I: pbuilder: network access will be disabled during build
I: Current time: Sun May 7 16:23:48 +14 2023
I: pbuilder-time-stamp: 1683426228
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [disulfinder_1.2.11-12.dsc]
I: copying [./disulfinder_1.2.11.orig.tar.gz]
I: copying [./disulfinder_1.2.11-12.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Jan 21 00:41:26 2022 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./disulfinder_1.2.11-12.dsc: no acceptable signature found
dpkg-source: info: extracting disulfinder in disulfinder-1.2.11
dpkg-source: info: unpacking disulfinder_1.2.11.orig.tar.gz
dpkg-source: info: unpacking disulfinder_1.2.11-12.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying variable_length_array
dpkg-source: info: applying unknown_escape
dpkg-source: info: applying gcc-6.patch
dpkg-source: info: applying gcc-7.patch
dpkg-source: info: applying cross.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/D01_modify_environment starting
debug: Running on jtx1a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 May 7 16:24 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4'
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=b0a7939aea464561a4d23d375a0901f1
LANG=C
LANGUAGE=it_CH:it
LC_ALL=C
MACHTYPE=arm-unknown-linux-gnueabihf
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnueabihf
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=31903
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.VW8aXGob/pbuilderrc_9PIF --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VW8aXGob/b2 --logfile b2/build.log --extrapackages usrmerge disulfinder_1.2.11-12.dsc'
SUDO_GID=114
SUDO_UID=108
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:3142/
I: uname -a
Linux i-capture-the-hostname 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash
-rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 67632 Sep 21 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 21 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 21 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 133220 Sep 21 2022 date
-rwxr-xr-x 1 root root 67732 Sep 21 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 21 2022 df
-rwxr-xr-x 1 root root 133632 Sep 21 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 21 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 23 23:51 login
-rwxr-xr-x 1 root root 133632 Sep 21 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 23 23:02 more
-rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount
-rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 21 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 9 May 7 16:24 sh -> /bin/bash
-rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 21 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 23 23:02 su
-rwxr-xr-x 1 root root 67584 Sep 21 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 21 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 21 2022 true
-rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount
-rwxr-xr-x 1 root root 67572 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <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 ... 19329 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-graph1.74-dev{a} libboost-graph1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libf2c2{a} libf2c2-dev{a} libfile-stripnondeterminism-perl{a} libicu-dev{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 42.4 MB of archives. After unpacking 290 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 24 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf icu-devtools armhf 72.1-3 [183 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf libboost1.74-dev armhf 1.74.0+ds1-20 [9510 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libboost-dev armhf 1.74.0.3 [4548 B]
Get: 34 http://deb.debian.org/debian bookworm/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-20 [432 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf libboost-graph1.74.0 armhf 1.74.0+ds1-20 [285 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf libicu-dev armhf 72.1-3 [10.1 MB]
Get: 37 http://deb.debian.org/debian bookworm/main armhf libboost-regex1.74-dev armhf 1.74.0+ds1-20 [543 kB]
Get: 38 http://deb.debian.org/debian bookworm/main armhf libboost-serialization1.74.0 armhf 1.74.0+ds1-20 [298 kB]
Get: 39 http://deb.debian.org/debian bookworm/main armhf libboost-serialization1.74-dev armhf 1.74.0+ds1-20 [368 kB]
Get: 40 http://deb.debian.org/debian bookworm/main armhf libboost-test1.74.0 armhf 1.74.0+ds1-20 [412 kB]
Get: 41 http://deb.debian.org/debian bookworm/main armhf libboost-test1.74-dev armhf 1.74.0+ds1-20 [517 kB]
Get: 42 http://deb.debian.org/debian bookworm/main armhf libboost-graph1.74-dev armhf 1.74.0+ds1-20 [1528 kB]
Get: 43 http://deb.debian.org/debian bookworm/main armhf libboost-graph-dev armhf 1.74.0.3 [4436 B]
Get: 44 http://deb.debian.org/debian bookworm/main armhf libf2c2 armhf 20140711-1 [113 kB]
Get: 45 http://deb.debian.org/debian bookworm/main armhf libf2c2-dev armhf 20140711-1 [121 kB]
Fetched 42.4 MB in 4s (11.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19329 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_armhf.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_armhf.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_armhf.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_armhf.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_armhf.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_armhf.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
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usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
removed '/etc/unsupported-skip-usrmerge-conversion'
The system has been successfully converted.
