https://launchpad.net/ubuntu/+source/disulfinder/1.2.11-8build1/+build/19101447 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-098 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu1 dpkg-dev_1.19.7ubuntu2 python-debian_0.1.36build1. Syncing the system clock with the buildd NTP service... 3 Apr 23:09:50 ntpdate[107097]: adjust time server 10.211.37.1 offset -0.000571 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 --image-type chroot /home/buildd/filecache-default/88ad86cb2b525f1abddded96eadf8014548f7845 Creating target for build PACKAGEBUILD-19101447 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 Starting target for build PACKAGEBUILD-19101447 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-19101447 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 Updating target for build PACKAGEBUILD-19101447 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [265 kB] Ign:2 http://archive-team.internal/bootstrap/riscv64 focal InRelease Get:3 http://archive-team.internal/bootstrap/riscv64 focal Release [757 B] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [265 kB] Ign:5 http://archive-team.internal/bootstrap/riscv64 focal Release.gpg Get:6 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 Packages [879 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main riscv64 Packages [694 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main Translation-en [501 kB] Get:9 http://ftpmaster.internal/ubuntu focal/universe riscv64 Packages [5395 kB] Get:10 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5127 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 Packages [20.7 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [22.9 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/universe riscv64 Packages [87.3 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [100 kB] Get:15 http://ftpmaster.internal/ubuntu focal-proposed/multiverse Translation-en [8856 B] Fetched 13.4 MB in 38s (356 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: coreutils liblocale-gettext-perl libperl5.30 libtext-charwidth-perl libtext-iconv-perl perl-base 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 6037 kB of archives. After this operation, 6144 B of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main riscv64 coreutils riscv64 8.30-3ubuntu2 [1158 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main riscv64 perl-base riscv64 5.30.0-9build1 [1419 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main riscv64 liblocale-gettext-perl riscv64 1.07-4 [16.5 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-charwidth-perl riscv64 0.04-10 [9460 B] Get:5 http://ftpmaster.internal/ubuntu focal/main riscv64 libtext-iconv-perl riscv64 1.7-7 [13.2 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main riscv64 libperl5.30 riscv64 5.30.0-9build1 [3422 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6037 kB in 2s (2939 kB/s) (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../coreutils_8.30-3ubuntu2_riscv64.deb ... Unpacking coreutils (8.30-3ubuntu2) over (8.30-3ubuntu2) ... Setting up coreutils (8.30-3ubuntu2) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../perl-base_5.30.0-9build1_riscv64.deb ... Unpacking perl-base (5.30.0-9build1) over (5.30.0-9build1) ... Setting up perl-base (5.30.0-9build1) ... (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4) over (1.07-4) ... Preparing to unpack .../libtext-charwidth-perl_0.04-10_riscv64.deb ... Unpacking libtext-charwidth-perl (0.04-10) over (0.04-10) ... Preparing to unpack .../libtext-iconv-perl_1.7-7_riscv64.deb ... Unpacking libtext-iconv-perl (1.7-7) over (1.7-7) ... Preparing to unpack .../libperl5.30_5.30.0-9build1_riscv64.deb ... Unpacking libperl5.30:riscv64 (5.30.0-9build1) over (5.30.0-9build1) ... Setting up libtext-iconv-perl (1.7-7) ... Setting up libtext-charwidth-perl (0.04-10) ... Setting up libperl5.30:riscv64 (5.30.0-9build1) ... Setting up liblocale-gettext-perl (1.07-4) ... Processing triggers for libc-bin (2.31-0ubuntu6~riscv64.1) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19101447 riscv64 focal -c chroot:build-PACKAGEBUILD-19101447 --arch=riscv64 --dist=focal --nolog disulfinder_1.2.11-8build1.dsc Initiating build PACKAGEBUILD-19101447 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-098 +==============================================================================+ | disulfinder 1.2.11-8build1 (riscv64) Fri, 03 Apr 2020 23:13:00 +0000 | +==============================================================================+ Package: disulfinder Version: 1.2.11-8build1 Source Version: 1.2.11-8build1 Distribution: focal Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19101447/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/disulfinder-7RcVxa/resolver-tuZ3FA' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- disulfinder_1.2.11-8build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/disulfinder-7RcVxa/disulfinder-1.2.11' with '<>' I: NOTICE: Log filtering will replace 'build/disulfinder-7RcVxa' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev, build-essential, fakeroot Filtered Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [388 B] Get:5 copy:/<>/apt_archive ./ Packages [474 B] Fetched 1819 B in 1s (2145 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libgpm2 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-dev libboost-graph-dev libboost-graph1.71-dev libboost-graph1.71.0 libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-test1.71-dev libboost-test1.71.0 libboost1.71-dev libbsd0 libcroco3 libdebhelper-perl libelf1 libf2c2 libf2c2-dev libfile-stripnondeterminism-perl libglib2.0-0 libicu-dev libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf tzdata Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc graphviz libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev icu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-dev libboost-graph-dev libboost-graph1.71-dev libboost-graph1.71.0 libboost-regex1.71-dev libboost-regex1.71.0 libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-test1.71-dev libboost-test1.71.0 libboost1.71-dev libbsd0 libcroco3 libdebhelper-perl libelf1 libf2c2 libf2c2-dev libfile-stripnondeterminism-perl libglib2.0-0 libicu-dev libicu66 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy tzdata 0 upgraded, 50 newly installed, 0 to remove and 0 not upgraded. 