Sun May 7 04:07:13 UTC 2023 I: starting to build freebayes/bookworm/armhf on jenkins on '2023-05-07 04:06'
Sun May 7 04:07:13 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_33/225/console.log
Sun May 7 04:07:13 UTC 2023 I: Downloading source for bookworm/freebayes=1.3.6-2
--2023-05-07 04:07:13-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/freebayes/freebayes_1.3.6-2.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2232 (2.2K) [text/prs.lines.tag]
Saving to: ‘freebayes_1.3.6-2.dsc’
0K .. 100% 164M=0s
2023-05-07 04:07:13 (164 MB/s) - ‘freebayes_1.3.6-2.dsc’ saved [2232/2232]
Sun May 7 04:07:15 UTC 2023 I: freebayes_1.3.6-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: freebayes
Binary: freebayes
Architecture: any
Version: 1.3.6-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Brad Chapman <chapmanb@50mail.com>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/ekg/freebayes
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/freebayes
Vcs-Git: https://salsa.debian.org/med-team/freebayes.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel <!nocheck>, libvcflib-tools <!nocheck>, debhelper
Package-List:
freebayes deb science optional arch=any
Checksums-Sha1:
2513323e336e02b5cc83d43c9f5b725579c0b75a 2898209 freebayes_1.3.6.orig.tar.gz
504b332ace3ff066468126e5559e058877bdfa0c 11440 freebayes_1.3.6-2.debian.tar.xz
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d668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044 2898209 freebayes_1.3.6.orig.tar.gz
2fbada9aaa038dc048d99a28e91201f4b57f240a5119fd01e83bdf3224e63872 11440 freebayes_1.3.6-2.debian.tar.xz
Files:
e8fe2bf8bb0139bb313744e5fb8e4105 2898209 freebayes_1.3.6.orig.tar.gz
cd9f68ade2865de3a9d15cab4fce73fe 11440 freebayes_1.3.6-2.debian.tar.xz
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Sun May 7 04:07:15 UTC 2023 I: Checking whether the package is not for us
Sun May 7 04:07:15 UTC 2023 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net.
Sun May 7 04:07:15 UTC 2023 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net.
Sun May 7 04:29:58 UTC 2023 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat May 6 16:07:26 -12 2023
I: pbuilder-time-stamp: 1683432446
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 [freebayes_1.3.6-2.dsc]
I: copying [./freebayes_1.3.6.orig.tar.gz]
I: copying [./freebayes_1.3.6-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Nov 1 01:45:15 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 ./freebayes_1.3.6-2.dsc: no acceptable signature found
dpkg-source: info: extracting freebayes in freebayes-1.3.6
dpkg-source: info: unpacking freebayes_1.3.6.orig.tar.gz
dpkg-source: info: unpacking freebayes_1.3.6-2.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3075/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='9feb12fccfd94457ab40a4dcd2694105'
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='3075'
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.7UXDtAQ8/pbuilderrc_VtEJ --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.7UXDtAQ8/b1 --logfile b1/build.log freebayes_1.3.6-2.dsc'
SUDO_GID='113'
SUDO_UID='107'
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 ff4a 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l 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/3075/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), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools, debhelper
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19329 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on meson; however:
Package meson is not installed.
pbuilder-satisfydepends-dummy depends on ninja-build; however:
Package ninja-build is not installed.
pbuilder-satisfydepends-dummy depends on pkg-config; however:
Package pkg-config is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbamtools-dev; however:
Package libbamtools-dev is not installed.
pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.0~rc2+dfsg-3~); however:
Package libvcflib-dev is not installed.
pbuilder-satisfydepends-dummy depends on libtabixpp-dev; however:
Package libtabixpp-dev is not installed.
pbuilder-satisfydepends-dummy depends on libseqlib-dev (>= 1.1.2+dfsg-5); however:
Package libseqlib-dev is not installed.
pbuilder-satisfydepends-dummy depends on bc; however:
Package bc is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on parallel; however:
Package parallel is not installed.
pbuilder-satisfydepends-dummy depends on libvcflib-tools; however:
Package libvcflib-tools is not installed.
pbuilder-satisfydepends-dummy depends on debhelper; however:
Package debhelper is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas3{a} libbrotli1{a} libbsd0{a} libbwa-dev{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp-dev{a} libjsoncpp25{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib-dev{a} libseqlib2{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib1{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6{a} littler{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} openssl{a} parallel{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samtools{a} sensible-utils{a} sysstat{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bcron cron curl libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx psmisc publicsuffix r-base-dev r-cran-abind r-cran-bit64 r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-domc r-cran-dplyr r-cran-formattable r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-interp r-cran-knitr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rsqlite r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-vdiffr r-cran-waldo r-cran-xml2 r-doc-html r-recommended shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 187 newly installed, 0 to remove and 0 not upgraded.
Need to get 110 MB of archives. After unpacking 259 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B]
Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf openssl armhf 3.0.8-1 [1373 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf ca-certificates all 20230311 [153 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 21 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 22 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 23 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 24 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf ucf all 3.0043+nmu1 [55.2 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 28 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf bc armhf 1.07.1-3 [104 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 35 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 36 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 37 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 38 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 39 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 40 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 41 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 42 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 43 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 44 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 45 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 46 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 47 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 48 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB]
Get: 49 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB]
Get: 50 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB]
Get: 51 http://deb.debian.org/debian bookworm/main armhf fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 52 http://deb.debian.org/debian bookworm/main armhf fontconfig-config armhf 2.14.1-4 [315 kB]
Get: 53 http://deb.debian.org/debian bookworm/main armhf libfontconfig1 armhf 2.14.1-4 [368 kB]
Get: 54 http://deb.debian.org/debian bookworm/main armhf fontconfig armhf 2.14.1-4 [448 kB]
Get: 55 http://deb.debian.org/debian bookworm/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-4 [130 kB]
Get: 56 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB]
Get: 57 http://deb.debian.org/debian bookworm/main armhf libbamtools-dev armhf 2.5.2+dfsg-4 [198 kB]
Get: 58 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB]
Get: 59 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB]
Get: 60 http://deb.debian.org/debian bookworm/main armhf libbwa-dev armhf 0.7.17-7+b2 [148 kB]
Get: 61 http://deb.debian.org/debian bookworm/main armhf libpixman-1-0 armhf 0.42.2-1 [465 kB]
Get: 62 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB]
Get: 63 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB]
Get: 64 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB]
Get: 65 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB]
Get: 66 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB]
Get: 67 http://deb.debian.org/debian bookworm/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get: 68 http://deb.debian.org/debian bookworm/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get: 69 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB]
Get: 70 http://deb.debian.org/debian bookworm/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB]
Get: 71 http://deb.debian.org/debian bookworm/main armhf libcairo2 armhf 1.16.0-7 [493 kB]
Get: 72 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB]
Get: 73 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB]
Get: 74 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB]
Get: 75 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB]
Get: 76 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB]
Get: 77 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB]
Get: 78 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB]
Get: 79 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB]
Get: 80 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB]