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/disulfinder-1.2.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 armhf
debian/rules clean
dh clean
dh_auto_clean
make -j4 distclean
make[1]: Entering directory '/build/disulfinder-1.2.11'
if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi
make[2]: Entering directory '/build/disulfinder-1.2.11/disulfind/src'
make -C NN clean
make -C Common clean
make -C SVM clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/NN'
rm -f *~ *.o brnn-train brnn-test
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Common'
make -C eig clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/SVM'
rm *~ *.o *.a *.exe SVMClassifier -f
make[4]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Common/eig'
rm *.o libeig.a *~ -f
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/NN'
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/SVM'
make[4]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Common/eig'
rm *.o libCommon.a Eig Norm *~ -f
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Common'
cd SVM && make clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/SVM'
rm *~ *.o *.a *.exe SVMClassifier -f
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/SVM'
cd Input && make clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Input'
rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Input'
cd Output && make clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Output'
rm *.o makeASCIIOutput makeHTMLOutput *~ -f
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/Output'
cd FSA-Alignment && make clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/FSA-Alignment'
rm *.o fold_automata viterbi_aligner timed_transitions *~ -f
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/FSA-Alignment'
cd BRNN && make clean
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/BRNN'
rm -f *.o core
rm -f ./RNNs/*.o ./RNNs/core disulfind-conn
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src/BRNN'
rm disulfinder disultrainer *.o *~ -f
make[2]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src'
rm -f *.[12345678] *.[12345678].gz
#if [ -d "disulfind" ]; then rm -rf disulfind; fi
if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi
rm -rf patch-stamp \
initial-clean-stamp \
"disulfinder-1.2.11.tar.gz" \
.pc
make[1]: Leaving directory '/build/disulfinder-1.2.11'
dh_clean
rm -f debian/debhelper-build-stamp
rm -rf debian/.debhelper/
rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars debian/files
rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/disulfinder-1.2.11'
dh_auto_build --no-parallel
make -j1 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/disulfinder-1.2.11'
make -C disulfind/src disulfinder
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o
In file included from Input/utils.h:2,
from Input/createBRNNDataset.h:1,
from Input/createBRNNDataset.cpp:2:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files
| ^~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o
In file included from Input/utils.h:2,
from Input/createKernelDataset.h:1,
from Input/createKernelDataset.cpp:2:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from Input/../Common/Matrix.h:10,
from Input/utils.h:1:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const char&>, std::tuple<>}; _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void createDataKernel(Protein&, std::ostream&, unsigned int, const GlobalDescriptorMaker&, const std::string&, bool)' at Input/createKernelDataset.cpp:39:35:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void createDataKernel(Protein&, std::ostream&, unsigned int, const GlobalDescriptorMaker&, const std::string&, bool)' at Input/createKernelDataset.cpp:42:38:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o
In file included from /usr/include/c++/12/vector:70,
from Input/../Common/Util.h:7,
from Input/Protein.cpp:11:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from Input/Protein.cpp:9:
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const char&>, std::tuple<>}; _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadProfile(std::istream&)' at Input/Protein.cpp:1071:34:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<char&&>, std::tuple<>}; _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Protein::AddDescriptors(std::vector<Protein>&)' at Input/Protein.cpp:199:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Protein::AddDescriptors(std::vector<Protein>&)' at Input/Protein.cpp:202:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Protein::AddDescriptors(std::vector<Protein>&)' at Input/Protein.cpp:205:32:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'static void Protein::AddDescriptors(std::vector<Protein>&)' at Input/Protein.cpp:225:39:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'static void Protein::AddDescriptors(std::vector<Protein>&)' at