridge partners
| ^~~~
BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder]
206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner
| ^~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)':
BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder]
241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set
| ^~~~~~~~~~~
BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder]
239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment
| ^~~~~
BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder]
245 | SSegment(char symbol):
| ^~~~~~~~
BRNN/rnn_util.cpp: In function 'void create_connectivity_input_data(const std::string&, const std::string&, int, int, const std::string&)':
BRNN/rnn_util.cpp:233:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Profile>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
233 | for(int i=0; i<pssm.size(); ++i)
| ~^~~~~~~~~~~~
BRNN/rnn_util.cpp:277:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Profile>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
277 | if(i >=0 && i < pssm.size())
| ~~^~~~~~~~~~~~~
BRNN/rnn_util.cpp: In function 'void rnn_predict_disulphides(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, int)':
BRNN/rnn_util.cpp:359:19: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int>, boost::no_property, boost::listS>::config::edges_size_type' {aka 'long unsigned int'} [-Wsign-compare]
359 | require(B == boost::num_edges(candidate) &&
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:348:16: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
348 | VertexId vertex_id = boost::get(boost::vertex_index, candidate);
| ^~~~~~~~~
BRNN/rnn_util.cpp:405:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
405 | for(int j=0; j<K && j<bestPatterns.size(); ++j) {
| ~^~~~~~~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:406:15: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int>, boost::no_property, boost::listS>::config::edges_size_type' {aka 'long unsigned int'} [-Wsign-compare]
406 | require(B == boost::num_edges(bestPatterns[j]) &&
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:407:15: warning: comparison of integer expressions of different signedness: 'int' and 'boost::detail::adj_list_gen<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int>, boost::no_property, boost::listS>::config::vertices_size_type' {aka 'long unsigned int'} [-Wsign-compare]
407 | B == boost::num_vertices(bestPatterns[j]) / 2,
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:378:18: warning: unused variable 'nodes' [-Wunused-variable]
378 | vector<Node*> *nodes = it.currenTONodes();
| ^~~~~
In file included from BRNN/rnn_util.cpp:5:
BRNN/RNNs/RecursiveNN.h: In instantiation of 'RecursiveNN<HA_Function, OA_Function, EMP>::RecursiveNN(const char*) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]':
BRNN/rnn_util.cpp:88:73: required from here
88 | rnn = new RecursiveNN<TanH, Sigmoid, MGradientDescent>(model.c_str());
| ^
BRNN/RNNs/RecursiveNN.h:1018:13: warning: unused variable 'trasd' [-Wunused-variable]
1018 | TrasdType trasd = Options::instance()->getTrasductionType();
| ^~~~~
BRNN/RNNs/RecursiveNN.h:1026:23: warning: variable 'indexes' set but not used [-Wunused-but-set-variable]
1026 | std::pair<int, int> indexes = Options::instance()->getLayersIndexes();
| ^~~~~~~
BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable 'default_precision' [-Wunused-variable]
1047 | int default_precision = is.precision();
| ^~~~~~~~~~~~~~~~~
In file included from BRNN/rnn_util.cpp:6:
BRNN/RNNs/StructureSearch.h: In instantiation of 'std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > > StructureSearch::ConnectivityPatternSearch(RNN<T1, T2, T3>*, const std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&, std::vector<float>&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]':
BRNN/rnn_util.cpp:396:37: required from here
396 | search.ConnectivityPatternSearch(rnn, candidates, bestScores);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/StructureSearch.h:977:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
977 | for(int i=0; i<_nodesInputs.size(); ++i)
| ~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/StructureSearch.h:984:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
984 | for(int i=0; i<candidates.size(); ++i) {
| ~^~~~~~~~~~~~~~~~~~
BRNN/RNNs/StructureSearch.h:980:7: warning: unused variable 'num_nodes' [-Wunused-variable]
980 | int num_nodes = _toNodes.size();
| ^~~~~~~~~
BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN<HA_Function, OA_Function, EMP>::fPropagateInput(std::vector<Node*>&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >]':
BRNN/RNNs/RecursiveNN.h:1356:3: required from 'void RecursiveNN<HA_Function, OA_Function, EMP>::propagateStructuredInput(std::vector<Node*>&, const std::pair<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]'
1356 | fPropagateInput(toNodes, sdags.first);
| ^~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:99:32: required from here