Get: 81 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB]
Get: 82 http://deb.debian.org/debian bookworm/main armhf libdatrie1 armhf 0.2.13-2+b1 [39.9 kB]
Get: 83 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB]
Get: 84 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB]
Get: 85 http://deb.debian.org/debian bookworm/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4+b1 [5220 B]
Get: 86 http://deb.debian.org/debian bookworm/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4+b1 [4732 B]
Get: 87 http://deb.debian.org/debian bookworm/main armhf libfastahack0 armhf 1.0.0+dfsg-10 [24.3 kB]
Get: 88 http://deb.debian.org/debian bookworm/main armhf libfastahack-dev armhf 1.0.0+dfsg-10 [27.9 kB]
Get: 89 http://deb.debian.org/debian bookworm/main armhf libfml0 armhf 0.1+git20190320.b499514-1+b1 [70.8 kB]
Get: 90 http://deb.debian.org/debian bookworm/main armhf libfml-dev armhf 0.1+git20190320.b499514-1+b1 [82.4 kB]
Get: 91 http://deb.debian.org/debian bookworm/main armhf libfribidi0 armhf 1.0.8-2.1 [63.1 kB]
Get: 92 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB]
Get: 93 http://deb.debian.org/debian bookworm/main armhf libglib2.0-0 armhf 2.74.6-2 [1227 kB]
Get: 94 http://deb.debian.org/debian bookworm/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB]
Get: 95 http://deb.debian.org/debian bookworm/main armhf libharfbuzz0b armhf 6.0.0+dfsg-3 [1893 kB]
Get: 96 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB]
Get: 97 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB]
Get: 98 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB]
Get: 99 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB]
Get: 100 http://deb.debian.org/debian bookworm/main armhf x11-common all 1:7.7+23 [252 kB]
Get: 101 http://deb.debian.org/debian bookworm/main armhf libice6 armhf 2:1.0.10-1 [51.9 kB]
Get: 102 http://deb.debian.org/debian bookworm/main armhf libjbig0 armhf 2.1-6.1 [27.1 kB]
Get: 103 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get: 104 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB]
Get: 105 http://deb.debian.org/debian bookworm/main armhf libjsoncpp-dev armhf 1.9.5-4 [26.4 kB]
Get: 106 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB]
Get: 107 http://deb.debian.org/debian bookworm/main armhf liblerc4 armhf 4.0.0+ds-2 [137 kB]
Get: 108 http://deb.debian.org/debian bookworm/main armhf libncurses6 armhf 6.4-2 [81.0 kB]
Get: 109 http://deb.debian.org/debian bookworm/main armhf libthai-data all 0.1.29-1 [176 kB]
Get: 110 http://deb.debian.org/debian bookworm/main armhf libthai0 armhf 0.1.29-1 [54.3 kB]
Get: 111 http://deb.debian.org/debian bookworm/main armhf libpango-1.0-0 armhf 1.50.12+ds-1 [188 kB]
Get: 112 http://deb.debian.org/debian bookworm/main armhf libpangoft2-1.0-0 armhf 1.50.12+ds-1 [40.9 kB]
Get: 113 http://deb.debian.org/debian bookworm/main armhf libpangocairo-1.0-0 armhf 1.50.12+ds-1 [30.3 kB]
Get: 114 http://deb.debian.org/debian bookworm/main armhf libpaper1 armhf 1.1.29 [11.9 kB]
Get: 115 http://deb.debian.org/debian bookworm/main armhf libpaper-utils armhf 1.1.29 [8400 B]
Get: 116 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get: 117 http://deb.debian.org/debian bookworm/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get: 118 http://deb.debian.org/debian bookworm/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get: 119 http://deb.debian.org/debian bookworm/main armhf libssw0 armhf 1.1-13 [21.2 kB]
Get: 120 http://deb.debian.org/debian bookworm/main armhf libseqlib2 armhf 1.2.0+dfsg-9 [136 kB]
Get: 121 http://deb.debian.org/debian bookworm/main armhf libssw-dev armhf 1.1-13 [24.3 kB]
Get: 122 http://deb.debian.org/debian bookworm/main armhf libseqlib-dev armhf 1.2.0+dfsg-9 [206 kB]
Get: 123 http://deb.debian.org/debian bookworm/main armhf libsm6 armhf 2:1.2.3-1 [33.0 kB]
Get: 124 http://deb.debian.org/debian bookworm/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12+b1 [33.0 kB]
Get: 125 http://deb.debian.org/debian bookworm/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12+b1 [38.2 kB]
Get: 126 http://deb.debian.org/debian bookworm/main armhf libtabixpp0 armhf 1.1.2-1 [8696 B]
Get: 127 http://deb.debian.org/debian bookworm/main armhf libtabixpp-dev armhf 1.1.2-1 [8532 B]
Get: 128 http://deb.debian.org/debian bookworm/main armhf libtcl8.6 armhf 8.6.13+dfsg-2 [922 kB]
Get: 129 http://deb.debian.org/debian bookworm/main armhf libwebp7 armhf 1.2.4-0.1 [242 kB]
Get: 130 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-5 [295 kB]
Get: 131 http://deb.debian.org/debian bookworm/main armhf libxft2 armhf 2.3.6-1 [53.8 kB]
Get: 132 http://deb.debian.org/debian bookworm/main armhf libxss1 armhf 1:1.2.3-1 [17.2 kB]
Get: 133 http://deb.debian.org/debian bookworm/main armhf libtk8.6 armhf 8.6.13-2 [689 kB]
Get: 134 http://deb.debian.org/debian bookworm/main armhf libvcflib1 armhf 1.0.3+dfsg-2 [128 kB]
Get: 135 http://deb.debian.org/debian bookworm/main armhf libvcflib-dev armhf 1.0.3+dfsg-2 [85.2 kB]
Get: 136 http://deb.debian.org/debian bookworm/main armhf zip armhf 3.0-13 [218 kB]
Get: 137 http://deb.debian.org/debian bookworm/main armhf unzip armhf 6.0-28 [152 kB]
Get: 138 http://deb.debian.org/debian bookworm/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 139 http://deb.debian.org/debian bookworm/main armhf libxt6 armhf 1:1.2.1-1.1 [157 kB]
Get: 140 http://deb.debian.org/debian bookworm/main armhf r-base-core armhf 4.2.2.20221110-2 [25.6 MB]
Get: 141 http://deb.debian.org/debian bookworm/main armhf r-cran-littler armhf 0.3.17-1 [93.4 kB]
Get: 142 http://deb.debian.org/debian bookworm/main armhf littler all 0.3.17-1 [14.4 kB]
Get: 143 http://deb.debian.org/debian bookworm/main armhf r-cran-pkgkitten all 0.2.2-2 [27.0 kB]
Get: 144 http://deb.debian.org/debian bookworm/main armhf r-cran-rcpp armhf 1.0.10-1 [2042 kB]
Get: 145 http://deb.debian.org/debian bookworm/main armhf r-cran-plyr armhf 1.8.8-1 [829 kB]
Get: 146 http://deb.debian.org/debian bookworm/main armhf r-cran-cli armhf 3.6.0-1 [1276 kB]
Get: 147 http://deb.debian.org/debian bookworm/main armhf r-cran-glue armhf 1.6.2-1 [151 kB]
Get: 148 http://deb.debian.org/debian bookworm/main armhf r-cran-gtable all 0.3.1+dfsg-1 [165 kB]
Get: 149 http://deb.debian.org/debian bookworm/main armhf r-cran-isoband armhf 0.2.7-1 [1610 kB]
Get: 150 http://deb.debian.org/debian bookworm/main armhf r-cran-rlang armhf 1.0.6-1 [1612 kB]
Get: 151 http://deb.debian.org/debian bookworm/main armhf r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB]
Get: 152 http://deb.debian.org/debian bookworm/main armhf r-cran-mass armhf 7.3-58.2-1 [1120 kB]
Get: 153 http://deb.debian.org/debian bookworm/main armhf r-cran-lattice armhf 0.20-45-3 [1176 kB]
Get: 154 http://deb.debian.org/debian bookworm/main armhf r-cran-nlme armhf 3.1.162-1 [2246 kB]
Get: 155 http://deb.debian.org/debian bookworm/main armhf r-cran-matrix armhf 1.5-3-1 [3758 kB]
Get: 156 http://deb.debian.org/debian bookworm/main armhf r-cran-mgcv armhf 1.8-41-1 [3127 kB]
Get: 157 http://deb.debian.org/debian bookworm/main armhf r-cran-farver armhf 2.1.1-1 [1391 kB]
Get: 158 http://deb.debian.org/debian bookworm/main armhf r-cran-labeling all 0.4.2-1 [62.7 kB]
Get: 159 http://deb.debian.org/debian bookworm/main armhf r-cran-colorspace armhf 2.1-0+dfsg-1 [1688 kB]
Get: 160 http://deb.debian.org/debian bookworm/main armhf r-cran-munsell all 0.5.0-2 [236 kB]
Get: 161 http://deb.debian.org/debian bookworm/main armhf r-cran-r6 all 2.5.1-1 [105 kB]
Get: 162 http://deb.debian.org/debian bookworm/main armhf r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get: 163 http://deb.debian.org/debian bookworm/main armhf r-cran-viridislite all 0.4.1-1 [1299 kB]
Get: 164 http://deb.debian.org/debian bookworm/main armhf r-cran-scales all 1.2.1-1 [614 kB]
Get: 165 http://deb.debian.org/debian bookworm/main armhf r-cran-fansi armhf 1.0.4-1 [609 kB]
Get: 166 http://deb.debian.org/debian bookworm/main armhf r-cran-magrittr armhf 2.0.3-1 [201 kB]
Get: 167 http://deb.debian.org/debian bookworm/main armhf r-cran-utf8 armhf 1.2.3-1 [129 kB]
Get: 168 http://deb.debian.org/debian bookworm/main armhf r-cran-vctrs armhf 0.5.2-1 [1342 kB]
Get: 169 http://deb.debian.org/debian bookworm/main armhf r-cran-pillar all 1.8.1+dfsg-1 [463 kB]
Get: 170 http://deb.debian.org/debian bookworm/main armhf r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get: 171 http://deb.debian.org/debian bookworm/main armhf r-cran-tibble armhf 3.1.8+dfsg-1 [513 kB]
Get: 172 http://deb.debian.org/debian bookworm/main armhf r-cran-withr all 2.5.0-1 [236 kB]
Get: 173 http://deb.debian.org/debian bookworm/main armhf r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB]
Get: 174 http://deb.debian.org/debian bookworm/main armhf r-cran-gridbase all 0.4-7-5 [163 kB]
Get: 175 http://deb.debian.org/debian bookworm/main armhf libvcflib-tools armhf 1.0.3+dfsg-2 [657 kB]
Get: 176 http://deb.debian.org/debian bookworm/main armhf ninja-build armhf 1.11.1-1 [122 kB]
Get: 177 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 178 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-2 [76.2 kB]
Get: 179 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-2 [131 kB]
Get: 180 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB]
Get: 181 http://deb.debian.org/debian bookworm/main armhf meson all 1.0.1-5 [548 kB]
Get: 182 http://deb.debian.org/debian bookworm/main armhf sysstat armhf 12.6.1-1 [575 kB]
Get: 183 http://deb.debian.org/debian bookworm/main armhf parallel all 20221122+ds-2 [1873 kB]
Get: 184 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB]
Get: 185 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get: 186 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
Get: 187 http://deb.debian.org/debian bookworm/main armhf samtools armhf 1.16.1-1 [575 kB]
Fetched 110 MB in 12s (8829 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:armhf.