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Get:39 http://ftpmaster.internal/ubuntu focal/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main riscv64 po-debconf all 1.0.21 [233 kB] Get:41 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libboost-test1.71.0 riscv64 1.71.0-6ubuntu5+riscv64.1 [421 kB] Get:42 http://ftpmaster.internal/ubuntu focal-proposed/main riscv64 debhelper all 12.10ubuntu1 [877 kB] Get:43 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libboost-test1.71-dev riscv64 1.71.0-6ubuntu5+riscv64.1 [2476 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main riscv64 icu-devtools riscv64 66.1-2ubuntu2 [177 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main riscv64 libboost-dev riscv64 1.71.0.0ubuntu1 [3600 B] Get:46 http://ftpmaster.internal/ubuntu focal/main riscv64 libicu-dev riscv64 66.1-2ubuntu2 [12.5 MB] Get:47 http://archive-team.internal/bootstrap/riscv64 focal/main riscv64 libboost-graph1.71-dev riscv64 1.71.0-6ubuntu5+riscv64.1 [577 kB] Get:48 http://ftpmaster.internal/ubuntu focal/universe riscv64 libboost-graph-dev riscv64 1.71.0.0ubuntu1 [3496 B] Get:49 http://ftpmaster.internal/ubuntu focal/universe riscv64 libf2c2 riscv64 20130926-3 [63.6 kB] Get:50 http://ftpmaster.internal/ubuntu focal/universe riscv64 libf2c2-dev riscv64 20130926-3 [148 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.7 MB in 8s (5461 kB/s) Selecting previously unselected package libbsd0:riscv64. (Reading database ... 9818 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2ubuntu3_riscv64.deb ... Unpacking bsdmainutils (11.1.2ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../02-libuchardet0_0.0.6-3build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.6-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4build1_riscv64.deb ... Unpacking groff-base (1.22.4-4build1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../04-libpipeline1_1.5.2-2build1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.2-2build1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.1-1_riscv64.deb ... 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Preparing to unpack .../49-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:riscv64 (1.5.2-2build1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-2) ... Setting up libglib2.0-0:riscv64 (2.64.1-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.10ubuntu1) ... Setting up libboost1.71-dev:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up libmagic1:riscv64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-4) ... Setting up tzdata (2019c-3ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Apr 3 23:18:42 UTC 2020. Universal Time is now: Fri Apr 3 23:18:42 UTC 2020. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:riscv64 (2.12-2) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libboost-test1.71.0:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up libuchardet0:riscv64 (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libf2c2:riscv64 (20130926-3) ... Setting up libboost-serialization1.71.0:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up libboost-dev:riscv64 (1.71.0.0ubuntu1) ... Setting up libf2c2-dev (20130926-3) ... Setting up libbsd0:riscv64 (0.10.0-1) ... Setting up libelf1:riscv64 (0.176-1.1build1) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libtool (2.4.6-13) ... Setting up libicu66:riscv64 (66.1-2ubuntu2) ... Setting up m4 (1.4.18-4) ... Setting up libboost-test1.71-dev:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libboost-serialization1.71-dev:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up icu-devtools (66.1-2ubuntu2) ... Setting up libboost-regex1.71.0:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up libboost-graph1.71.0:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up libicu-dev:riscv64 (66.1-2ubuntu2) ... Setting up libxml2:riscv64 (2.9.10+dfsg-4build1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-regex1.71-dev:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up libcroco3:riscv64 (0.6.13-1) ... Setting up libboost-graph1.71-dev:riscv64 (1.71.0-6ubuntu5+riscv64.1) ... Setting up libboost-graph-dev:riscv64 (1.71.0.0ubuntu1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.10ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu6~riscv64.1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-21-generic #25-Ubuntu SMP Tue Mar 31 01:57:06 UTC 2020 riscv64 (riscv64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-8ubuntu1 gcc-9_9.3.0-8ubuntu1 libc6-dev_2.31-0ubuntu6~riscv64.1 libstdc++-9-dev_9.3.0-8ubuntu1 libstdc++6_10-20200324-1ubuntu1 linux-libc-dev_5.4.0-21.25 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.1 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 binutils-riscv64-linux-gnu_2.34-5ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-8ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 file_1:5.38-4 findutils_4.7.0-1ubuntu1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-8ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200324-1ubuntu1 gcc-8-base_8.4.0-3ubuntu1 gcc-9_9.3.0-8ubuntu1 gcc-9-base_9.3.0-8ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 icu-devtools_66.1-2ubuntu2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libapt-pkg6.0_2.0.1 libarchive-zip-perl_1.67-2 libassuan0_2.5.3-7ubuntu2 libatomic1_10-20200324-1ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-5ubuntu1 libblkid1_2.34-0.1ubuntu8 libboost-dev_1.71.0.0ubuntu1 libboost-graph-dev_1.71.0.0ubuntu1 libboost-graph1.71-dev_1.71.0-6ubuntu5+riscv64.1 libboost-graph1.71.0_1.71.0-6ubuntu5+riscv64.1 libboost-regex1.71-dev_1.71.0-6ubuntu5+riscv64.1 libboost-regex1.71.0_1.71.0-6ubuntu5+riscv64.1 libboost-serialization1.71-dev_1.71.0-6ubuntu5+riscv64.1 libboost-serialization1.71.0_1.71.0-6ubuntu5+riscv64.1 libboost-test1.71-dev_1.71.0-6ubuntu5+riscv64.1 libboost-test1.71.0_1.71.0-6ubuntu5+riscv64.1 libboost1.71-dev_1.71.0-6ubuntu5+riscv64.