99 | rnn->propagateStructuredInput(*nodes, *dpags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1390 | require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!");
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1415:45: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare]
1415 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) {
BRNN/RNNs/RecursiveNN.h:1418:45: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
1418 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) {
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
1384 | VertexId vertex_id = boost::get(boost::vertex_index, sdag);
| ^~~~~~~~~
BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN<HA_Function, OA_Function, EMP>::bPropagateInput(std::vector<Node*>&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >]':
BRNN/RNNs/RecursiveNN.h:1359:19: required from 'void RecursiveNN<HA_Function, OA_Function, EMP>::propagateStructuredInput(std::vector<Node*>&, const std::pair<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >, boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]'
1359 | if(_process_dr) bPropagateInput(toNodes, sdags.second);
| ^~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:99:32: required from here
99 | rnn->propagateStructuredInput(*nodes, *dpags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Node*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1470 | for(int t=0; t<toNodes.size(); t++) {
| ~^~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1471:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
1471 | require(_n == toNodes[t]->_encodedInput.size(), "Error!");
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1492:45: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare]
1492 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) {
BRNN/RNNs/RecursiveNN.h:1495:45: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
1495 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) {
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1465:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
1465 | VertexId vertex_id = boost::get(boost::vertex_index, sdag);
| ^~~~~~~~~
BRNN/RNNs/StructureSearch.h: In instantiation of 'float StructureSearch::RNNMeasure(const DPAG&, RNN<T1, T2, T3>*, std::vector<Node*>&, std::vector<float>&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN; DPAG = boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> >]':
BRNN/RNNs/StructureSearch.h:990:17: required from 'std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > > StructureSearch::ConnectivityPatternSearch(RNN<T1, T2, T3>*, const std::vector<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, boost::property<boost::vertex_index_t, unsigned int>, boost::property<boost::edge_index_t, unsigned int> > >&, std::vector<float>&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]'
990 | RNNMeasure(candidates[i], net_scorer, _toNodes, localScores);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/rnn_util.cpp:396:37: required from here
396 | search.ConnectivityPatternSearch(rnn, candidates, bestScores);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/StructureSearch.h:186:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Node*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
186 | for(int i=0; i<toNodes.size(); i++) {
| ~^~~~~~~~~~~~~~~
make -C Common lib
make[4]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Vector.cpp -o Vector.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Util.cpp -o Util.o
Util.cpp: In function 'std::vector<std::__cxx11::basic_string<char> > Util::tokenize(const std::string&, const std::string&, bool)':
Util.cpp:135:12: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
135 | delete str;
| ^~~
Util.cpp:127:38: note: returned from 'void* operator new [](std::size_t)'
127 | char *str = new char[s.length()+1];
| ^
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c CommonMethods.cpp -o CommonMethods.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c ConfusionMatrix.cpp -o ConfusionMatrix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Exception.cpp -o Exception.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Statistics.cpp -o Statistics.o
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balanc.o eig/balanc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balbak.o eig/balbak.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/cdiv.o eig/cdiv.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/elmhes.o eig/elmhes.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/eltran.o eig/eltran.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr.o eig/hqr.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr2.o eig/hqr2.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/rg.o eig/rg.c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c coords.cpp -o coords.o
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/d_sign.o eig/d_sign.c