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Unpacking libpython3.11-minimal:armhf (3.11.2-6) ...
Selecting previously unselected package libexpat1:armhf.
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Setting up libpython3.11-minimal:armhf (3.11.2-6) ...
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Unpacking python3-minimal (3.11.2-1+b1) ...
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invoke-rc.d: could not determine current runlevel
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update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Creating config file /etc/R/Renviron with new version
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Setting up r-cran-magrittr (2.0.3-1) ...
Setting up libseqlib2:armhf (1.2.0+dfsg-9) ...
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Setting up python3-pkg-resources (66.1.1-1) ...
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Setting up r-cran-gridbase (0.4-7-5) ...
Setting up littler (0.3.17-1) ...
Setting up python3-setuptools (66.1.1-1) ...
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Setting up r-cran-fansi (1.0.4-1) ...
Setting up r-cran-mass (7.3-58.2-1) ...
Setting up libseqlib-dev:armhf (1.2.0+dfsg-9) ...
Setting up meson (1.0.1-5) ...
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Processing triggers for libc-bin (2.36-9) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
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done.
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/freebayes-1.3.6/ && 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 > ../freebayes_1.3.6-2_source.changes
dpkg-buildpackage: info: source package freebayes
dpkg-buildpackage: info: source version 1.3.6-2
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 --buildsystem=meson --builddir=build
dh_auto_clean -O--buildsystem=meson -O--builddir=build
dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build
dh_clean -O--buildsystem=meson -O--builddir=build
debian/rules binary
dh binary --buildsystem=meson --builddir=build
dh_update_autotools_config -O--buildsystem=meson -O--builddir=build
dh_autoreconf -O--buildsystem=meson -O--builddir=build
dh_auto_configure -O--buildsystem=meson -O--builddir=build
cd build && LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf
The Meson build system
Version: 1.0.1
Source dir: /build/freebayes-1.3.6
Build dir: /build/freebayes-1.3.6/build
Build type: native build
Project name: freebayes
Project version: 1.3.6
C compiler for the host machine: cc (gcc 12.2.0 "cc (Debian 12.2.0-14) 12.2.0")
C linker for the host machine: cc ld.bfd 2.40
C++ compiler for the host machine: c++ (gcc 12.2.0 "c++ (Debian 12.2.0-14) 12.2.0")
C++ linker for the host machine: c++ ld.bfd 2.40
Host machine cpu family: arm
Host machine cpu: armv7l
Found pkg-config: /usr/bin/pkg-config (1.8.1)
Run-time dependency zlib found: YES 1.2.13
Run-time dependency liblzma found: YES 5.4.1
Run-time dependency threads found: YES
Library tabixpp found: YES
Run-time dependency htslib found: YES 1.16
Library tabixpp found: YES
Run-time dependency libvcflib found: YES 1.0
Run-time dependency libseqlib found: YES 1.0
Compiler for C++ supports arguments -fpermissive: YES
Compiler for C++ supports arguments -Wno-reorder: YES
Compiler for C++ supports arguments -Wno-sign-compare: YES
Compiler for C++ supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
Program prove found: YES (/usr/bin/prove)
Build targets in project: 3
freebayes 1.3.6
User defined options
buildtype : plain
libdir : lib/arm-linux-gnueabihf
localstatedir: /var
prefix : /usr
sysconfdir : /etc
wrap_mode : nodownload
Found ninja-1.11.1 at /usr/bin/ninja
dh_auto_build -O--buildsystem=meson -O--builddir=build
cd build && LC_ALL=C.UTF-8 ninja -j3 -v
[1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp
[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp
In file included from /usr/include/c++/12/vector:70,
from ../src/Bias.h:8,
from ../src/Bias.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void Bias::open(std::string&)’ at ../src/Bias.cpp:32:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp
[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp
[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp
../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’:
../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch]
160 | switch (this->type) {
| ^
../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch]
In file included from /usr/include/c++/12/vector:70,
from ../src/Allele.h:8,
from ../src/Allele.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::vector<Allele>&, bool (*)(Allele&, Allele&))’ at ../src/Allele.cpp:815:38:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::vector<Allele>&, bool (*)(Allele&, Allele&))’ at ../src/Allele.cpp:808:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::vector<Allele>&)’ at ../src/Allele.cpp:835:38:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::vector<Allele>&)’ at ../src/Allele.cpp:828:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::__cxx11::list<Allele>&, bool (*)(Allele&, Allele&))’ at ../src/Allele.cpp:795:38:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::__cxx11::list<Allele>&, bool (*)(Allele&, Allele&))’ at ../src/Allele.cpp:788:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<Allele> alleleUnion(std::vector<Allele>&, std::vector<Allele>&)’ at ../src/Allele.cpp:1489:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Allele> genotypeAllelesFromAlleleGroups(std::vector<std::vector<Allele*> >&)’ at ../src/Allele.cpp:862:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Allele> genotypeAllelesFromAlleles(std::vector<Allele>&)’ at ../src/Allele.cpp:889:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Allele> genotypeAllelesFromAlleles(std::vector<Allele*>&)’ at ../src/Allele.cpp:871:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Allele> genotypeAllelesFromAlleleGroups(std::vector<std::vector<Allele> >&)’ at ../src/Allele.cpp:880:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../src/Allele.h:10:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Allele&>, std::tuple<>}; _Key = Allele; _Val = std::pair<const Allele, int>; _KeyOfValue = std::_Select1st<std::pair<const Allele, int> >; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::map<Allele, int> countAlleles(std::vector<Allele*>&)’ at ../src/Allele.cpp:516:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::map<Allele, int> countAlleles(std::vector<Allele*>&)’ at ../src/Allele.cpp:518:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::map<Allele, int> countAlleles(std::__cxx11::list<Allele*>&)’ at ../src/Allele.cpp:576:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::map<Allele, int> countAlleles(std::__cxx11::list<Allele*>&)’ at ../src/Allele.cpp:578:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<Allele> uniqueAlleles(std::__cxx11::list<Allele*>&)’ at ../src/Allele.cpp:598:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::map<Allele, int> countAlleles(std::vector<Allele>&)’ at ../src/Allele.cpp:562:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::map<Allele, int> countAlleles(std::vector<Allele>&)’ at ../src/Allele.cpp:564:26:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp
In file included from /usr/include/c++/12/vector:70,
from ../src/Dirichlet.h:4,
from ../src/Dirichlet.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double dirichletln(const std::vector<long double>&, const std::vector<int>&, long double)’ at ../src/Dirichlet.cpp:43:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double dirichletln(const std::vector<long double>&, const std::vector<int>&, long double)’ at ../src/Dirichlet.cpp:49:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double dirichlet(const std::vector<long double>&, const std::vector<int>&, long double)’ at ../src/Dirichlet.cpp:13:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double dirichlet(const std::vector<long double>&, const std::vector<int>&, long double)’ at ../src/Dirichlet.cpp:19:27:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp
[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/DataLikelihood.h:20,
from ../src/DataLikelihood.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/DataLikelihood.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../src/DataLikelihood.h:5:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<Genotype*, long double>}; _Tp = std::pair<Genotype*, long double>; _Alloc = std::allocator<std::pair<Genotype*, long double> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<Genotype*, long double> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {SampleDataLikelihood}; _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<SampleDataLikelihood>::iterator’ changed in GCC 7.1
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<Genotype*, long double>}; _Tp = std::pair<Genotype*, long double>; _Alloc = std::allocator<std::pair<Genotype*, long double> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<Genotype*, long double>; _Alloc = std::allocator<std::pair<Genotype*, long double> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<std::pair<Genotype*, long double> > probObservedAllelesGivenGenotypes(Sample&, std::vector<Genotype*>&, Bias&, std::vector<Allele>&, Contamination&, std::map<std::__cxx11::basic_string<char>, double>&, Parameters&)’ at ../src/DataLikelihood.cpp:183:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Genotype*, long double>*, std::vector<std::pair<Genotype*, long double> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SampleDataLikelihood}; _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void calculateSampleDataLikelihoods(Samples&, Results&, AlleleParser*, std::map<int, std::vector<Genotype> >&, Parameters&, bool, Bias&, std::vector<Allele>&, Contamination&, std::map<std::__cxx11::basic_string<char>, double>&, std::map<std::__cxx11::basic_string<char>, std::vector<std::vector<SampleDataLikelihood> > >&, std::map<std::__cxx11::basic_string<char>, std::vector<std::vector<SampleDataLikelihood> > >&, std::map<std::__cxx11::basic_string<char>, std::vector<std::vector<SampleDataLikelihood> > >&)’ at ../src/DataLikelihood.cpp:268:33:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/bits/stl_tree.h:63,
from /usr/include/c++/12/map:60,
from ../src/FBFasta.h:12,
from ../src/FBFasta.cpp:9:
/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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Iterator2 = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Compare = bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)]’:
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSequence(std::string)’:
../src/FBFasta.cpp:273:20: warning: pointer ‘seq’ used after ‘void free(void*)’ [-Wuse-after-free]
273 | s.resize((pend - pbegin)/sizeof(char));
| ~~~~~^~~~~~~~
