I: pbuilder: network access will be disabled during build
I: Current time: Sat May 13 07:14:07 -12 2023
I: pbuilder-time-stamp: 1684005247
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 [igor_1.4.0+dfsg-4.dsc]
I: copying [./igor_1.4.0+dfsg.orig.tar.xz]
I: copying [./igor_1.4.0+dfsg-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Nov 5 07:49:36 2022 -12
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 ./igor_1.4.0+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting igor in igor-1.4.0+dfsg
dpkg-source: info: unpacking igor_1.4.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking igor_1.4.0+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying get_autoreconf_to_work.patch
dpkg-source: info: applying inline_fix.patch
dpkg-source: info: applying fix-gcc-10.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/12627/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='4ff23738313a4842bd421c695c5ba8bd'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='12627'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gBCkimTT/pbuilderrc_HTCR --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gBCkimTT/b1 --logfile b1/build.log igor_1.4.0+dfsg-4.dsc'
SUDO_GID='114'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux jtx1b 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 23 09:24 bash
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 67632 Sep 20 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 133220 Sep 20 2022 date
-rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 20 2022 df
-rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
-rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
-rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
-rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 20 2022 true
-rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
-rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/12627/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), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so
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 libjemalloc-dev; however:
Package libjemalloc-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgsl-dev; however:
Package libgsl-dev is not installed.
pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however:
Package libblas-dev is not installed.
Package libblas.so 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} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu72{a} libjemalloc-dev{a} libjemalloc2{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, 37 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.6 MB of archives. After unpacking 78.3 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 libblas3 armhf 3.11.0-2 [105 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf libblas-dev armhf 3.11.0-2 [115 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libgslcblas0 armhf 2.7.1+dfsg-3+b1 [87.7 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf libgsl27 armhf 2.7.1+dfsg-3+b1 [773 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf libgsl-dev armhf 2.7.1+dfsg-3+b1 [975 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf libjemalloc2 armhf 5.3.0-1 [206 kB]
Get: 37 http://deb.debian.org/debian bookworm/main armhf libjemalloc-dev armhf 5.3.0-1 [341 kB]
Fetched 20.6 MB in 2s (9651 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(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.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../22-libelf1_0.188-2.1_armhf.deb ...
Unpacking libelf1:armhf (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_armhf.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../24-libicu72_72.1-3_armhf.deb ...
Unpacking libicu72:armhf (72.1-3) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_armhf.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../30-libblas3_3.11.0-2_armhf.deb ...
Unpacking libblas3:armhf (3.11.0-2) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../31-libblas-dev_3.11.0-2_armhf.deb ...
Unpacking libblas-dev:armhf (3.11.0-2) ...
Selecting previously unselected package libgslcblas0:armhf.
Preparing to unpack .../32-libgslcblas0_2.7.1+dfsg-3+b1_armhf.deb ...
Unpacking libgslcblas0:armhf (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package libgsl27:armhf.
Preparing to unpack .../33-libgsl27_2.7.1+dfsg-3+b1_armhf.deb ...
Unpacking libgsl27:armhf (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../34-libgsl-dev_2.7.1+dfsg-3+b1_armhf.deb ...
Unpacking libgsl-dev (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package libjemalloc2:armhf.
Preparing to unpack .../35-libjemalloc2_5.3.0-1_armhf.deb ...
Unpacking libjemalloc2:armhf (5.3.0-1) ...
Selecting previously unselected package libjemalloc-dev.
Preparing to unpack .../36-libjemalloc-dev_5.3.0-1_armhf.deb ...