ar rvs libCommon.a Vector.o Util.o CommonMethods.o ConfusionMatrix.o Exception.o Statistics.o eig/balanc.o eig/balbak.o eig/cdiv.o eig/elmhes.o eig/eltran.o eig/hqr.o eig/hqr2.o eig/rg.o coords.o eig/d_sign.o
ar: creating libCommon.a
a - Vector.o
a - Util.o
a - CommonMethods.o
a - ConfusionMatrix.o
a - Exception.o
a - Statistics.o
a - eig/balanc.o
a - eig/balbak.o
a - eig/cdiv.o
a - eig/elmhes.o
a - eig/eltran.o
a - eig/hqr.o
a - eig/hqr2.o
a - eig/rg.o
a - coords.o
a - eig/d_sign.o
make[4]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src/Common'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/disulfinder-1.2.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c disulfinder.cpp -o disulfinder.o
In file included from Input/utils.h:2,
from disulfinder.cpp:8:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files
| ^~~~~~~~
g++ -o disulfinder disulfinder.o Input/GlobalDescriptor.o Input/createBRNNDataset.o Input/createKernelDataset.o Input/makeWindow.o Input/makeSparseVector.o Input/Protein.o Input/buildXfolds.o SVM/SVMClassifier.o Output/makeHTMLOutput.o Output/utils.o Output/makeASCIIOutput.o FSA-Alignment/fsa.o FSA-Alignment/viterbi_aligner.o NN/multi-array.o NN/array.o NN/brnn-model.o NN/brnn-test.o BRNN/RNNs/Node.o BRNN/RNNs/StructureSearch.o BRNN/RNNs/DataSet.o BRNN/RNNs/DPAG.o BRNN/RNNs/Options.o BRNN/protein_util.o BRNN/blast_util.o BRNN/rnn_util.o -Wl,-z,relro -Wl,-z,now -LCommon/ -lCommon
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src'
sed -e 's|__datadir__||g;s|__docdir__|/usr/share/doc/disulfinder|g;s|__pkgdatadir__||g;s|__PREFIX__|/usr|g;s|__sysconfdir__||g;s|__VERSION__|1.2.11|g;' "disulfinder.pod" | \
pod2man -c 'User Commands' -r '1.2.11' -name DISULFINDER > "disulfinder.1"
make[2]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11'
make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-KM81m0SM
create-stamp debian/debhelper-build-stamp
dh_prep
rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars
rm -fr -- debian/.debhelper/generated/disulfinder/ debian/disulfinder/ debian/tmp/ debian/.debhelper/generated/disulfinder-data/ debian/disulfinder-data/
rm -f debian/disulfinder-data.debhelper.log debian/disulfinder.debhelper.log
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11'
/usr/bin/make DESTDIR=/build/reproducible-path/disulfinder-1.2.11/debian/disulfinder prefix=/usr install
make[2]: Entering directory '/build/reproducible-path/disulfinder-1.2.11'
/usr/bin/make -C disulfind/src install
make[3]: Entering directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src'
mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/bin
cp disulfinder /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/bin/
mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder
mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models
cp -r ../Models /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ && find /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ -depth -ignore_readdir_race -name .svn -execdir rm -rf {} \;
rm -rf /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models/conn/data/sequences_w5
rm -rf /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Predictions
rm -rf /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/tmp
make[3]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11/disulfind/src'
mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1 && cp disulfinder.1 /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1/
mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples && cp examples/res_id_* /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples/
make[2]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11'
make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/disulfinder-1.2.11'
dh_install
mkdir -p /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder
mv /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/* /build/reproducible-path/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder
make[1]: Leaving directory '/build/reproducible-path/disulfinder-1.2.11'
dh_installdocs
install -m0755 -d debian/disulfinder/usr/share/doc/disulfinder
cp --reflink=auto -a ./debian/upstream/metadata debian/disulfinder/usr/share/doc/disulfinder
cp --reflink=auto -a ./debian/README.test debian/disulfinder/usr/share/doc/disulfinder
cp --reflink=auto -a ./debian/tests/installation-test debian/disulfinder/usr/share/doc/disulfinder
chmod -R u\+rw,go=rX debian/disulfinder/usr/share/doc
install -p -m0644 debian/copyright debian/disulfinder/usr/share/doc/disulfinder/copyright
install -m0755 -d debian/disulfinder-data/usr/share/doc/disulfinder-data
install -p -m0644 debian/copyright debian/disulfinder-data/usr/share/doc/disulfinder-data/copyright
dh_installchangelogs
install -m0755 -d debian/disulfinder-data/usr/share/doc/disulfinder-data
install -p -m0644 debian/.debhelper/generated/disulfinder-data/dh_installchangelogs.dch.trimmed debian/disulfinder-data/usr/share/doc/disulfinder-data/changelog.Debian
install -p -m0644 ./ChangeLog debian/disulfinder-data/usr/share/doc/disulfinder-data/changelog