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu6~riscv64.1 libc-dev-bin_2.31-0ubuntu6~riscv64.1 libc6_2.31-0ubuntu6~riscv64.1 libc6-dev_2.31-0ubuntu6~riscv64.1 libcap-ng0_0.7.9-2.1build1 libcc1-0_10-20200324-1ubuntu1 libcom-err2_1.45.5-2ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10ubuntu4 libcrypt1_1:4.4.10-10ubuntu4 libctf-nobfd0_2.34-5ubuntu1 libctf0_2.34-5ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_12.10ubuntu1 libdpkg-perl_1.19.7ubuntu3 libelf1_0.176-1.1build1 libext2fs2_1.45.5-2ubuntu1 libf2c2_20130926-3 libf2c2-dev_20130926-3 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.3.0-8ubuntu1 libgcc-s1_10-20200324-1ubuntu1 libgcc1_1:10-20200324-1ubuntu1 libgcrypt20_1.8.5-5ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_10-20200324-1ubuntu1 libgpg-error0_1.37-1 libgpm2_1.20.7-5 libhogweed5_3.5.1+really3.5.1-2 libicu-dev_66.1-2ubuntu2 libicu66_66.1-2ubuntu2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 liblocale-gettext-perl_1.07-4 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: disulfinder Binary: disulfinder, disulfinder-data Architecture: any all Version: 1.2.11-8build1 Maintainer: Debian Med Packaging Team Uploaders: Guy Yachdav , Laszlo Kajan , Andreas Tille Homepage: http://disulfind.dsi.unifi.it/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/disulfinder Vcs-Git: https://salsa.debian.org/med-team/disulfinder.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), libboost-dev, libboost-graph-dev, libf2c2-dev Package-List: disulfinder deb science optional arch=any disulfinder-data deb science optional arch=all Checksums-Sha1: 275abbe8b4ac8e7f83d8a38c81c7f75c0ec7481e 2480613 disulfinder_1.2.11.orig.tar.gz 409668614cadcef6bdd51841eeb7e16465e4b927 7676 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dpkg-source: info: applying gcc-7.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19101447 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19101447 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19101447 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package disulfinder dpkg-buildpackage: info: source version 1.2.11-8build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 fakeroot debian/rules clean dh clean dh_auto_clean make -j4 distclean make[1]: Entering directory '/<>' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory '/<>/disulfind/src' make -C NN clean make -C Common clean make -C SVM clean make[3]: Entering directory '/<>/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Entering directory '/<>/disulfind/src/Common' make -C eig clean make[3]: Entering directory '/<>/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[4]: Entering directory '/<>/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[3]: Leaving directory '/<>/disulfind/src/NN' make[3]: Leaving directory '/<>/disulfind/src/SVM' make[4]: Leaving directory '/<>/disulfind/src/Common/eig' rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory '/<>/disulfind/src/Common' cd SVM && make clean make[3]: Entering directory '/<>/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/<>/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory '/<>/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory '/<>/disulfind/src/Input' cd Output && make clean make[3]: Entering directory '/<>/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory '/<>/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory '/<>/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory '/<>/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory '/<>/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory '/<>/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory '/<>/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 '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars debian/files rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --no-parallel make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>' make -C disulfind/src disulfinder make[3]: Entering directory '/<>/disulfind/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o In file included from Input/utils.h:2, from Input/GlobalDescriptor.cpp:3: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o In file included from Input/utils.h:2, from Input/createBRNNDataset.h:1, from Input/createBRNNDataset.cpp:2: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o In file included from Input/utils.h:2, from Input/createKernelDataset.h:1, from Input/createKernelDataset.cpp:2: Input/Protein.h:19:20: warning: ‘aa_three_codes’ defined but not used [-Wunused-variable] 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o Output/makeHTMLOutput.cpp: In function ‘void makeHTMLOutput(std::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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o Output/makeASCIIOutput.cpp: In function ‘void makeASCIIOutput(std::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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/array.cpp -o NN/array.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DataSet.cpp -o BRNN/RNNs/DataSet.o In file included from BRNN/RNNs/DataSet.cpp:1: BRNN/RNNs/DataSet.h:19:1: warning: ‘typedef’ was ignored in this declaration 19 | typedef struct StructuredInstanceTemplate { | ^~~~~~~ In file included from BRNN/RNNs/DataSet.cpp:1: BRNN/RNNs/DataSet.h: In constructor ‘DataSet::iterator::iterator(DataSet&)’: BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function ‘bool DataSet::iterator::operator++()’: BRNN/RNNs/DataSet.h:116:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 116 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 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 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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DPAG.cpp -o BRNN/RNNs/DPAG.o BRNN/RNNs/DPAG.cpp: In function ‘float PRMeasure(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:48:7: warning: unused variable ‘global_predicted_positives’ [-Wunused-variable] 48 | int global_predicted_positives = boost::num_edges(g), | ^~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:49:5: warning: unused variable ‘global_actual_positives’ [-Wunused-variable] 49 | global_actual_positives = boost::num_edges(gtarget), | ^~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:52:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 52 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘float PrecisionMeasure(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:302:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 302 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘std::pair globalPRMeasure(const DPAG&, const DPAG&, int&, int&, int&, int&, int&, int&, float&)’: BRNN/RNNs/DPAG.cpp:361:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 361 | Vertex_d graphNode, targetNode, targetNode1; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘ConfusionTable getPredictionIndexes(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:560:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 559 | require(true_positives + true_negatives + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | false_positives + false_negatives == | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 561 | boost::num_vertices(gpred) * (boost::num_vertices(gpred)-1) / 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:471:9: warning: unused variable ‘weight’ [-Wunused-variable] 471 | float weight = 1.0 / boost::num_vertices(gpred); | ^~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘float RecallMeasure(const DPAG&, const DPAG&, std::vector&)’: BRNN/RNNs/DPAG.cpp:573:12: warning: unused variable ‘graphNode’ [-Wunused-variable] 573 | Vertex_d graphNode, targetNode; | ^~~~~~~~~ BRNN/RNNs/DPAG.cpp: In function ‘bool equal(const DPAG&, const DPAG&)’: BRNN/RNNs/DPAG.cpp:746:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 746 | for(int i=0; i, boost::property >, boost::adjacency_list, boost::property > > dpag_to_rnndpag(const DPAG&)’: BRNN/RNNs/DPAG.cpp:832:24: warning: comparison of integer expressions of different signedness: ‘boost::vec_adj_list_vertex_id_map, 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:839:22: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} and ‘boost::vec_adj_list_vertex_id_map, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 839 | if(children.front() == vertex_id[*v_i]+1) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:844:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 844 | for(int i=0; i, int>::value_type’ {aka ‘int’} and ‘boost::vec_adj_list_vertex_id_map, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 862 | if((*it).second.front() == vertex_id[*v_i]-1) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:867:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 867 | for(int i=0; i<(*it).second.size(); i++) | ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable ‘node’ [-Wunused-variable] 813 | Vertex_d node; | ^~~~ BRNN/RNNs/DPAG.cpp: In function ‘DPAG rnndpag_to_dpag(const std::pair, boost::property >, boost::adjacency_list, boost::property > >&)’: BRNN/RNNs/DPAG.cpp:878:12: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 878 | VertexId vertex_id = boost::get(boost::vertex_index, g);; | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Options.cpp -o BRNN/RNNs/Options.o BRNN/RNNs/Options.cpp: In member function ‘virtual void Options::parse_config(const string&)’: BRNN/RNNs/Options.cpp:30:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const 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 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 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 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 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 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 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 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::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 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 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 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 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 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 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 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 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::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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/protein_util.cpp -o BRNN/protein_util.o In file included from BRNN/protein_util.cpp:1: BRNN/protein_util.h: In constructor ‘Residue::Residue(int, int, char, float, float, float, float, float, char)’: BRNN/protein_util.h:209:16: warning: ‘Residue::_coord’ will be initialized after [-Wreorder] 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++/9/cassert:44, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp: In member function ‘void Chain::setSShydrophobicity()’: BRNN/protein_util.cpp:365:31: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 365 | assert(resHydrScales.size() == numResidues()); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:380:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 380 | if(r_i >= resHydrScales.size()) r_i = resHydrScales.size()-1; | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/cassert:44, from BRNN/protein_util.cpp:2: BRNN/protein_util.cpp:386:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 386 | assert(hAvg.size() == (*c_it).numResidues()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ BRNN/protein_util.cpp:391:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 391 | for(int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 401 | assert(seq_pos == resHydrScales.size()); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/blast_util.cpp -o BRNN/blast_util.o BRNN/blast_util.cpp: In member function ‘void PSSM::parsePsiBlastReport(const char*)’: BRNN/blast_util.cpp:34:13: warning: unused variable ‘prof’ [-Wunused-variable] 34 | Profile prof; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/rnn_util.cpp -o BRNN/rnn_util.o