../src/FBFasta.cpp:272:9: note: call to ‘void free(void*)’ here
272 | free(seq);
| ~~~~^~~~~
../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSubSequence(std::string, int, int)’:
../src/FBFasta.cpp:316:20: warning: pointer ‘seq’ used after ‘void free(void*)’ [-Wuse-after-free]
316 | s.resize((pend - pbegin)/sizeof(char));
| ~~~~~^~~~~~~~
../src/FBFasta.cpp:315:9: note: call to ‘void free(void*)’ here
315 | free(seq);
| ~~~~^~~~~
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = FB::FastaIndexEntry; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >]’,
inlined from ‘std::string FB::FastaReference::sequenceNameStartingWith(std::string)’ at ../src/FBFasta.cpp:285:37:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from ../src/FBFasta.h:18:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1809:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1809 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../src/FBFasta.h:15:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const FB::FastaIndexEntry&}; _Tp = FB::FastaIndexEntry; _Alloc = std::allocator<FB::FastaIndexEntry>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<FB::FastaIndexEntry>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Distance = int; _Tp = FB::FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:232:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
232 | if (__comp(__first + __secondChild,
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
233 | __first + (__secondChild - 1)))
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1631:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1631 | if (__comp(__i, __first))
| ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’,
inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’ 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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = FB::FastaIndexEntry; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >]’,
inlined from ‘std::ostream& FB::operator<<(std::ostream&, FastaIndex&)’ at ../src/FBFasta.cpp:84:45:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, FB::FastaIndexEntry> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = FB::FastaIndexEntry; _Alloc = std::allocator<FB::FastaIndexEntry>]’,
inlined from ‘std::ostream& FB::operator<<(std::ostream&, FastaIndex&)’ at ../src/FBFasta.cpp:84:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘std::ostream& FB::operator<<(std::ostream&, FastaIndex&)’ at ../src/FBFasta.cpp:86:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’ 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<FB::FastaIndexEntry*, vector<FB::FastaIndexEntry> >; _Compare = bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘std::ostream& FB::operator<<(std::ostream&, FastaIndex&)’ at ../src/FBFasta.cpp:86:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ 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<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp
[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp
[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/ResultData.h:10,
from ../src/Marginals.h:7,
from ../src/Marginals.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/Marginals.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../src/Marginals.h:5:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<Genotype* const&>, std::tuple<>}; _Key = Genotype*; _Val = std::pair<Genotype* const, long double>; _KeyOfValue = std::_Select1st<std::pair<Genotype* const, long double> >; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Genotype*; _Tp = long double; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’,
inlined from ‘long double marginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:57:34:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Genotype*; _Tp = long double; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’,
inlined from ‘long double marginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:62:34:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Genotype*; _Tp = long double; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’,
inlined from ‘long double marginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:78:31:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘long double marginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:79:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Genotype*; _Tp = long double; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’,
inlined from ‘long double marginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:83:62:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:151:45:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:161:49:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:170:49:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Genotype*; _Tp = long double; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’,
inlined from ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:185:31:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:186:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Genotype*; _Tp = long double; _Compare = std::less<Genotype*>; _Alloc = std::allocator<std::pair<Genotype* const, long double> >]’,
inlined from ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’ at ../src/Marginals.cpp:190:62:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Genotype*, std::pair<Genotype* const, long double>, std::_Select1st<std::pair<Genotype* const, long double> >, std::less<Genotype*>, std::allocator<std::pair<Genotype* const, long double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/AlleleParser.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/AlleleParser.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../src/AlleleParser.h:11:
/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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Distance = int; _Tp = pair<Allele, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/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<Allele*, vector<Allele> >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from ../src/AlleleParser.h:7:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’ at ../src/AlleleParser.cpp:1011:22:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/string:50:
/usr/include/c++/12/bits/stl_algobase.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<bool (*)(const Allele&)>]’:
/usr/include/c++/12/bits/stl_algobase.h:2131:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
2131 | __remove_if(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_algobase.h:2131:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
189 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<Allele, int> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(const_iterator, value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:350:5: note: parameter passing for argument of type ‘std::vector<Allele>::const_iterator’ changed in GCC 7.1
350 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:366:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
366 | _M_realloc_insert(begin() + __n, std::move(__v));
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void AlleleParser::updateInputVariants(long int, int)’ at ../src/AlleleParser.cpp:2432:50:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void AlleleParser::updateInputVariants(long int, int)’ at ../src/AlleleParser.cpp:2435:122:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void AlleleParser::getInputVariantsInRegion(std::string&, long int, long int)’ at ../src/AlleleParser.cpp:2302:42:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void AlleleParser::getInputVariantsInRegion(std::string&, long int, long int)’ at ../src/AlleleParser.cpp:2305:122:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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 Allele*, vector<Allele> >; _ForwardIterator = Allele*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ 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 Allele*, std::vector<Allele> >’ 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 Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 Allele*, std::vector<Allele> >; _Tp = Allele; _Alloc = std::allocator<Allele>]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ 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 Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Predicate = bool (*)(const Allele&)]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1016:28:
/usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
877 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
878 | __gnu_cxx::__ops::__pred_iter(__pred));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1016:18:
/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1057:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Predicate = bool (*)(const Allele&)]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1062:28:
/usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
877 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
878 | __gnu_cxx::__ops::__pred_iter(__pred));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1062:18:
/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Predicate = bool (*)(const Allele&)]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1094:28:
/usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
877 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
878 | __gnu_cxx::__ops::__pred_iter(__pred));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’ at ../src/AlleleParser.cpp:1094:18:
/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘RegisteredAlignment::RegisteredAlignment(const RegisteredAlignment&)’ at ../src/AlleleParser.h:47:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = RegisteredAlignment; _Args = {const RegisteredAlignment&}; _Tp = RegisteredAlignment]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = RegisteredAlignment; _Args = {const RegisteredAlignment&}; _Tp = RegisteredAlignment]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::deque<_Tp, _Alloc>::_M_push_back_aux(_Args&& ...) [with _Args = {const RegisteredAlignment&}; _Tp = RegisteredAlignment; _Alloc = std::allocator<RegisteredAlignment>]’ at /usr/include/c++/12/bits/deque.tcc:501:30:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ 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 Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘RegisteredAlignment::RegisteredAlignment(const RegisteredAlignment&)’ at ../src/AlleleParser.h:47:7,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = RegisteredAlignment; _Args = {const RegisteredAlignment&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = _Deque_iterator<RegisteredAlignment, const RegisteredAlignment&, const RegisteredAlignment*>; _ForwardIterator = _Deque_iterator<RegisteredAlignment, RegisteredAlignment&, RegisteredAlignment*>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21,