Unpacking libjemalloc-dev (5.3.0-1) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/igor-1.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../igor_1.4.0+dfsg-4_source.changes
dpkg-buildpackage: info: source package igor
dpkg-buildpackage: info: source version 1.4.0+dfsg-4
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
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/igor-1.4.0+dfsg'
dh_auto_clean
rm -rf docs/latex
rm -rf docs/html
rm -rf config.guess config.sub
make[1]: Leaving directory '/build/igor-1.4.0+dfsg'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:14: installing './compile'
configure.ac:14: installing './config.guess'
configure.ac:14: installing './config.sub'
configure.ac:7: installing './install-sh'
configure.ac:7: installing './missing'
igor_src/Makefile.am: installing './depcomp'
dh_auto_configure
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
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checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
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checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
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checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc... (cached) gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking whether g++ supports C++11 features by default... yes
checking for g++ option to support OpenMP... -fopenmp
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for inline... inline
checking for size_t... yes
checking for pow... yes
checking for sqrt... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating igor_src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in igor_src (/build/igor-1.4.0+dfsg/igor_src)
configure: WARNING: no configuration information is in igor_src
dh_auto_build
make -j3
make[1]: Entering directory '/build/igor-1.4.0+dfsg'
make all-recursive
make[2]: Entering directory '/build/igor-1.4.0+dfsg'
Making all in igor_src
make[3]: Entering directory '/build/igor-1.4.0+dfsg/igor_src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Bestscenarioscounter.o `test -f 'Bestscenarioscounter.cpp' || echo './'`Bestscenarioscounter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp
In file included from /usr/include/c++/12/vector:70,
from /usr/include/c++/12/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Bestscenarioscounter.h:29,
from Bestscenarioscounter.cpp:26:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]':
/usr/include/c++/12/bits/vector.tcc:407:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::iterator' changed in GCC 7.1
407 | 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 = {long double&, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >&, std::__cxx11::list<int, std::allocator<int> >&}; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(const_iterator, _Args&& ...) [with _Args = {long double&, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >&, std::__cxx11::list<int, std::allocator<int> >&}; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]':
/usr/include/c++/12/bits/vector.tcc:375:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' changed in GCC 7.1
375 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:395:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >' changed in GCC 7.1
395 | _M_insert_aux(begin() + __n, std::move(__tmp._M_val()));
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:398:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >' changed in GCC 7.1
398 | _M_realloc_insert(begin() + __n, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double&, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >&, std::__cxx11::list<int, std::allocator<int> >&}; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]',
inlined from 'virtual void Best_scenarios_counter::count_scenario(long double, double, const std::string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)' at Bestscenarioscounter.cpp:77:41:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(const_iterator, _Args&& ...) [with _Args = {long double&, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >&, std::__cxx11::list<int, std::allocator<int> >&}; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]',
inlined from 'virtual void Best_scenarios_counter::count_scenario(long double, double, const std::string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)' at Bestscenarioscounter.cpp:84:36:
/usr/include/c++/12/bits/stl_vector.h:1342:32: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' changed in GCC 7.1
1342 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(const_iterator, _Args&& ...) [with _Args = {long double&, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >&, std::__cxx11::list<int, std::allocator<int> >&}; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]',
inlined from 'virtual void Best_scenarios_counter::count_scenario(long double, double, const std::string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)' at Bestscenarioscounter.cpp:112:36:
/usr/include/c++/12/bits/stl_vector.h:1342:32: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' changed in GCC 7.1
1342 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp
Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar]
1590 | else if ((*iter)=='14'){
| ^~~~
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/bits/forward_list.h:38,
from /usr/include/c++/12/forward_list:38,
from Aligner.h:29,
from Aligner.cpp:27:
/usr/include/c++/12/bits/predefined_ops.h: In function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Iterator2 = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]':
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used
| ^~~~~~~~~~