In file included from BRNN/rnn_util.cpp:4: BRNN/RNNs/DataSet.h:19:1: warning: ‘typedef’ was ignored in this declaration 19 | typedef struct StructuredInstanceTemplate { | ^~~~~~~ In file included from BRNN/rnn_util.cpp:4: BRNN/RNNs/DataSet.h: In constructor ‘DataSet::iterator::iterator(DataSet&)’: BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 86 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h: In member function ‘bool DataSet::iterator::operator++()’: BRNN/RNNs/DataSet.h:116:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 116 | require(num_nodes == (*_nodes_targets_iter).size(), | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/DataSet.h:135:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 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 string&, const string&, int, int, const string&)’: BRNN/rnn_util.cpp:233:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 233 | for(int i=0; i::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 string&, const string&, const string&, const string&, const string&, const string&, int)’: BRNN/rnn_util.cpp:359:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::edges_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 359 | require(B == boost::num_edges(candidate) && | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:348:16: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 348 | VertexId vertex_id = boost::get(boost::vertex_index, candidate); | ^~~~~~~~~ BRNN/rnn_util.cpp:405:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, boost::property > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 405 | for(int j=0; j, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::edges_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 406 | require(B == boost::num_edges(bestPatterns[j]) && | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:407:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::detail::adj_list_gen, boost::property >, boost::vecS, boost::vecS, boost::bidirectionalS, boost::property, boost::property, boost::no_property, boost::listS>::config::vertices_size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 407 | B == boost::num_vertices(bestPatterns[j]) / 2, | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/rnn_util.cpp:378:18: warning: unused variable ‘nodes’ [-Wunused-variable] 378 | vector *nodes = it.currenTONodes(); | ^~~~~ In file included from BRNN/rnn_util.cpp:5: BRNN/RNNs/RecursiveNN.h: In instantiation of ‘RecursiveNN::RecursiveNN(const char*) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]’: BRNN/rnn_util.cpp:88:73: required from here BRNN/RNNs/RecursiveNN.h:1018:13: warning: unused variable ‘trasd’ [-Wunused-variable] 1018 | TrasdType trasd = Options::instance()->getTrasductionType(); | ^~~~~ In file included from BRNN/rnn_util.cpp:5: BRNN/RNNs/RecursiveNN.h:1026:23: warning: variable ‘indexes’ set but not used [-Wunused-but-set-variable] 1026 | std::pair indexes = Options::instance()->getLayersIndexes(); | ^~~~~~~ BRNN/RNNs/RecursiveNN.h:1047:7: warning: unused variable ‘default_precision’ [-Wunused-variable] 1047 | int default_precision = is.precision(); | ^~~~~~~~~~~~~~~~~ In file included from BRNN/rnn_util.cpp:6: BRNN/RNNs/StructureSearch.h: In instantiation of ‘std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]’: BRNN/rnn_util.cpp:396:65: required from here BRNN/RNNs/StructureSearch.h:977:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 977 | for(int i=0; i<_nodesInputs.size(); ++i) | ~^~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/StructureSearch.h:984:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector, boost::property > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 984 | for(int i=0; i::fPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]’: BRNN/RNNs/RecursiveNN.h:1356:3: required from ‘void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]’ BRNN/rnn_util.cpp:99:47: required from here BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1390 | require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!"); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1415:38: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘int’ [-Wsign-compare] 1415 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1418:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1418 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable ‘vertex_id’ set but not used [-Wunused-but-set-variable] 1384 | VertexId vertex_id = boost::get(boost::vertex_index, sdag); | ^~~~~~~~~ BRNN/RNNs/RecursiveNN.h: In instantiation of ‘void RecursiveNN::bPropagateInput(std::vector&, const DPAG&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent; DPAG = boost::adjacency_list, boost::property >]’: BRNN/RNNs/RecursiveNN.h:1359:19: required from ‘void RecursiveNN::propagateStructuredInput(std::vector&, const std::pair, boost::property >, boost::adjacency_list, boost::property > >&) [with HA_Function = TanH; OA_Function = Sigmoid; EMP = MGradientDescent]’ BRNN/rnn_util.cpp:99:47: required from here BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1470 | for(int t=0; t::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1471 | require(_n == toNodes[t]->_encodedInput.size(), "Error!"); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BRNN/RNNs/RecursiveNN.h:1492:38: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘int’ [-Wsign-compare] 1492 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) { BRNN/RNNs/RecursiveNN.h:1495:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 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); | ^~~~~~~~~ In file included from BRNN/rnn_util.cpp:6: BRNN/RNNs/StructureSearch.h: In instantiation of ‘float StructureSearch::RNNMeasure(const DPAG&, RNN*, std::vector&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN; DPAG = boost::adjacency_list, boost::property >]’: BRNN/RNNs/StructureSearch.h:989:11: required from ‘std::vector, boost::property > > StructureSearch::ConnectivityPatternSearch(RNN*, const std::vector, boost::property > >&, std::vector&) [with T1 = TanH; T2 = Sigmoid; T3 = MGradientDescent; RNN = RecursiveNN]’ BRNN/rnn_util.cpp:396:65: required from here BRNN/RNNs/StructureSearch.h:186:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 186 | for(int i=0; i>/disulfind/src/Common' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Util.cpp -o Util.