Input/Protein.cpp:242:37:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:323:29:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:338:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:341:18:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:342:18:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:345:18:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:346:18:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:350:21:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:364:36:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:366:55:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadCB513(std::istream&)' at Input/Protein.cpp:366:29:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:487:24:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:506:29:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:518:36:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:520:55:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadHSSP(std::istream&, double)' at Input/Protein.cpp:520:29:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1315:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1316:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1321:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1322:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1323:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadTDB(std::istream&)' at Input/Protein.cpp:1337:33:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1111:32:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1116:34:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1120:34:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void Protein::ReadPsiBlast0(std::istream&)' at Input/Protein.cpp:1122:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1235:31:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1242:34:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1249:29:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1256:45:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = char; _Tp = double; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1258:29:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1265:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Protein::ReadPsiBlast2(std::istream&, double)' at Input/Protein.cpp:1271:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o
Output/makeHTMLOutput.cpp: In function 'void makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)':
Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~~
Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
162 | char * altname[2] = {"Second","Third"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o
Output/makeASCIIOutput.cpp: In function 'void makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)':
Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~~
Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
144 | char * altname[2] = {"SECOND","THIRD"};
| ^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o
In file included from /usr/include/c++/12/vector:70,
from FSA-Alignment/fsa.h:3,
from FSA-Alignment/fsa.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Transition}; _Tp = Transition; _Alloc = std::allocator<Transition>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Transition>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Transition}; _Tp = Transition; _Alloc = std::allocator<Transition>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Transition; _Alloc = std::allocator<Transition>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void FiniteStateAutomata::Read(std::istream&)' at FSA-Alignment/fsa.cpp:80:34:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/viterbi_aligner.cpp -o FSA-Alignment/viterbi_aligner.o
In file included from /usr/include/c++/12/vector:70,
from FSA-Alignment/../Common/Matrix.h:8,
from FSA-Alignment/../Common/CommonMethods.h:15,
from FSA-Alignment/viterbi_aligner.h:2,
from FSA-Alignment/viterbi_aligner.cpp:3:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void Matrix<DATATYPE>::Read(std::istream&) [with DATATYPE = double]' at FSA-Alignment/../Common/Matrix.h:403:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/multi-array.cpp -o NN/multi-array.o
In file included from /usr/include/c++/12/vector:70,
from NN/multi-array.cpp:2:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'REAL* ReadArray(std::istream&, int&)' at NN/multi-array.cpp:292:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/array.cpp -o NN/array.o
In file included from /usr/include/c++/12/vector:70,
from NN/array.cpp:2:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void VECTOR::Read(std::istream&)' at NN/array.cpp:172:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void COLLECTIONA::Read(std::istream&)' at NN/array.cpp:246:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-model.cpp -o NN/brnn-model.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c NN/brnn-test.cpp -o NN/brnn-test.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Node.cpp -o BRNN/RNNs/Node.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/StructureSearch.cpp -o BRNN/RNNs/StructureSearch.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DataSet.cpp -o BRNN/RNNs/DataSet.o
In file included from BRNN/RNNs/DataSet.cpp:1:
BRNN/RNNs/DataSet.h:19:1: warning: 'typedef' was ignored in this declaration