install -m0755 -d debian/disulfinder/usr/share/doc/disulfinder
install -p -m0644 debian/.debhelper/generated/disulfinder/dh_installchangelogs.dch.trimmed debian/disulfinder/usr/share/doc/disulfinder/changelog.Debian
install -p -m0644 ./ChangeLog debian/disulfinder/usr/share/doc/disulfinder/changelog
dh_installman
man-recode --to-code UTF-8 --suffix .dh-new debian/disulfinder/usr/share/man/man1/disulfinder.1
mv debian/disulfinder/usr/share/man/man1/disulfinder.1.dh-new debian/disulfinder/usr/share/man/man1/disulfinder.1
chmod 0644 -- debian/disulfinder/usr/share/man/man1/disulfinder.1
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
cd debian/disulfinder
cd debian/disulfinder-data
chmod a-x usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/man/man1/disulfinder.1
chmod a-x usr/share/doc/disulfinder-data/changelog usr/share/doc/disulfinder-data/changelog.Debian
gzip -9nf usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/man/man1/disulfinder.1
gzip -9nf usr/share/doc/disulfinder-data/changelog usr/share/doc/disulfinder-data/changelog.Debian
cd '/build/reproducible-path/disulfinder-1.2.11'
cd '/build/reproducible-path/disulfinder-1.2.11'
dh_fixperms
find debian/disulfinder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/disulfinder-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/disulfinder-data/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
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-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
dwz -- debian/disulfinder/usr/bin/disulfinder
dh_strip -a
install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/b4
objcopy --only-keep-debug --compress-debug-sections debian/disulfinder/usr/bin/disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/b4/6c52ce9e26c72acd3a0be4db6d26bd2fad5b53.debug
chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/b4/6c52ce9e26c72acd3a0be4db6d26bd2fad5b53.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/b4/6c52ce9e26c72acd3a0be4db6d26bd2fad5b53.debug debian/disulfinder/usr/bin/disulfinder
install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc
ln -s disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc/disulfinder-dbgsym
install -m0755 -d debian/.debhelper/disulfinder
dh_makeshlibs -a
rm -f debian/disulfinder/DEBIAN/shlibs
dh_shlibdeps -a
install -m0755 -d debian/disulfinder/DEBIAN
dpkg-shlibdeps -Tdebian/disulfinder.substvars debian/disulfinder/usr/bin/disulfinder
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb
install -m0755 -d debian/disulfinder/DEBIAN
install -m0755 -d debian/disulfinder-data/DEBIAN
dh_gencontrol
install -m0755 -d debian/disulfinder-data/DEBIAN
echo misc:Depends= >> debian/disulfinder-data.substvars
echo misc:Pre-Depends= >> debian/disulfinder-data.substvars
dpkg-gencontrol -pdisulfinder-data -ldebian/changelog -Tdebian/disulfinder-data.substvars -cdebian/control -Pdebian/disulfinder-data
install -m0755 -d debian/disulfinder/DEBIAN
echo misc:Depends= >> debian/disulfinder.substvars
echo misc:Pre-Depends= >> debian/disulfinder.substvars
install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN
dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -cdebian/control -Pdebian/.debhelper/disulfinder/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=disulfinder-dbgsym "-DDepends=disulfinder (= \${binary:Version})" "-DDescription=debug symbols for disulfinder" -DBuild-Ids=b46c52ce9e26c72acd3a0be4db6d26bd2fad5b53 -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/disulfinder-data/DEBIAN/control
chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -cdebian/control -Pdebian/disulfinder
chmod 0644 -- debian/disulfinder/DEBIAN/control
dh_md5sums
install -m0755 -d debian/disulfinder/DEBIAN
install -m0755 -d debian/disulfinder-data/DEBIAN
cd debian/disulfinder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/disulfinder-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/disulfinder/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN
cd debian/.debhelper/disulfinder/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/disulfinder-data/DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/disulfinder ..
dpkg-deb --root-owner-group --build debian/.debhelper/disulfinder/dbgsym-root ..
dpkg-deb: building package 'disulfinder-dbgsym' in '../disulfinder-dbgsym_1.2.11-12_arm64.deb'.
dpkg-deb --root-owner-group --build debian/disulfinder-data ..
dpkg-deb: building package 'disulfinder' in '../disulfinder_1.2.11-12_arm64.deb'.
dpkg-deb: building package 'disulfinder-data' in '../disulfinder-data_1.2.11-12_all.deb'.
dpkg-genbuildinfo --build=binary -O../disulfinder_1.2.11-12_arm64.buildinfo
dpkg-genchanges --build=binary -O../disulfinder_1.2.11-12_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)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/169441 and its subdirectories
I: Current time: Fri Feb 20 01:41:50 -12 2026
I: pbuilder-time-stamp: 1771594910
Sat Jan 18 07:18:52 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net.