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Statistics.cpp -o Statistics.o cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balanc.o eig/balanc.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balbak.o eig/balbak.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/cdiv.o eig/cdiv.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/elmhes.o eig/elmhes.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/eltran.o eig/eltran.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr.o eig/hqr.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr2.o eig/hqr2.c cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/rg.o eig/rg.c g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c coords.cpp -o coords.o cc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/<>/disulfind/src/Common' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -LCommon/ -lCommon make[3]: Leaving directory '/<>/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 '/<>' make[1]: Leaving directory '/<>' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a rm -f -- debian/disulfinder.substvars rm -fr -- debian/.debhelper/generated/disulfinder/ debian/disulfinder/ debian/tmp/ rm -f debian/disulfinder.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/<>' /usr/bin/make DESTDIR=/<>/debian/disulfinder prefix=/usr install make[2]: Entering directory '/<>' /usr/bin/make -C disulfind/src install make[3]: Entering directory '/<>/disulfind/src' mkdir -p /<>/debian/disulfinder/usr/bin cp disulfinder /<>/debian/disulfinder/usr/bin/ mkdir -p /<>/debian/disulfinder/usr/share/disulfinder mkdir -p /<>/debian/disulfinder/usr/share/disulfinder/Models cp -r ../Models /<>/debian/disulfinder/usr/share/disulfinder/ && find /<>/debian/disulfinder/usr/share/disulfinder/ -depth -ignore_readdir_race -name .svn -execdir rm -rf {} \; rm -rf /<>/debian/disulfinder/usr/share/disulfinder/Models/conn/data/sequences_w5 rm -rf /<>/debian/disulfinder/usr/share/disulfinder/Predictions rm -rf /<>/debian/disulfinder/usr/share/disulfinder/tmp make[3]: Leaving directory '/<>/disulfind/src' mkdir -p /<>/debian/disulfinder/usr/share/man/man1 && cp disulfinder.1 /<>/debian/disulfinder/usr/share/man/man1/ mkdir -p /<>/debian/disulfinder/usr/share/doc/disulfinder/examples && cp examples/res_id_* /<>/debian/disulfinder/usr/share/doc/disulfinder/examples/ make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install install -d debian/.debhelper/generated/disulfinder install -d debian/.debhelper/generated/disulfinder-data mkdir -p /<>/debian/disulfinder-data/usr/share/disulfinder mv /<>/debian/disulfinder/usr/share/disulfinder/* /<>/debian/disulfinder-data/usr/share/disulfinder make[1]: Leaving directory '/<>' dh_installdocs -a cp --reflink=auto -a ./debian/upstream/metadata debian/disulfinder/usr/share/doc/disulfinder cp --reflink=auto -a ./debian/README.test debian/disulfinder/usr/share/doc/disulfinder cp --reflink=auto -a ./debian/tests/installation-test debian/disulfinder/usr/share/doc/disulfinder chown -R 0:0 debian/disulfinder/usr/share/doc chmod -R u\+rw,go=rX debian/disulfinder/usr/share/doc install -p -m0644 debian/copyright debian/disulfinder/usr/share/doc/disulfinder/copyright dh_installchangelogs -a install -p -m0644 debian/changelog debian/disulfinder/usr/share/doc/disulfinder/changelog.Debian dh_installman -a 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 -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/disulfinder chmod a-x usr/share/doc/disulfinder/changelog.Debian usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb usr/share/man/man1/disulfinder.1 gzip -9nf usr/share/doc/disulfinder/changelog.Debian usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb usr/share/man/man1/disulfinder.1 cd '/<>' dh_fixperms -a find debian/disulfinder -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/disulfinder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/disulfinder/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/disulfinder/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/disulfinder/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_strip -a install -d debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c2 objcopy --only-keep-debug --compress-debug-sections debian/disulfinder/usr/bin/disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c2/ce23712f8cff0057271b16590c6b0bbdead9bf.debug chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c2/ce23712f8cff0057271b16590c6b0bbdead9bf.debug chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/c2/ce23712f8cff0057271b16590c6b0bbdead9bf.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/c2/ce23712f8cff0057271b16590c6b0bbdead9bf.debug debian/disulfinder/usr/bin/disulfinder install -d debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc ln -s disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/share/doc/disulfinder-dbgsym dh_makeshlibs -a rm -f debian/disulfinder/DEBIAN/shlibs dh_shlibdeps -a install -d debian/disulfinder/DEBIAN dpkg-shlibdeps -Tdebian/disulfinder.substvars debian/disulfinder/usr/bin/disulfinder dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/disulfinder.substvars echo misc:Pre-Depends= >> debian/disulfinder.substvars install -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -Pdebian/.debhelper/disulfinder/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=disulfinder-dbgsym "-DDepends=disulfinder (= \${binary:Version})" "-DDescription=debug symbols for disulfinder" -DBuild-Ids=c2ce23712f8cff0057271b16590c6b0bbdead9bf -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -Pdebian/disulfinder -UMulti-Arch chmod 0644 -- debian/disulfinder/DEBIAN/control chown 0:0 -- debian/disulfinder/DEBIAN/control dh_md5sums -a cd debian/disulfinder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/disulfinder/DEBIAN/md5sums chown 0:0 -- debian/disulfinder/DEBIAN/md5sums