inlined from ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::_Deque_iterator<RegisteredAlignment, const RegisteredAlignment&, const RegisteredAlignment*>; _ForwardIterator = std::_Deque_iterator<RegisteredAlignment, RegisteredAlignment&, RegisteredAlignment*>; bool _TrivialValueTypes = false]’ at /usr/include/c++/12/bits/stl_uninitialized.h:137:58,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = _Deque_iterator<RegisteredAlignment, const RegisteredAlignment&, const RegisteredAlignment*>; _ForwardIterator = _Deque_iterator<RegisteredAlignment, RegisteredAlignment&, RegisteredAlignment*>]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:41,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = _Deque_iterator<RegisteredAlignment, const RegisteredAlignment&, const RegisteredAlignment*>; _ForwardIterator = _Deque_iterator<RegisteredAlignment, RegisteredAlignment&, RegisteredAlignment*>; _Tp = RegisteredAlignment]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:63:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ 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<Allele*, std::vector<Allele> >’ changed in GCC 7.1
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1901:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’ at ../src/AlleleParser.cpp:3047:35:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Predicate = bool (*)(const Allele&)]’,
inlined from ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’ at ../src/AlleleParser.cpp:3151:32:
/usr/include/c++/12/bits/stl_algo.h:877:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
877 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
878 | __gnu_cxx::__ops::__pred_iter(__pred));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’ at ../src/AlleleParser.cpp:3151:22:
/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = AllelePositionCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’ at ../src/AlleleParser.cpp:3158:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ 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<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’ 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<Allele*, vector<Allele> >; _Compare = AllelePositionCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’ at ../src/AlleleParser.cpp:3158:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ 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<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1901:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’ at ../src/AlleleParser.cpp:3878:40:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’ at ../src/AlleleParser.cpp:3950:33:
/usr/include/c++/12/bits/stl_vector.h:1389:30: note: parameter passing for argument of type ‘std::vector<Allele>::const_iterator’ changed in GCC 7.1
1389 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’ at ../src/AlleleParser.cpp:3957:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = AllelePairIntCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’ at ../src/AlleleParser.cpp:3961:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ 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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = AllelePairIntCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’ at ../src/AlleleParser.cpp:3961:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’ at ../src/AlleleParser.cpp:3988:33:
/usr/include/c++/12/bits/stl_vector.h:1389:30: note: parameter passing for argument of type ‘std::vector<Allele>::const_iterator’ changed in GCC 7.1
1389 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘RegisteredAlignment::RegisteredAlignment(const RegisteredAlignment&)’ at ../src/AlleleParser.h:47:7,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = RegisteredAlignment; _Args = {const RegisteredAlignment&}; _Tp = RegisteredAlignment]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = RegisteredAlignment; _Args = {const RegisteredAlignment&}; _Tp = RegisteredAlignment]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::deque<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RegisteredAlignment; _Alloc = std::allocator<RegisteredAlignment>]’ at /usr/include/c++/12/bits/stl_deque.h:1543:30,
inlined from ‘void AlleleParser::removeRegisteredAlignmentsOverlappingPosition(long unsigned int)’ at ../src/AlleleParser.cpp:2144:38:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp
In file included from /usr/include/c++/12/vector:70,
from ../src/Utility.h:7,
from ../src/Multinomial.h:4,
from ../src/Multinomial.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double multinomialSamplingProb(const std::vector<long double>&, const std::vector<int>&)’ at ../src/Multinomial.cpp:14:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double multinomialSamplingProbLn(const std::vector<long double>&, const std::vector<int>&)’ at ../src/Multinomial.cpp:29:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp
In file included from /usr/include/c++/12/algorithm:61,
from ../src/Genotype.h:7,
from ../src/Genotype.cpp:1:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Distance = int; _Tp = pair<Allele, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/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<Allele*, vector<Allele> >; _Distance = int; _Tp = Allele; _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<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _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<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from ../src/Genotype.h:5:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<Allele> Genotype::alternateAlleles(std::string&)’ at ../src/Genotype.cpp:35:30:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {GenotypeElement}; _Tp = GenotypeElement; _Alloc = std::allocator<GenotypeElement>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<GenotypeElement>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double GenotypeCombo::hweExpectedFrequencyln(Genotype*)’ at ../src/Genotype.cpp:1425:36:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<long double> Genotype::alleleProbabilities()’ at ../src/Genotype.cpp:239:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<long double> GenotypeCombo::alleleProbs()’ at ../src/Genotype.cpp:679:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<long double> Genotype::alleleProbabilities(Bias&)’ at ../src/Genotype.cpp:253:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::pair<Allele, int> >::iterator’ changed in GCC 7.1
/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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
In file included from /usr/include/c++/12/map:60,
from ../src/Genotype.h:10:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Allele&>, std::tuple<>}; _Key = Allele; _Val = std::pair<const Allele, GenotypeCombo>; _KeyOfValue = std::_Select1st<std::pair<const Allele, GenotypeCombo> >; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, GenotypeCombo> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, GenotypeCombo>, std::_Select1st<std::pair<const Allele, GenotypeCombo> >, std::less<Allele>, std::allocator<std::pair<const Allele, GenotypeCombo> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = GenotypeCombo; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, GenotypeCombo> >]’,
inlined from ‘void addAllHomozygousCombos(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::vector<Allele>&, long double, bool, bool, bool, bool, bool, bool, long double)’ at ../src/Genotype.cpp:1320:59:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, GenotypeCombo>, std::_Select1st<std::pair<const Allele, GenotypeCombo> >, std::less<Allele>, std::allocator<std::pair<const Allele, GenotypeCombo> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Allele&>, std::tuple<>}; _Key = Allele; _Val = std::pair<const Allele, int>; _KeyOfValue = std::_Select1st<std::pair<const Allele, int> >; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = GenotypeCombo; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, GenotypeCombo> >]’,
inlined from ‘void combinePopulationCombos(std::__cxx11::list<GenotypeCombo>&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::list<GenotypeCombo> >&)’ at ../src/Genotype.cpp:1871:64:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, GenotypeCombo>, std::_Select1st<std::pair<const Allele, GenotypeCombo> >, std::less<Allele>, std::allocator<std::pair<const Allele, GenotypeCombo> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector: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 Allele*, vector<Allele> >; _ForwardIterator = Allele*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ 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 Allele*, std::vector<Allele> >’ 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 Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<Allele>; _Args = {const std::vector<Allele, std::allocator<Allele> >&}; _Tp = std::vector<Allele>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<Allele>; _Args = {const std::vector<Allele, std::allocator<Allele> >&}; _Tp = std::vector<Allele>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::vector<Allele, std::allocator<Allele> >&}; _Tp = std::vector<Allele>; _Alloc = std::allocator<std::vector<Allele> >]’ at /usr/include/c++/12/bits/vector.tcc:462:28:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘std::vector<std::vector<ValueType> > multichoose(int, std::vector<ValueType>&) [with T = Allele]’ at /usr/include/vcflib/multichoose.h:58:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ 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 Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::vector<Allele>; _Args = {const std::vector<Allele, std::allocator<Allele> >&}; _Tp = std::vector<Allele>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::vector<Allele>; _Args = {const std::vector<Allele, std::allocator<Allele> >&}; _Tp = std::vector<Allele>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::vector<Allele>; _Alloc = std::allocator<std::vector<Allele> >]’ at /usr/include/c++/12/bits/stl_vector.h:1281:30,
inlined from ‘std::vector<std::vector<ValueType> > multichoose(int, std::vector<ValueType>&) [with T = Allele]’ at /usr/include/vcflib/multichoose.h:59:26:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:340:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
254 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_heap.h:254:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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<Allele*, vector<Allele> >; _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<Allele*, std::vector<Allele> >’ 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<Allele*, std::vector<Allele> >’ changed in GCC 7.1