19 | typedef struct StructuredInstanceTemplate {
| ^~~~~~~
BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)':
BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
86 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()':
BRNN/RNNs/DataSet.h:116:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
116 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h:135:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
135 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.cpp: In constructor 'DataSet::DataSet(const char*, const char*)':
BRNN/RNNs/DataSet.cpp:69:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
69 | if(pos == string::npos)
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.cpp: In member function 'bool DataSet::loadInstances(const char*)':
BRNN/RNNs/DataSet.cpp:141:7: warning: unused variable 'ng' [-Wunused-variable]
141 | int ng = 1;
| ^~
BRNN/RNNs/DataSet.cpp: At global scope:
BRNN/RNNs/DataSet.cpp:14:12: warning: 'int one(const dirent*)' defined but not used [-Wunused-function]
14 | static int one(const struct dirent* unused) {
| ^~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/DPAG.cpp -o BRNN/RNNs/DPAG.o
BRNN/RNNs/DPAG.cpp: In function 'float PRMeasure(const DPAG&, const DPAG&, std::vector<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 '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 '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>, unsigned int>::value_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
832 | if(vertex_id[*v_i] != n_vertices-1) {
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:839:29: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_t, unsigned int>, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare]
839 | if(children.front() == vertex_id[*v_i]+1)
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:844:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka '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>, unsigned int>::value_type' {aka 'unsigned int'} [-Wsign-compare]
862 | if((*it).second.front() == vertex_id[*v_i]-1)
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:867:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
867 | for(int i=0; i<(*it).second.size(); i++)
| ~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DPAG.cpp:813:12: warning: unused variable 'node' [-Wunused-variable]
813 | Vertex_d node;
| ^~~~
BRNN/RNNs/DPAG.cpp: In function 'DPAG rnndpag_to_dpag(const std::pair<boost::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/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/RNNs/Options.cpp -o BRNN/RNNs/Options.o
BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_config(const std::string&)':
BRNN/RNNs/Options.cpp:30:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
30 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:36:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
36 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:42:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
42 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:47:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
47 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:61:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
61 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:79:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
79 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:85:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
85 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:90:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
90 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:99:29: warning: comparison of integer expressions of different signedness: 'std::vector<bool>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
99 | if(_input_mask.size() != _input_dimension)
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp: In member function 'virtual void Options::parse_args(int, char**)':
BRNN/RNNs/Options.cpp:138:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
138 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:144:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
144 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:150:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
150 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:155:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
155 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:169:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
169 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:187:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
187 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:193:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
193 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:198:12: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const unsigned int'} [-Wsign-compare]
198 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
BRNN/RNNs/Options.cpp:207:29: warning: comparison of integer expressions of different signedness: 'std::vector<bool>::size_type' {aka '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/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/protein_util.cpp -o BRNN/protein_util.o