cd debian/.debhelper/disulfinder/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --build debian/disulfinder .. install -d debian/.debhelper/scratch-space/build-disulfinder dpkg-deb --build debian/.debhelper/disulfinder/dbgsym-root debian/.debhelper/scratch-space/build-disulfinder INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing disulfinder (in debian/disulfinder); do_strip: , oemstrip: pkgstriptranslations: processing disulfinder-dbgsym (in debian/.debhelper/disulfinder/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/disulfinder/DEBIAN/control, package disulfinder, directory debian/disulfinder pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: Truncating usr/share/doc/disulfinder/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package disulfinder ... pkgstripfiles: No PNG files. dpkg-deb: building package 'disulfinder' in '../disulfinder_1.2.11-8build1_riscv64.deb'. pkgstripfiles: processing control file: debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control, package disulfinder-dbgsym, directory debian/.debhelper/disulfinder/dbgsym-root dpkg-deb: building package 'disulfinder-dbgsym' in 'debian/.debhelper/scratch-space/build-disulfinder/disulfinder-dbgsym_1.2.11-8build1_riscv64.deb'. Renaming disulfinder-dbgsym_1.2.11-8build1_riscv64.deb to disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb mv debian/.debhelper/scratch-space/build-disulfinder/disulfinder-dbgsym_1.2.11-8build1_riscv64.deb ../disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../disulfinder_1.2.11-8build1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2020-04-03T23:51:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ disulfinder_1.2.11-8build1_riscv64.changes: ------------------------------------------- Format: 1.8 Date: Sun, 22 Mar 2020 16:38:22 +0100 Source: disulfinder Binary: disulfinder Architecture: riscv64 Version: 1.2.11-8build1 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: disulfinder - cysteines disulfide bonding state and connectivity predictor Changes: disulfinder (1.2.11-8build1) focal; urgency=medium . * No-change rebuild for libgcc-s1 package name change. Checksums-Sha1: 77ceef122c0affb9f8f72ce696dcd9ac47e17555 2956052 disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb bd7529878d5950820479c52889202d5d187b72a0 5824 disulfinder_1.2.11-8build1_riscv64.buildinfo 143a902eaa8d53f11d77ccdbde9863edd6663382 218624 disulfinder_1.2.11-8build1_riscv64.deb Checksums-Sha256: ade39c7fee1959d8b9eaca7ab746647013230b8f89099a32330c8ea0fd9897ed 2956052 disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb 05a02fe67ff4d4ba72645ac2755f3704a1aa8f1ba3f97c9e409f858e896c7087 5824 disulfinder_1.2.11-8build1_riscv64.buildinfo ffd934336665d3cee84313bfbc4b0b6b17422fbcab532c1ae2fad3e65e020933 218624 disulfinder_1.2.11-8build1_riscv64.deb Files: 695f891936ee521e5b600db85e6f46e0 2956052 debug optional disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb cc20a44c9d937eeab3751850ddd1db8d 5824 science optional disulfinder_1.2.11-8build1_riscv64.buildinfo d03be283b1c95791d03afffb7fe450dc 218624 science optional disulfinder_1.2.11-8build1_riscv64.deb /<>/disulfinder_1.2.11-8build1_riscv64.changes.new could not be renamed to /<>/disulfinder_1.2.11-8build1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: disulfinder Binary: disulfinder disulfinder-data Architecture: riscv64 Version: 1.2.11-8build1 Checksums-Md5: 695f891936ee521e5b600db85e6f46e0 2956052 disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb d03be283b1c95791d03afffb7fe450dc 218624 disulfinder_1.2.11-8build1_riscv64.deb Checksums-Sha1: 77ceef122c0affb9f8f72ce696dcd9ac47e17555 2956052 disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb 143a902eaa8d53f11d77ccdbde9863edd6663382 218624 disulfinder_1.2.11-8build1_riscv64.deb Checksums-Sha256: ade39c7fee1959d8b9eaca7ab746647013230b8f89099a32330c8ea0fd9897ed 2956052 disulfinder-dbgsym_1.2.11-8build1_riscv64.ddeb ffd934336665d3cee84313bfbc4b0b6b17422fbcab532c1ae2fad3e65e020933 218624 disulfinder_1.2.11-8build1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Fri, 03 Apr 2020 23:51:46 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.1-4ubuntu6), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu4), base-passwd (= 3.5.47), bash (= 5.0-6ubuntu1), binutils (= 2.34-5ubuntu1), binutils-common (= 2.34-5ubuntu1), binutils-riscv64-linux-gnu (= 2.34-5ubuntu1), bsdmainutils (= 11.1.2ubuntu3), bsdutils (= 1:2.34-0.1ubuntu8), build-essential (= 12.8ubuntu1), bzip2 (= 1.0.8-2), coreutils (= 8.30-3ubuntu2), cpp (= 4:9.3.0-1ubuntu2), cpp-9 (= 9.3.0-8ubuntu1), dash (= 0.5.10.2-6), debconf (= 1.5.73), debhelper (= 12.10ubuntu1), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.6.3-2), diffutils (= 1:3.7-3), dpkg (= 1.19.7ubuntu3), dpkg-dev (= 1.19.7ubuntu3), dwz (= 0.13-5), file (= 1:5.38-4), findutils (= 4.7.0-1ubuntu1), g++ (= 4:9.3.0-1ubuntu2), g++-9 (= 9.3.0-8ubuntu1), gcc (= 4:9.3.0-1ubuntu2), gcc-10-base (= 10-20200324-1ubuntu1), gcc-9 (= 9.3.0-8ubuntu1), gcc-9-base (= 9.3.0-8ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.4-1), groff-base (= 1.22.4-4build1), gzip (= 1.10-0ubuntu4), hostname (= 3.23), icu-devtools (= 66.1-2ubuntu2), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-6), libarchive-zip-perl (= 1.67-2), libatomic1 (= 10-20200324-1ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-2ubuntu6), libaudit1 (= 1:2.8.5-2ubuntu6), libbinutils (= 2.34-5ubuntu1), libblkid1 (= 2.34-0.1ubuntu8), libboost-dev (= 1.71.0.0ubuntu1), libboost-graph-dev (= 1.71.0.0ubuntu1), libboost-graph1.71-dev (= 1.71.0-6ubuntu5+riscv64.1), libboost-graph1.71.0 (= 1.71.0-6ubuntu5+riscv64.1), libboost-regex1.71-dev (= 1.71.0-6ubuntu5+riscv64.1), libboost-regex1.71.0 (= 1.71.0-6ubuntu5+riscv64.1), libboost-serialization1.71-dev (= 1.71.0-6ubuntu5+riscv64.1), libboost-serialization1.71.0 (= 1.71.0-6ubuntu5+riscv64.1), libboost-test1.71-dev (= 1.71.0-6ubuntu5+riscv64.1), libboost-test1.71.0 (= 1.71.0-6ubuntu5+riscv64.1), libboost1.71-dev (= 1.71.0-6ubuntu5+riscv64.