Deletion.cpp:909:98: note: candidate 1: 'operator+(const char*, int)' (built-in)
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Deletion.h:29,
from Deletion.cpp:26:
Utils.h:69:13: note: candidate 2: 'std::string operator+(const std::string&, Seq_side)'
69 | std::string operator+(const std::string& , Seq_side );
| ^~~~~~~~
Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class);
| ^~~~~~~~~~~
Deletion.cpp:1173:88: note: candidate 1: 'operator+(const char*, int)' (built-in)
Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from Utils.h:31,
from Aligner.h:37:
/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
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'Matrix<double> read_substitution_matrix(const std::string&, std::string)' at Aligner.cpp:1581:25:
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const':
Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type]
1705 | }
| ^
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Alignment_data>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::unordered_map<int, std::vector<Alignment_data> > read_alignments_seq_csv(std::string, double, bool)' at Aligner.cpp:788:38:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Dinuclmarkov.cpp:147:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
| ^~~~~~~~~~~
Dinuclmarkov.cpp:147:95: note: candidate 1: 'operator+(const char*, int)' (built-in)
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Dinuclmarkov.h:32,
from Dinuclmarkov.cpp:26:
Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
Dinuclmarkov.cpp: In member function 'virtual std::queue<int> Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::unordered_map<Seq_type, std::__cxx11::basic_string<char> >&, std::mt19937_64&) const':
Dinuclmarkov.cpp:211:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
211 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
| ^~~~~~~~~~~
Dinuclmarkov.cpp:211:95: note: candidate 1: 'operator+(const char*, int)' (built-in)
Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map<int, double>&, std::queue<std::shared_ptr<Rec_Event> >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const':
Dinuclmarkov.cpp:565:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
| ^~~~~~~~~~~
Dinuclmarkov.cpp:565:95: note: candidate 1: 'operator+(const char*, int)' (built-in)
Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from Aligner.h:35:
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]' at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from 'std::__detail::_Hashtable_alloc<_NodeAlloc>::__node_type* std::__detail::_Hashtable_alloc<_NodeAlloc>::_M_allocate_node(_Args&& ...) [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]' at /usr/include/c++/12/bits/hashtable_policy.h:1968:36:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Distance = int; _Tp = Alignment_data; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]',
inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]' at /usr/include/c++/12/bits/stl_algo.h:1887:34,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]' at /usr/include/c++/12/bits/stl_algo.h:1921:38:
/usr/include/c++/12/bits/stl_algo.h:85:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
85 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
87 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
89 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
94 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
96 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]',
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]' at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'std::unordered_map<int, std::pair<std::__cxx11::basic_string<char>, std::unordered_map<Gene_class, std::vector<Alignment_data> > > > read_alignments_seq_csv_score_range(std::string, Gene_class, double, bool, std::vector<std::pair<const int, const std::__cxx11::basic_string<char> > >, std::unordered_map<int, std::pair<std::__cxx11::basic_string<char>, std::unordered_map<Gene_class, std::vector<Alignment_data> > > >)' at Aligner.cpp:827:8:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'std::unordered_map<int, std::pair<std::__cxx11::basic_string<char>, std::unordered_map<Gene_class, std::vector<Alignment_data> > > > read_alignments_seq_csv_score_range(std::string, Gene_class, double, bool, std::vector<std::pair<const int, const std::__cxx11::basic_string<char> > >, std::unordered_map<int, std::pair<std::__cxx11::basic_string<char>, std::unordered_map<Gene_class, std::vector<Alignment_data> > > >)' at Aligner.cpp:827:8:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp
In file included from /usr/include/c++/12/vector:70,
from /usr/include/c++/12/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Errorscounter.h:29,
from Errorscounter.cpp:26:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple<double, unsigned int, unsigned int>; _Alloc = std::allocator<std::tuple<double, unsigned int, unsigned int> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(const_iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple<double, unsigned int, unsigned int>; _Alloc = std::allocator<std::tuple<double, unsigned int, unsigned int> >]':
/usr/include/c++/12/bits/vector.tcc:375:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator' changed in GCC 7.1
375 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:398:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >' changed in GCC 7.1
398 | _M_realloc_insert(begin() + __n, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple<double, unsigned int, unsigned int>; _Alloc = std::allocator<std::tuple<double, unsigned int, unsigned int> >]',