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1901:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >; _ForwardIterator = Allele*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Allele*, vector<Allele> >; _ForwardIterator = Allele*]’ 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 Allele*, vector<Allele> >; _ForwardIterator = Allele*; _Tp = Allele]’ 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 Allele*, std::vector<Allele> >; _Tp = Allele; _Alloc = std::allocator<Allele>]’ 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 = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/vector.tcc:232:44,
inlined from ‘Genotype::Genotype(std::vector<Allele>&)’ at ../src/Genotype.h:56:19:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Allele*, std::vector<Allele> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘Genotype::Genotype(std::vector<Allele>&)’ at ../src/Genotype.h:57:13:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ 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<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<Allele*, vector<Allele> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘Genotype::Genotype(std::vector<Allele>&)’ at ../src/Genotype.h:57:13:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ 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<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {GenotypeElement}; _Tp = GenotypeElement; _Alloc = std::allocator<GenotypeElement>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = GenotypeElement; _Alloc = std::allocator<GenotypeElement>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘Genotype::Genotype(std::vector<Allele>&)’ at ../src/Genotype.h:60:28:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<GenotypeElement*, std::vector<GenotypeElement> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Genotype; _Alloc = std::allocator<Genotype>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<Genotype> allPossibleGenotypes(int, std::vector<Allele>&)’ at ../src/Genotype.cpp:358:28:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
In function ‘void std::__sort_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1901:23,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_heap.h:425:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
425 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1900:25,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1629:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1629 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::vector<std::pair<Allele, int> > alternateAlleles(GenotypeCombo&, std::string)’ at ../src/Genotype.cpp:1666:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Allele; _Tp = int; _Compare = std::less<Allele>; _Alloc = std::allocator<std::pair<const Allele, int> >]’,
inlined from ‘std::vector<std::pair<Allele, int> > alternateAlleles(GenotypeCombo&, std::string)’ at ../src/Genotype.cpp:1668:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<Allele, std::pair<const Allele, int>, std::_Select1st<std::pair<const Allele, int> >, std::less<Allele>, std::allocator<std::pair<const Allele, int> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::vector<std::pair<Allele, int> > alternateAlleles(GenotypeCombo&, std::string)’ at ../src/Genotype.cpp:1676:35:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = AllelePairIntCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘std::vector<std::pair<Allele, int> > alternateAlleles(GenotypeCombo&, std::string)’ at ../src/Genotype.cpp:1680:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’ 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<pair<Allele, int>*, vector<pair<Allele, int> > >; _Compare = AllelePairIntCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘std::vector<std::pair<Allele, int> > alternateAlleles(GenotypeCombo&, std::string)’ at ../src/Genotype.cpp:1680:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ 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::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleLikelihoodCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool sortSampleDataLikelihoodsScaledByMarginals(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:754:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleLikelihoodCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool sortSampleDataLikelihoodsScaledByMarginals(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:754:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleMarginalCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool sortSampleDataLikelihoodsByMarginals(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:708:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleMarginalCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool sortSampleDataLikelihoodsByMarginals(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:708:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleDataLikelihoodCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘void sortSampleDataLikelihoods(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:699:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleDataLikelihoodCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘void sortSampleDataLikelihoods(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:699:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleMarginalAndObsCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool sortSampleDataLikelihoodsByMarginalsAndObs(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:731:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleMarginalAndObsCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘bool sortSampleDataLikelihoodsByMarginalsAndObs(std::vector<SampleDataLikelihood>&)’ at ../src/Genotype.cpp:731:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp
In file included from /usr/include/c++/12/set:60,
from ../src/NonCall.h:6,
from ../src/NonCall.cpp:1:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, NonCall>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, NonCall> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, NonCall> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, NonCall>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, NonCall> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, NonCall> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61,
from ../src/NonCall.h:7:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = NonCall; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, NonCall> >]’,
inlined from ‘void NonCalls::aggregatePerSample(std::map<std::__cxx11::basic_string<char>, NonCall>&)’ at ../src/NonCall.cpp:39:52:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, NonCall>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, NonCall> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, NonCall> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = NonCall; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, NonCall> >]’,
inlined from ‘void NonCalls::record(const std::string&, long int, const Samples&)’ at ../src/NonCall.cpp:62:37:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, NonCall>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, NonCall> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, NonCall> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp
In file included from /usr/include/c++/12/algorithm:61,
from ../src/Result.h:6,
from ../src/Result.cpp:1:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleDataLikelihoodCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘void Result::sortDataLikelihoods()’ at ../src/Result.cpp:5:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’ 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<SampleDataLikelihood*, vector<SampleDataLikelihood> >; _Compare = SampleDataLikelihoodCompare]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘void Result::sortDataLikelihoods()’ at ../src/Result.cpp:5:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp
[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp
[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp
[21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp
In file included from /usr/include/c++/12/vector:70,
from ../src/Utility.h:7,
from ../src/Utility.cpp:3:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double jointQuality(const std::vector<short int>&)’ at ../src/Utility.cpp:77:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘double entropy(const std::string&)’ at ../src/Utility.cpp:100749:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../ttmath/ttmathint.h:48,
from ../ttmath/ttmathbig.h:46,
from ../ttmath/ttmath.h:58,
from ../src/Utility.h:18:
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with unsigned int value_size = 2]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Exp(const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:326:10,
inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25:
../ttmath/ttmathuint.h:2740:43: warning: ‘x.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../src/Utility.cpp: In function ‘BigFloat big_exp(long double)’:
../src/Utility.cpp:361:14: note: ‘x’ declared here
361 | BigFloat x, result;
| ^
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with unsigned int value_size = 2]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Exp(const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:326:10,
inlined from ‘BigFloat big_exp(long double)’ at ../src/Utility.cpp:363:25:
../ttmath/ttmathuint.h:2740:43: warning: ‘x.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[1]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../src/Utility.cpp: In function ‘BigFloat big_exp(long double)’:
../src/Utility.cpp:361:14: note: ‘x’ declared here
361 | BigFloat x, result;
| ^
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with unsigned int value_size = 2]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ttmath::Big<exp, man> ttmath::Big<exp, man>::operator+(const ttmath::Big<exp, man>&) const [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:5570:15,
inlined from ‘long double logsumexp_probs(const std::vector<long double>&)’ at ../src/Utility.cpp:381:48:
../ttmath/ttmathuint.h:2740:43: warning: ‘maxNb.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../src/Utility.cpp: In function ‘long double logsumexp_probs(const std::vector<long double>&)’:
../src/Utility.cpp:380:14: note: ‘maxNb’ declared here
380 | BigFloat maxNb; maxNb.FromDouble(maxN);
| ^~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator<long double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘long double poissonPvalLn(int, int)’ at ../src/Utility.cpp:253:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with unsigned int value_size = 2]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with unsigned int value_size = 2]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with unsigned int exp = 8; unsigned int man = 2]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<8, 2>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<8, 2>::mantissa.ttmath::UInt<2>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/ResultData.h:10,