Sat Jan 18 07:18:52 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net.
Sat Jan 18 07:21:27 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net.
Sat Jan 18 07:21:27 UTC 2025 I: disulfinder_1.2.11-12_arm64.changes:
Format: 1.8
Date: Thu, 20 Jan 2022 11:36:56 +0100
Source: disulfinder
Binary: disulfinder disulfinder-data disulfinder-dbgsym
Architecture: all arm64
Version: 1.2.11-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
disulfinder - cysteines disulfide bonding state and connectivity predictor
disulfinder-data - data files for predictor of disulfide bonds in proteins
Changes:
disulfinder (1.2.11-12) unstable; urgency=medium
.
* Upstream download vanished
* Standards-Version: 4.6.0 (routine-update)
* Add missing build dependency on dh addon.
* Apply multi-arch hints.
+ disulfinder-data: Add Multi-Arch: foreign.
Checksums-Sha1:
c0e3f8d8ba191891b6fa3e0c43936bfc7945ceaa 1125600 disulfinder-data_1.2.11-12_all.deb
6fbb8e44f99a5178efe7b7eca7111c3e6bd20973 3538036 disulfinder-dbgsym_1.2.11-12_arm64.deb
048fc186677e9ba4727003dc6fb34b56d8ff4eae 5848 disulfinder_1.2.11-12_arm64.buildinfo
0a98082d2fa0bfa2e3558de692ce8215110b77b1 217832 disulfinder_1.2.11-12_arm64.deb
Checksums-Sha256:
d9660f8b02ffd7c141d78ca63c2b801bf9330b800885ea60e7f0830d2f82aa92 1125600 disulfinder-data_1.2.11-12_all.deb
f8475c9babcd82e2dab8371471c46e74629a6d34b99b1ca24d85eb17443a4fdb 3538036 disulfinder-dbgsym_1.2.11-12_arm64.deb
23c4cc25d4e519adb707491d06c24d5749aa0cc42d10feea1a940047f4e36019 5848 disulfinder_1.2.11-12_arm64.buildinfo
f125909f1c415a994800fd1a9298ef305d19266553e853bdade4dc3f60c8544e 217832 disulfinder_1.2.11-12_arm64.deb
Files:
a63e8d964808d1fe0f57a27a95107fc7 1125600 science optional disulfinder-data_1.2.11-12_all.deb
8eca80c193efc4c9b70c3831f67e2009 3538036 debug optional disulfinder-dbgsym_1.2.11-12_arm64.deb
66f234b28c84a29122306a0c222eb1f4 5848 science optional disulfinder_1.2.11-12_arm64.buildinfo
bac4cb48e93792fd5f173c4b9bd725ab 217832 science optional disulfinder_1.2.11-12_arm64.deb
Sat Jan 18 07:21:28 UTC 2025 I: diffoscope 285 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_14-78773.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/disulfinder_1.2.11-12.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/disulfinder_1.2.11-12.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/disulfinder_1.2.11-12.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/b1/disulfinder_1.2.11-12_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.uAkknBhY/b2/disulfinder_1.2.11-12_arm64.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: 0.359s)
0.359s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.056s)
0.056s 12 calls diffoscope.comparators.binary.FilesystemFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 633ms
CPU time consumed: 633ms
Sat Jan 18 07:21:29 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists.
Sat Jan 18 07:21:29 UTC 2025 I: disulfinder from trixie built successfully and reproducibly on arm64.
Sat Jan 18 07:21:30 UTC 2025 I: Submitting .buildinfo files to external archives:
Sat Jan 18 07:21:30 UTC 2025 I: Submitting 8.0K b1/disulfinder_1.2.11-12_arm64.buildinfo.asc
Sat Jan 18 07:21:31 UTC 2025 I: Submitting 8.0K b2/disulfinder_1.2.11-12_arm64.buildinfo.asc
Sat Jan 18 07:21:32 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Jan 18 07:21:32 UTC 2025 I: Done submitting .buildinfo files.
Sat Jan 18 07:21:32 UTC 2025 I: Removing signed disulfinder_1.2.11-12_arm64.buildinfo.asc files:
removed './b1/disulfinder_1.2.11-12_arm64.buildinfo.asc'
removed './b2/disulfinder_1.2.11-12_arm64.buildinfo.asc'