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.31-0ubuntu6~riscv64.1), libc-dev-bin (= 2.31-0ubuntu6~riscv64.1), libc6 (= 2.31-0ubuntu6~riscv64.1), libc6-dev (= 2.31-0ubuntu6~riscv64.1), libcap-ng0 (= 0.7.9-2.1build1), libcc1-0 (= 10-20200324-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.10-10ubuntu4), libcrypt1 (= 1:4.4.10-10ubuntu4), libctf-nobfd0 (= 2.34-5ubuntu1), libctf0 (= 2.34-5ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu2), libdebconfclient0 (= 0.251ubuntu1), libdebhelper-perl (= 12.10ubuntu1), libdpkg-perl (= 1.19.7ubuntu3), libelf1 (= 0.176-1.1build1), libf2c2 (= 20130926-3), libf2c2-dev (= 20130926-3), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.6.3-2), libgcc-9-dev (= 9.3.0-8ubuntu1), libgcc-s1 (= 10-20200324-1ubuntu1), libgcc1 (= 1:10-20200324-1ubuntu1), libgcrypt20 (= 1.8.5-5ubuntu1), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.1-1), libgmp10 (= 2:6.2.0+dfsg-4), libgomp1 (= 10-20200324-1ubuntu1), libgpg-error0 (= 1.37-1), libicu-dev (= 66.1-2ubuntu2), libicu66 (= 66.1-2ubuntu2), libisl22 (= 0.22.1-1), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.34-0.1ubuntu8), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libpam-modules (= 1.3.1-5ubuntu4), libpam-modules-bin (= 1.3.1-5ubuntu4), libpam-runtime (= 1.3.1-5ubuntu4), libpam0g (= 1.3.1-5ubuntu4), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12build1), libperl5.30 (= 5.30.0-9build1), libpipeline1 (= 1.5.2-2build1), libselinux1 (= 3.0-1build2), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.34-0.1ubuntu8), libstdc++-9-dev (= 9.3.0-8ubuntu1), libstdc++6 (= 10-20200324-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 244.3-1ubuntu1), libtinfo6 (= 6.2-0ubuntu2), libtool (= 2.4.6-13), libuchardet0 (= 0.0.6-3build1), libudev1 (= 244.3-1ubuntu1), libunistring2 (= 0.9.10-2), libuuid1 (= 2.34-0.1ubuntu8), libxml2 (= 2.9.10+dfsg-4build1), libzstd1 (= 1.4.4+dfsg-3), linux-libc-dev (= 5.4.0-21.25), login (= 1:4.8.1-1ubuntu3), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.2.1-1.2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-0ubuntu2), ncurses-bin (= 6.2-0ubuntu2), patch (= 2.7.6-6), perl (= 5.30.0-9build1), perl-base (= 5.30.0-9build1), perl-modules-5.30 (= 5.30.0-9build1), po-debconf (= 1.0.21), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-2.1ubuntu1), tar (= 1.30+dfsg-7), tzdata (= 2019c-3ubuntu1), util-linux (= 2.34-0.1ubuntu8), xz-utils (= 5.2.4-1), zlib1g (= 1:1.2.11.dfsg-2ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1584891502" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ disulfinder_1.2.11-8build1_riscv64.deb -------------------------------------- new Debian package, version 2.0. size 218624 bytes: control archive=1304 bytes. 1382 bytes, 25 lines control 691 bytes, 9 lines md5sums Package: disulfinder Version: 1.2.11-8build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 458 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.4), libstdc++6 (>= 5.2), disulfinder-data Section: science Priority: optional Homepage: http://disulfind.dsi.unifi.it/ Description: cysteines disulfide bonding state and connectivity predictor 'disulfinder' is for predicting the disulfide bonding state of cysteines and their disulfide connectivity starting from sequence alone. Disulfide bridges play a major role in the stabilization of the folding process for several proteins. Prediction of disulfide bridges from sequence alone is therefore useful for the study of structural and functional properties of specific proteins. In addition, knowledge about the disulfide bonding state of cysteines may help the experimental structure determination process and may be useful in other genomic annotation tasks. . 'disulfinder' predicts disulfide patterns in two computational stages: (1) the disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary classifier; (2) cysteines that are known to participate in the formation of bridges are paired by a Recursive Neural Network to obtain a connectivity pattern. drwxr-xr-x root/root 0 2020-03-22 15:38 ./ drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/ drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/bin/ -rwxr-xr-x root/root 433744 2020-03-22 15:38 ./usr/bin/disulfinder drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/ drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/disulfinder/ drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/doc/disulfinder/ -rw-r--r-- root/root 971 2018-09-23 15:15 ./usr/share/doc/disulfinder/README.test -rw-r--r-- root/root 1375 2020-03-22 15:38 ./usr/share/doc/disulfinder/changelog.Debian.gz -rw-r--r-- root/root 2159 2018-09-23 15:15 ./usr/share/doc/disulfinder/copyright drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/doc/disulfinder/examples/ -rw-r--r-- root/root 5977 2020-03-22 15:38 ./usr/share/doc/disulfinder/examples/res_id_41483.blastPsiMatTmb.gz -rw-r--r-- root/root 3609 2020-03-22 15:38 ./usr/share/doc/disulfinder/examples/res_id_41483.expected_result -rw-r--r-- root/root 713 2018-09-23 15:15 ./usr/share/doc/disulfinder/installation-test -rw-r--r-- root/root 1535 2018-09-23 15:15 ./usr/share/doc/disulfinder/metadata drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/man/ drwxr-xr-x root/root 0 2020-03-22 15:38 ./usr/share/man/man1/ -rw-r--r-- root/root 3630 2020-03-22 15:38 ./usr/share/man/man1/disulfinder.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 94824 Build-Time: 1956 Distribution: focal Host Architecture: riscv64 Install-Time: 325 Job: disulfinder_1.2.11-8build1.dsc Machine Architecture: riscv64 Package: disulfinder Package-Time: 2335 Source-Version: 1.2.11-8build1 Space: 94824 Status: successful Version: 1.2.11-8build1 -------------------------------------------------------------------------------- Finished at 2020-04-03T23:51:55Z Build needed 00:38:55, 94824k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 Scanning for processes to kill in build PACKAGEBUILD-19101447 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 Stopping target for build PACKAGEBUILD-19101447 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=focal --arch=riscv64 PACKAGEBUILD-19101447 Removing build PACKAGEBUILD-19101447