from ../src/ResultData.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/ResultData.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../src/Genotype.h:10,
from ../src/ResultData.h:7:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘vcflib::Variant& Results::vcf(vcflib::Variant&, BigFloat, long double, Samples&, std::string, std::vector<Allele>&, std::map<std::__cxx11::basic_string<char>, int>, int, std::vector<std::__cxx11::basic_string<char> >&, int, GenotypeCombo&, std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, std::map<Allele*, std::set<Allele*> >&, std::map<int, std::vector<Genotype> >&, std::vector<std::__cxx11::basic_string<char> >&, AlleleParser*)’ at ../src/ResultData.cpp:40:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]’,
inlined from ‘vcflib::Variant& Results::vcf(vcflib::Variant&, BigFloat, long double, Samples&, std::string, std::vector<Allele>&, std::map<std::__cxx11::basic_string<char>, int>, int, std::vector<std::__cxx11::basic_string<char> >&, int, GenotypeCombo&, std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, std::map<Allele*, std::set<Allele*> >&, std::map<int, std::vector<Genotype> >&, std::vector<std::__cxx11::basic_string<char> >&, AlleleParser*)’ at ../src/ResultData.cpp:591:66:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]’,
inlined from ‘vcflib::Variant& Results::vcf(vcflib::Variant&, BigFloat, long double, Samples&, std::string, std::vector<Allele>&, std::map<std::__cxx11::basic_string<char>, int>, int, std::vector<std::__cxx11::basic_string<char> >&, int, GenotypeCombo&, std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, std::map<Allele*, std::set<Allele*> >&, std::map<int, std::vector<Genotype> >&, std::vector<std::__cxx11::basic_string<char> >&, AlleleParser*)’ at ../src/ResultData.cpp:599:62:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[23/27] rm -f libfreebayes_common.a && gcc-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o
[24/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp
[25/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblzma.so -pthread /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libvcflib.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libsmithwaterman.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libdisorder.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libfastahack.so /usr/lib/arm-linux-gnueabihf/libseqlib.so /usr/lib/libbwa.a /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libtabixpp.so -Wl,--end-group
[26/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/freebayes.cpp:29:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/freebayes.cpp:9:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../src/freebayes.cpp:12:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SampleDataLikelihood&}; _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<SampleDataLikelihood>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/list:63,
from ../src/Utility.h:8,
from ../src/Parameters.h:14,
from ../src/freebayes.cpp:26:
/usr/include/c++/12/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const GenotypeCombo&}; _Tp = GenotypeCombo; _Alloc = std::allocator<GenotypeCombo>]’:
/usr/include/c++/12/bits/stl_list.h:2003:8: note: parameter passing for argument of type ‘std::__cxx11::list<GenotypeCombo>::iterator’ changed in GCC 7.1
2003 | _M_insert(iterator __position, _Args&&... __args)
| ^~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’,
inlined from ‘void Results::update(SampleDataLikelihoods&)’ at ../src/ResultData.h:39:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from ../src/freebayes.cpp:13:
/usr/include/c++/12/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]’:
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator’ changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/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 SampleDataLikelihood*, vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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 SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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 SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const SampleDataLikelihood*, vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*]’ 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 SampleDataLikelihood*, vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*; _Tp = SampleDataLikelihood]’ 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 SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’ 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 = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’ at /usr/include/c++/12/bits/vector.tcc:232:44,
inlined from ‘static _OI std::__copy_move<false, false, std::random_access_iterator_tag>::__copy_m(_II, _II, _OI) [with _II = std::vector<SampleDataLikelihood>*; _OI = std::vector<SampleDataLikelihood>*]’ at /usr/include/c++/12/bits/stl_algobase.h:385:18:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ 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 SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const SampleDataLikelihood*, vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*]’ 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 SampleDataLikelihood*, vector<SampleDataLikelihood> >; _ForwardIterator = SampleDataLikelihood*; _Tp = SampleDataLikelihood]’ 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 = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘void std::_Construct(_Tp*, _Args&& ...) [with _Tp = vector<SampleDataLikelihood>; _Args = {vector<SampleDataLikelihood, allocator<SampleDataLikelihood> >&}]’ at /usr/include/c++/12/bits/stl_construct.h:119:7,
inlined from ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<vector<SampleDataLikelihood>*, vector<vector<SampleDataLikelihood> > >; _ForwardIterator = vector<SampleDataLikelihood>*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:120:21:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:273:38:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:321:38:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = double; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> >]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:349:82:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, double> > >::const_iterator’ changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = GenotypeCombo; _Alloc = std::allocator<GenotypeCombo>]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:484:50:
/usr/include/c++/12/bits/stl_list.h:1306:24: note: parameter passing for argument of type ‘std::_List_iterator<GenotypeCombo>’ changed in GCC 7.1
1306 | { this->_M_insert(end(), __x); }
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator<long double>]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:529:33:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:580:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:615:38:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = GenotypeCombo; _Alloc = std::allocator<GenotypeCombo>]’,
inlined from ‘int main(int, char**)’ at ../src/freebayes.cpp:634:65:
/usr/include/c++/12/bits/stl_list.h:1306:24: note: parameter passing for argument of type ‘std::_List_iterator<GenotypeCombo>’ changed in GCC 7.1
1306 | { this->_M_insert(end(), __x); }
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~
[27/27] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblzma.so -pthread /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libtabixpp.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libvcflib.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libsmithwaterman.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libdisorder.so /usr/lib/gcc/arm-linux-gnueabihf/12/../../../arm-linux-gnueabihf/libfastahack.so /usr/lib/arm-linux-gnueabihf/libseqlib.so /usr/lib/libbwa.a -Wl,--end-group
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/freebayes-1.3.6'
mkdir -p test/bash-tap/
ln -s -t test/bash-tap /build/freebayes-1.3.6/debian/bash-tap/*
mkdir -p test/test-simple-bash
ln -s -t test/test-simple-bash /build/freebayes-1.3.6/debian/test-simple-bash/*
dh_auto_test -- -v --timeout-multiplier 100
cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=3 meson test -v --timeout-multiplier 100
ninja: no work to do.
ninja: Entering directory `/build/freebayes-1.3.6/build'
ninja: no work to do.
1/5 T00 RUNNING
>>> MALLOC_PERTURB_=12 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t
2/5 T01 RUNNING
>>> MALLOC_PERTURB_=166 /usr/bin/prove -e bash -v t/01_call_variants.t
3/5 T01b RUNNING
>>> MALLOC_PERTURB_=143 /usr/bin/prove -e bash -v t/01b_call_variants.t
1/5 T00 OK 3.21s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/00_region_and_target_handling.t ..
1..12
ok 1 - ref:4-5 ref:6-7 are empty
ok 2 - ref:4 ref:6 are empty
ok 3 - ref:5-6 ref:7-8
ok 4 - ref:5 ref:7
ok 5 - ref:5-
ok 6 - full output
ok 7 - --targets t/../00_region_and_target_handling.t.bed
ok 8 - --region ref
ok 9 - ref:1,0-
ok 10 - ref:1,0-1,1
ok 11 - ref:0-1
ok 12 - region outside of bounds error
ok
All tests successful.
Files=1, Tests=12, 2 wallclock secs ( 0.12 usr 0.02 sys + 0.38 cusr 0.32 csys = 0.84 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
4/5 T02 RUNNING
>>> MALLOC_PERTURB_=154 /usr/bin/prove -e bash -v t/02_multi_bam.t
4/5 T02 OK 3.61s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/02_multi_bam.t ..
1..7
ok 1 - freebayes calls from two identical BAMs
ok 2 - freebayes calls from two BAMs with different samples for different read groups
ok 3 - freebayes calls from two BAMs with different technologies for different read groups
ok 4 - freebayes rejects two BAMs with different samples for same read groups
ok 5 - freebayes rejects two BAMs with different technologies for same read groups
ok 6 - freebayes calls multiple alts from two different BAMs
ok 7 - freebayes rejects two BAMs with the same name
ok
All tests successful.
Files=1, Tests=7, 3 wallclock secs ( 0.09 usr 0.01 sys + 0.39 cusr 0.30 csys = 0.79 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
5/5 T03 RUNNING
>>> MALLOC_PERTURB_=82 /usr/bin/prove -e bash -v t/03_reference_bases.t
5/5 T03 OK 1.85s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/03_reference_bases.t ..
1..3
ok 1 - freebayes rejects invalid reference
ok 2 - freebayes does not put uppercase IUPAC bases in VCFs
ok 3 - freebayes does not put lowercase IUPAC bases in VCFs
ok
All tests successful.
Files=1, Tests=3, 1 wallclock secs ( 0.09 usr 0.01 sys + 0.11 cusr 0.08 csys = 0.29 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
3/5 T01b OK 59.08s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/01b_call_variants.t ..