In file included from BRNN/protein_util.cpp:1:
BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder]
211 | int _bp1, _bp2; // bridge partners
| ^~~~
BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder]
206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner
| ^~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)':
BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder]
241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set
| ^~~~~~~~~~~
BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder]
239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment
| ^~~~~
BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder]
245 | SSegment(char symbol):
| ^~~~~~~~
In file included from /usr/include/c++/12/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 '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 '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 '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 '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 'unsigned int'} [-Wsign-compare]
401 | assert(seq_pos == resHydrScales.size());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c BRNN/rnn_util.cpp -o BRNN/rnn_util.o
In file included from BRNN/rnn_util.cpp:4:
BRNN/RNNs/DataSet.h:19:1: warning: 'typedef' was ignored in this declaration
19 | typedef struct StructuredInstanceTemplate {
| ^~~~~~~
BRNN/RNNs/DataSet.h: In constructor 'DataSet::iterator::iterator(DataSet&)':
BRNN/RNNs/DataSet.h:86:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
86 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h: In member function 'bool DataSet::iterator::operator++()':
BRNN/RNNs/DataSet.h:116:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
116 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/DataSet.h:135:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
135 | require(num_nodes == (*_nodes_targets_iter).size(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from BRNN/rnn_util.cpp:7:
BRNN/protein_util.h: In constructor 'Residue::Residue(int, int, char, float, float, float, float, float, char)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:213:3: warning: when initialized here [-Wreorder]
213 | Residue(int index, int sindex, char symbol, float x, float y, float z, float hydr, float acc, char ssbridge):
| ^~~~~~~
BRNN/protein_util.h: In copy constructor 'Residue::Residue(const Residue&)':
BRNN/protein_util.h:209:16: warning: 'Residue::_coord' will be initialized after [-Wreorder]
209 | Coordinate3D _coord; // residue representative coordinates
| ^~~~~~
BRNN/protein_util.h:208:9: warning: 'float Residue::_hydr' [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:208:16: warning: 'Residue::_acc' will be initialized after [-Wreorder]
208 | float _hydr, _acc; // residue hydrophobicity and acc. values
| ^~~~
BRNN/protein_util.h:207:17: warning: 'char Residue::_ssbridge' [-Wreorder]
207 | char _symbol, _ssbridge; // one char standard amino acid symbol and ss bond indicator
| ^~~~~~~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h:211:13: warning: 'Residue::_bp2' will be initialized after [-Wreorder]
211 | int _bp1, _bp2; // bridge partners
| ^~~~
BRNN/protein_util.h:206:24: warning: 'int Residue::_ssp' [-Wreorder]
206 | int _index, _sindex, _ssp; // DSSP index, sequential index and disulfide bond partner
| ^~~~
BRNN/protein_util.h:219:3: warning: when initialized here [-Wreorder]
219 | Residue(const Residue& r):
| ^~~~~~~
BRNN/protein_util.h: In constructor 'SSegment::SSegment(char)':
BRNN/protein_util.h:241:16: warning: 'SSegment::_baricentre' will be initialized after [-Wreorder]
241 | Coordinate3D _baricentre; // baricentrum of C_alpha atoms set
| ^~~~~~~~~~~
BRNN/protein_util.h:239:18: warning: 'SSegment::Hydrophobicity SSegment::_hydr' [-Wreorder]
239 | Hydrophobicity _hydr; // hydropatic tendency (?!) of the segment
| ^~~~~
BRNN/protein_util.h:245:3: warning: when initialized here [-Wreorder]
245 | SSegment(char symbol):
| ^~~~~~~~
BRNN/rnn_util.cpp: In function 'void create_connectivity_input_data(const std::string&, const std::string&, int, int, const std::string&)':
BRNN/rnn_util.cpp:233:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Profile>::size_type' {aka '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 '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 '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 '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 '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 '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
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
BRNN/RNNs/StructureSearch.h:977:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
977 | for(int i=0; i<_nodesInputs.size(); ++i)
| ~^~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/StructureSearch.h:984:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<boost::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 '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]'
BRNN/rnn_util.cpp:99:32: required from here