inlined from 'virtual void Errors_counter::count_scenario(long double, double, const std::string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)' at Errorscounter.cpp:94:42:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(const_iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple<double, unsigned int, unsigned int>; _Alloc = std::allocator<std::tuple<double, unsigned int, unsigned int> >]',
inlined from 'virtual void Errors_counter::count_scenario(long double, double, const std::string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)' at Errorscounter.cpp:101:37:
/usr/include/c++/12/bits/stl_vector.h:1342:32: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator' changed in GCC 7.1
1342 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(const_iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple<double, unsigned int, unsigned int>; _Alloc = std::allocator<std::tuple<double, unsigned int, unsigned int> >]',
inlined from 'virtual void Errors_counter::count_scenario(long double, double, const std::string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)' at Errorscounter.cpp:111:37:
/usr/include/c++/12/bits/stl_vector.h:1342:32: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator' changed in GCC 7.1
1342 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp
Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class);
| ^~~~~~~~~~~
Genechoice.cpp:908:94: note: candidate 1: 'operator+(const char*, int)' (built-in)
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Genechoice.h:29,
from Genechoice.cpp:26:
Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/bits/hashtable_policy.h:35,
from /usr/include/c++/12/bits/hashtable.h:35,
from /usr/include/c++/12/unordered_map:46,
from Rec_Event.h:30:
/usr/include/c++/12/bits/predefined_ops.h: In function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]':
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from Rec_Event.h:32:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, const int&, const int&, double}; _Tp = std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>; _Alloc = std::allocator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> >]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In file included from /usr/include/c++/12/queue:62,
from Errorrate.h:38:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31:
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: 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/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: 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/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1844 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1844:5: 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/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from Rec_Event.h:32,
from Model_Parms.h:33,
from GenModel.h:32,
from GenModel.cpp:28:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Alignment_data&}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<Alignment_data>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from Aligner.h:35,
from Rec_Event.h:41:
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<D_position_comparator>]':
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]' at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from 'std::__detail::_Hashtable_alloc<_NodeAlloc>::__node_type* std::__detail::_Hashtable_alloc<_NodeAlloc>::_M_allocate_node(_Args&& ...) [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]' at /usr/include/c++/12/bits/hashtable_policy.h:1968:36:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
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 = Alignment_data; _Alloc = std::allocator<Alignment_data>]',
inlined from 'std::vector<std::tuple<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::unordered_map<Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> >, std::hash<Gene_class>, std::equal_to<Gene_class>, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > > > > > > get_best_aligns(const std::vector<std::tuple<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::unordered_map<Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> >, std::hash<Gene_class>, std::equal_to<Gene_class>, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > > > > > >&, Gene_class)' at GenModel.cpp:686:64:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/vector.tcc:232:44,
inlined from 'std::vector<std::tuple<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::unordered_map<Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> >, std::hash<Gene_class>, std::equal_to<Gene_class>, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > > > > > > get_best_aligns(const std::vector<std::tuple<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::unordered_map<Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> >, std::hash<Gene_class>, std::equal_to<Gene_class>, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > > > > > >&, Gene_class)' at GenModel.cpp:689:16:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from Utils.h:31:
/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/queue:62,
from Rec_Event.h:37:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Distance = int; _Tp = tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
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 'virtual void Hypermutation_full_Nmer_errorrate::update()' at HypermutationfullNmererrorrate.cpp:961:35:
/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 function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'virtual void Hypermutation_full_Nmer_errorrate::update()' at HypermutationfullNmererrorrate.cpp:966:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void Hypermutation_full_Nmer_errorrate::build_upper_bound_matrix(size_t, size_t)' at HypermutationfullNmererrorrate.cpp:292:26:
/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 function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'virtual void Hypermutation_full_Nmer_errorrate::build_upper_bound_matrix(size_t, size_t)' at HypermutationfullNmererrorrate.cpp:294:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual const double& Hypermutation_full_Nmer_errorrate::get_err_rate_upper_bound(size_t, size_t)' at HypermutationfullNmererrorrate.cpp:249:27:
/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 function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'virtual const double& Hypermutation_full_Nmer_errorrate::get_err_rate_upper_bound(size_t, size_t)' at HypermutationfullNmererrorrate.cpp:251:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]',
inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]' at /usr/include/c++/12/bits/stl_algo.h:1887:34,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]' at /usr/include/c++/12/bits/stl_algo.h:1921:38:
/usr/include/c++/12/bits/stl_algo.h:85:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
85 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
87 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
89 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
94 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
96 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]',
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]' at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, const int&, const int&, double}; _Tp = std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>; _Alloc = std::allocator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> >]',
inlined from 'virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)' at Genechoice.cpp:1360:65:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]',
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)' at Genechoice.cpp:1371:10:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]' at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from 'virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)' at Genechoice.cpp:1371:10:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]' at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from 'std::__detail::_ReuseOrAllocNode<_NodeAlloc>::__node_type* std::__detail::_ReuseOrAllocNode<_NodeAlloc>::operator()(_Args&& ...) const [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]' at /usr/include/c++/12/bits/hashtable_policy.h:177:35:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]' at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from 'std::__detail::_ReuseOrAllocNode<_NodeAlloc>::__node_type* std::__detail::_ReuseOrAllocNode<_NodeAlloc>::operator()(_Args&& ...) const [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]' at /usr/include/c++/12/bits/hashtable_policy.h:177:35,
inlined from 'void std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _Hash, _RangeHash, _Unused, _RehashPolicy, _Traits>::_M_assign(_Ht&&, const _NodeGenerator&) [with _Ht = const std::_Hashtable<Gene_class, std::pair<const Gene_class, std::vector<Alignment_data> >, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data> > >, std::__detail::_Select1st, std::equal_to<Gene_class>, std::hash<Gene_class>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >&; _NodeGenerator = std::__detail::_ReuseOrAllocNode<std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> > >; _Key = Gene_class; _Value = std::pair<const Gene_class, std::vector<Alignment_data> >; _Alloc = std::allocator<std::pair<const Gene_class, std::vector<Alignment_data> > >; _ExtractKey = std::__detail::_Select1st; _Equal = std::equal_to<Gene_class>; _Hash = std::hash<Gene_class>; _RangeHash = std::__detail::_Mod_range_hashing; _Unused = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits<true, false, true>]' at /usr/include/c++/12/bits/hashtable.h:1357:24:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp
In file included from Errorrate.h:29,
from Hypermutationglobalerrorrate.h:30,
from Hypermutationglobalerrorrate.cpp:27:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Insertion.cpp:244:93: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class);
| ^~~~~~~~~~~
Insertion.cpp:244:93: note: candidate 1: 'operator+(const char*, int)' (built-in)
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Insertion.h:30,
from Insertion.cpp:27:
Utils.h:68:13: note: candidate 2: 'std::string operator+(const std::string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp
In file included from /usr/include/c++/12/vector:70,
from Rec_Event.h:32,
from Model_Parms.h:33,
from Model_Parms.cpp:30:
/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
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference 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 Model_Parms::read_model_parms(std::string)' at Model_Parms.cpp:718:32:
/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::vector<_Tp, _Alloc>::reference 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 Model_Parms::read_model_parms(std::string)' at Model_Parms.cpp:721:32:
/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::vector<_Tp, _Alloc>::reference 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 Model_Parms::read_model_parms(std::string)' at Model_Parms.cpp:759:31:
/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::vector<_Tp, _Alloc>::reference 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 Model_Parms::read_model_parms(std::string)' at Model_Parms.cpp:762:31:
/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp
In file included from Errorrate.h:29,
from Singleerrorrate.h:30,
from Singleerrorrate.cpp:27:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp
main.cpp: In function 'int main(int, char**)':