1..10
ok 1 - running in parallel makes no difference
ok 2 - freebayes handles spaces in file names
ok 3 - freebayes handles region and variant input even with : in contig names
ok 4 - freebayes can handle spliced reads
ok 5 - freebayes produces the expected number of lines of gVCF output
ok 6 - freebayes produces the expected number of lines of gVCF output
ok 7 - freebayes produces the expected number of lines of gVCF output
ok 8 - the CNV map may be used to specify per-sample copy numbers
ok 9 - freebayes makes the expected number of calls when capping coverage
ok 10 - freebayes correctly uses CNV map with multiple entries
ok
All tests successful.
Files=1, Tests=10, 58 wallclock secs ( 0.12 usr 0.02 sys + 23.20 cusr 1.69 csys = 25.03 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
2/5 T01 OK 91.55s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
stdout:
t/01_call_variants.t ..
1..16
ok 1 - variant calling recovers most of the GiAB variants in a test region
ok 2 - freebayes produces the same number of calls if targeted per site or called without targets
ok 3 - a targets bed file can be used with the same effect as running by region
ok 4 - reading from stdin or not makes no difference
ok 5 - freebayes processes all alignments in BAM input
ok 6 - freebayes processes all alignments in CRAM input
ok 7 - freebayes correctly handles variant input
ok 8 - freebayes puts required variants in output
ok 9 - freebayes limits calls to input variants correctly
ok 10 - freebayes reports all input variants even when there is no input data
ok 11 - freebayes handles region and variant input
ok 12 - freebayes limits to variant input correctly when region is given
ok 13 - freebayes handles variant input and reading from stdin
ok 14 - freebayes limits to variant input when reading from stdin
ok 15 - freebayes handles region, stdin, and variant input
ok 16 - !
ok
All tests successful.
Files=1, Tests=16, 91 wallclock secs ( 0.12 usr 0.00 sys + 32.95 cusr 8.34 csys = 41.41 CPU)
Result: PASS
stderr:
[E::idx_find_and_load] Could not retrieve index file for '-'
Random access with SetRegion not available for STDIN reading (no index file)
ERROR(freebayes): Could not SetRegion to q:1..10000
t/01_call_variants.t: line 107: 29579 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
Ok: 5
Expected Fail: 0
Fail: 0
Unexpected Pass: 0
Skipped: 0
Timeout: 0
Full log written to /build/freebayes-1.3.6/build/meson-logs/testlog.txt
rm test/bash-tap/*
rm test/test-simple-bash/*
make[1]: Leaving directory '/build/freebayes-1.3.6'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=meson -O--builddir=build
dh_prep -O--buildsystem=meson -O--builddir=build
dh_auto_install --destdir=debian/freebayes/ -O--buildsystem=meson -O--builddir=build
cd build && DESTDIR=/build/freebayes-1.3.6/debian/freebayes LC_ALL=C.UTF-8 ninja install
[0/1] Installing files.
Installing freebayes to /build/freebayes-1.3.6/debian/freebayes/usr/bin
Installing bamleftalign to /build/freebayes-1.3.6/debian/freebayes/usr/bin
dh_install -O--buildsystem=meson -O--builddir=build
dh_installdocs -O--buildsystem=meson -O--builddir=build
dh_installchangelogs -O--buildsystem=meson -O--builddir=build
dh_installexamples -O--buildsystem=meson -O--builddir=build
dh_installsystemduser -O--buildsystem=meson -O--builddir=build
dh_perl -O--buildsystem=meson -O--builddir=build
dh_link -O--buildsystem=meson -O--builddir=build
dh_strip_nondeterminism -O--buildsystem=meson -O--builddir=build
dh_compress -O--buildsystem=meson -O--builddir=build
dh_fixperms -O--buildsystem=meson -O--builddir=build
dh_missing -O--buildsystem=meson -O--builddir=build
dh_dwz -a -O--buildsystem=meson -O--builddir=build
dh_strip -a -O--buildsystem=meson -O--builddir=build
dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build
dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build
dpkg-shlibdeps: warning: debian/freebayes/usr/bin/freebayes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/freebayes/usr/bin/bamleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -O--buildsystem=meson -O--builddir=build
dh_gencontrol -O--buildsystem=meson -O--builddir=build
dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -O--buildsystem=meson -O--builddir=build
dh_builddeb -O--buildsystem=meson -O--builddir=build
dpkg-deb: building package 'freebayes' in '../freebayes_1.3.6-2_armhf.deb'.
dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.6-2_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../freebayes_1.3.6-2_armhf.buildinfo
dpkg-genchanges --build=binary -O../freebayes_1.3.6-2_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/3075 and its subdirectories
I: Current time: Sat May 6 16:29:19 -12 2023
I: pbuilder-time-stamp: 1683433759
Sun May 7 04:30:00 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt64c-armhf-rb.debian.net.
Sun May 7 04:30:00 UTC 2023 I: Preparing to do remote build '2' on virt64c-armhf-rb.debian.net.
Sun May 7 04:35:47 UTC 2023 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net.
Sun May 7 04:35:52 UTC 2023 I: freebayes_1.3.6-2_armhf.changes:
Format: 1.8
Date: Tue, 01 Nov 2022 14:38:51 +0100
Source: freebayes
Binary: freebayes freebayes-dbgsym
Architecture: armhf
Version: 1.3.6-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
freebayes - Bayesian haplotype-based polymorphism discovery and genotyping
Changes:
freebayes (1.3.6-2) unstable; urgency=medium
.
* install scripts (+ python3 dependency accordingly)
* Standards-Version: 4.6.1 (routine-update)
Checksums-Sha1:
5a548eb9552385dbf4ec0483b7de275f64353046 6473716 freebayes-dbgsym_1.3.6-2_armhf.deb
f3dfd31c42ee67f918f817d3bad1f035b4592fc0 9859 freebayes_1.3.6-2_armhf.buildinfo
7e874cb9c7785c5e2f516babbc9240ca0ecc5651 1417576 freebayes_1.3.6-2_armhf.deb
Checksums-Sha256:
0d611fbf0c5d40c486f4e6dfbd83a9f2a722bfbad40b755ad14030aaf3540248 6473716 freebayes-dbgsym_1.3.6-2_armhf.deb
6d52a83be15457c18f171eb3cbd05fa2b394dbf2f356a33ba55dfef016215cf5 9859 freebayes_1.3.6-2_armhf.buildinfo
4cbf22181a527572763d9aee96bb0081794a3fc18e21e35b6c2dfd5a44c3b549 1417576 freebayes_1.3.6-2_armhf.deb
Files:
dd6a76ba24f854ba192badaa8666e988 6473716 debug optional freebayes-dbgsym_1.3.6-2_armhf.deb
749c92ad40aef8fde043b938f0b351e4 9859 science optional freebayes_1.3.6-2_armhf.buildinfo
7b6bf33d758af373e5adfa2cb4dc9c8f 1417576 science optional freebayes_1.3.6-2_armhf.deb
Sun May 7 04:35:53 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.7UXDtAQ8/freebayes_1.3.6-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.7UXDtAQ8/freebayes_1.3.6-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.7UXDtAQ8/freebayes_1.3.6-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.7UXDtAQ8/b1/freebayes_1.3.6-2_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.7UXDtAQ8/b2/freebayes_1.3.6-2_armhf.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.384s)
0.384s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.101s)
0.100s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Sun May 7 04:35:54 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Sun May 7 04:35:54 UTC 2023 I: freebayes from bookworm built successfully and reproducibly on armhf.
Sun May 7 04:35:56 UTC 2023 I: Submitting .buildinfo files to external archives:
Sun May 7 04:35:56 UTC 2023 I: Submitting 12K b1/freebayes_1.3.6-2_armhf.buildinfo.asc
Sun May 7 04:35:58 UTC 2023 I: Submitting 12K b2/freebayes_1.3.6-2_armhf.buildinfo.asc
Sun May 7 04:35:58 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun May 7 04:35:58 UTC 2023 I: Done submitting .buildinfo files.
Sun May 7 04:35:58 UTC 2023 I: Removing signed freebayes_1.3.6-2_armhf.buildinfo.asc files:
removed './b1/freebayes_1.3.6-2_armhf.buildinfo.asc'
removed './b2/freebayes_1.3.6-2_armhf.buildinfo.asc'