BRNN/RNNs/RecursiveNN.h:1390:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'unsigned int'} [-Wsign-compare]
1390 | require(_n == toNodes[t]->_encodedInput.size(), "Error in input dim!");
| ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1415:45: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare]
1415 | out_i!=out_end && edge_id[*out_i] < _v; ++out_i) {
BRNN/RNNs/RecursiveNN.h:1418:45: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
1418 | for(int i=_n + edge_id[*out_i]*_m; i<_n + _m*(edge_id[*out_i] + 1); i++) {
| ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BRNN/RNNs/RecursiveNN.h:1384:12: warning: variable 'vertex_id' set but not used [-Wunused-but-set-variable]
1384 | VertexId vertex_id = boost::get(boost::vertex_index, sdag);
| ^~~~~~~~~
BRNN/RNNs/RecursiveNN.h: In instantiation of 'void RecursiveNN<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]'
BRNN/rnn_util.cpp:99:32: required from here
BRNN/RNNs/RecursiveNN.h:1470:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Node*>::size_type' {aka '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 '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]'
BRNN/rnn_util.cpp:396:37: required from here
BRNN/RNNs/StructureSearch.h:186:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Node*>::size_type' {aka 'unsigned int'} [-Wsign-compare]
186 | for(int i=0; i<toNodes.size(); i++) {
| ~^~~~~~~~~~~~~~~
make -C Common lib
make[4]: Entering directory '/build/disulfinder-1.2.11/disulfind/src/Common'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -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/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c CommonMethods.cpp -o CommonMethods.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c ConfusionMatrix.cpp -o ConfusionMatrix.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Exception.cpp -o Exception.o
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c Statistics.cpp -o Statistics.o
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balanc.o eig/balanc.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/balbak.o eig/balbak.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/cdiv.o eig/cdiv.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/elmhes.o eig/elmhes.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/eltran.o eig/eltran.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr.o eig/hqr.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o eig/hqr2.o eig/hqr2.c
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -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 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -O3 -Wall -Wno-deprecated -c coords.cpp -o coords.o
cc -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -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 '/build/disulfinder-1.2.11/disulfind/src/Common'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/disulfinder-1.2.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c disulfinder.cpp -o disulfinder.o
In file included from Input/utils.h:2,
from disulfinder.cpp:8:
Input/Protein.h:19:20: warning: 'aa_three_codes' defined but not used [-Wunused-variable]
19 | static const char *aa_three_codes[23] = {
| ^~~~~~~~~~~~~~
Input/Protein.h:17:20: warning: 'tdb_aa_codes' defined but not used [-Wunused-variable]
17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files
| ^~~~~~~~~~~~
Input/Protein.h:16:20: warning: 'aa_codes' defined but not used [-Wunused-variable]
16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files
| ^~~~~~~~
g++ -o disulfinder disulfinder.o Input/GlobalDescriptor.o Input/createBRNNDataset.o Input/createKernelDataset.o Input/makeWindow.o Input/makeSparseVector.o Input/Protein.o Input/buildXfolds.o SVM/SVMClassifier.o Output/makeHTMLOutput.o Output/utils.o Output/makeASCIIOutput.o FSA-Alignment/fsa.o FSA-Alignment/viterbi_aligner.o NN/multi-array.o NN/array.o NN/brnn-model.o NN/brnn-test.o BRNN/RNNs/Node.o BRNN/RNNs/StructureSearch.o BRNN/RNNs/DataSet.o BRNN/RNNs/DPAG.o BRNN/RNNs/Options.o BRNN/protein_util.o BRNN/blast_util.o BRNN/rnn_util.o -Wl,-z,relro -Wl,-z,now -LCommon/ -lCommon
make[3]: Leaving directory '/build/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/disulfinder-1.2.11'
make[1]: Leaving directory '/build/disulfinder-1.2.11'
dh_auto_test
rm -fr -- /tmp/dh-xdg-rundir-wRPBJsOZ
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/disulfinder-1.2.11'
/usr/bin/make DESTDIR=/build/disulfinder-1.2.11/debian/disulfinder prefix=/usr install
make[2]: Entering directory '/build/disulfinder-1.2.11'
/usr/bin/make -C disulfind/src install
make[3]: Entering directory '/build/disulfinder-1.2.11/disulfind/src'
mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/bin
cp disulfinder /build/disulfinder-1.2.11/debian/disulfinder/usr/bin/
mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder
mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models
cp -r ../Models /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ && find /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/ -depth -ignore_readdir_race -name .svn -execdir rm -rf {} \;