main.cpp:257:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
257 | system(&("man igor")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~
main.cpp:289:32: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
289 | freopen(argv[++carg_i],"a+",stdout);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1565:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1565 | system(&("mkdir " + cl_path )[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1716:23: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1716 | system(&("mkdir " + cl_path + "run_demo")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1750:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
1750 | system(&("mkdir " + cl_path + "aligns")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2058:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
2058 | system(&("mkdir " + cl_path + batchname + "output")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2062:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
2062 | system(&("mkdir " + cl_path + batchname + "inference")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2068:39: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
2068 | system(&("mkdir " + cl_path + batchname + "evaluate")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2078:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
2078 | system(&("mkdir " + cl_path + batchname + "generated")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Deletion.h:29,
from main.cpp:28:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In file included from /usr/include/c++/12/vector:63,
from Rec_Event.h:32:
/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]':
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]',
inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]' at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from 'std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]' at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from 'static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]' at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from 'std::__detail::_Hashtable_alloc<_NodeAlloc>::__node_type* std::__detail::_Hashtable_alloc<_NodeAlloc>::_M_allocate_node(_Args&& ...) [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]' at /usr/include/c++/12/bits/hashtable_policy.h:1968:36:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl
libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/build/igor-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp
make[3]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src'
make[3]: Entering directory '/build/igor-1.4.0+dfsg'
make[3]: Leaving directory '/build/igor-1.4.0+dfsg'
make[2]: Leaving directory '/build/igor-1.4.0+dfsg'
make[1]: Leaving directory '/build/igor-1.4.0+dfsg'
dh_auto_test
make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1
make[1]: Entering directory '/build/igor-1.4.0+dfsg'
Making check in igor_src
make[2]: Entering directory '/build/igor-1.4.0+dfsg/igor_src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src'
make[2]: Entering directory '/build/igor-1.4.0+dfsg'
make[2]: Leaving directory '/build/igor-1.4.0+dfsg'
make[1]: Leaving directory '/build/igor-1.4.0+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_installdirs
dh_auto_install --destdir=debian/igor/
make -j1 install DESTDIR=/build/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/igor-1.4.0+dfsg'
Making install in igor_src
make[2]: Entering directory '/build/igor-1.4.0+dfsg/igor_src'
make[3]: Entering directory '/build/igor-1.4.0+dfsg/igor_src'
/bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c igor '/build/igor-1.4.0+dfsg/debian/igor/usr/bin'
libtool: install: /usr/bin/install -c igor /build/igor-1.4.0+dfsg/debian/igor/usr/bin/igor
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src'
make[2]: Leaving directory '/build/igor-1.4.0+dfsg/igor_src'
make[2]: Entering directory '/build/igor-1.4.0+dfsg'
make[3]: Entering directory '/build/igor-1.4.0+dfsg'
/bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/bin'
/usr/bin/install -c scripts/igor-compute_pgen '/build/igor-1.4.0+dfsg/debian/igor/usr/bin'
mkdir -p /build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models
cp -r models/* /build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models
/bin/mkdir -p '/build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo'
/usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/build/igor-1.4.0+dfsg/debian/igor/usr/share/igor/demo'
make[3]: Leaving directory '/build/igor-1.4.0+dfsg'
make[2]: Leaving directory '/build/igor-1.4.0+dfsg'
make[1]: Leaving directory '/build/igor-1.4.0+dfsg'
dh_installdocs
dh_installchangelogs
dh_installexamples
debian/rules override_dh_installman
make[1]: Entering directory '/build/igor-1.4.0+dfsg'
mv debian/igor1 debian/igor.1
dh_installman
make[1]: Leaving directory '/build/igor-1.4.0+dfsg'
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/igor-1.4.0+dfsg'
dh_fixperms
find debian -name "*.fasta" -exec chmod -x \{\} \;
make[1]: Leaving directory '/build/igor-1.4.0+dfsg'
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/igor/usr/bin/igor contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against libblas.so.3 (it uses none of the library's symbols)
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-4_armhf.deb'.
dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../igor_1.4.0+dfsg-4_armhf.buildinfo
dpkg-genchanges --build=binary -O../igor_1.4.0+dfsg-4_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: 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/12627 and its subdirectories
I: Current time: Sat May 13 07:19:24 -12 2023
I: pbuilder-time-stamp: 1684005564