rm -rf /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Models/conn/data/sequences_w5
rm -rf /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/Predictions
rm -rf /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/tmp
make[3]: Leaving directory '/build/disulfinder-1.2.11/disulfind/src'
mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1 && cp disulfinder.1 /build/disulfinder-1.2.11/debian/disulfinder/usr/share/man/man1/
mkdir -p /build/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples && cp examples/res_id_* /build/disulfinder-1.2.11/debian/disulfinder/usr/share/doc/disulfinder/examples/
make[2]: Leaving directory '/build/disulfinder-1.2.11'
make[1]: Leaving directory '/build/disulfinder-1.2.11'
debian/rules override_dh_install
make[1]: Entering directory '/build/disulfinder-1.2.11'
dh_install
mkdir -p /build/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder
mv /build/disulfinder-1.2.11/debian/disulfinder/usr/share/disulfinder/* /build/disulfinder-1.2.11/debian/disulfinder-data/usr/share/disulfinder
make[1]: Leaving directory '/build/disulfinder-1.2.11'
dh_installdocs
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/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
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
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-data/changelog usr/share/doc/disulfinder-data/changelog.Debian
chmod a-x usr/share/doc/disulfinder/changelog usr/share/doc/disulfinder/changelog.Debian usr/share/man/man1/disulfinder.1
gzip -9nf 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
cd '/build/disulfinder-1.2.11'
cd '/build/disulfinder-1.2.11'
dh_fixperms
find debian/disulfinder ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/disulfinder-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/disulfinder/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder-data/usr/share/doc -type f -a -true -a ! -regex 'debian/disulfinder-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/disulfinder-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
find debian/disulfinder/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder-data -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644
find debian/disulfinder/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x
dh_missing
dh_dwz -a
dwz -- debian/disulfinder/usr/bin/disulfinder
dh_strip -a
install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/cf
objcopy --only-keep-debug --compress-debug-sections debian/disulfinder/usr/bin/disulfinder debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/cf/399386bfb96a46706e6adee57920297c48866c.debug
chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/usr/lib/debug/.build-id/cf/399386bfb96a46706e6adee57920297c48866c.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/cf/399386bfb96a46706e6adee57920297c48866c.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: debian/disulfinder/usr/bin/disulfinder contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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 -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 -Pdebian/.debhelper/disulfinder/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=disulfinder-dbgsym "-DDepends=disulfinder (= \${binary:Version})" "-DDescription=debug symbols for disulfinder" -DBuild-Ids=cf399386bfb96a46706e6adee57920297c48866c -DSection=debug -UMulti-Arch -UReplaces -UBreaks
chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/control
dpkg-gencontrol -pdisulfinder -ldebian/changelog -Tdebian/disulfinder.substvars -Pdebian/disulfinder
chmod 0644 -- debian/disulfinder-data/DEBIAN/control
chmod 0644 -- debian/disulfinder/DEBIAN/control
dh_md5sums
install -m0755 -d debian/disulfinder-data/DEBIAN
install -m0755 -d debian/disulfinder/DEBIAN
cd debian/disulfinder >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
cd debian/disulfinder-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/disulfinder/DEBIAN/md5sums
install -m0755 -d debian/.debhelper/disulfinder/dbgsym-root/DEBIAN
cd debian/.debhelper/disulfinder/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
chmod 0644 -- debian/.debhelper/disulfinder/dbgsym-root/DEBIAN/md5sums
chmod 0644 -- debian/disulfinder-data/DEBIAN/md5sums
dh_builddeb
dpkg-deb --root-owner-group --build debian/disulfinder ..
dpkg-deb --root-owner-group --build debian/.debhelper/disulfinder/dbgsym-root ..
dpkg-deb --root-owner-group --build debian/disulfinder-data ..
dpkg-deb: building package 'disulfinder-dbgsym' in '../disulfinder-dbgsym_1.2.11-12_armhf.deb'.
dpkg-deb: building package 'disulfinder-data' in '../disulfinder-data_1.2.11-12_all.deb'.
dpkg-deb: building package 'disulfinder' in '../disulfinder_1.2.11-12_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../disulfinder_1.2.11-12_armhf.buildinfo
dpkg-genchanges --build=binary -O../disulfinder_1.2.11-12_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/31903/tmp/hooks/B01_cleanup finished
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/31903 and its subdirectories
I: Current time: Sun May 7 16:29:39 +14 2023
I: pbuilder-time-stamp: 1683426579