freebayes →
1.3.6-2 →
armhf → 2022-11-04 04:32:50
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| freebayes 1.3.6-2 (armhf) Fri, 04 Nov 2022 04:05:59 +0000 |
+==============================================================================+
Package: freebayes
Version: 1.3.6-2
Source Version: 1.3.6-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-0bdffe15-6dd9-4898-89a5-577fcf48fff8' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/freebayes-OiAhJZ/resolver-pSiMpb' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 11s (2500 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'freebayes' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/freebayes.git
Please use:
git clone https://salsa.debian.org/med-team/freebayes.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2912 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main freebayes 1.3.6-2 (dsc) [2232 B]
Get:2 http://172.17.4.1/private bookworm-staging/main freebayes 1.3.6-2 (tar) [2898 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main freebayes 1.3.6-2 (diff) [11.4 kB]
Fetched 2912 kB in 0s (6674 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/freebayes-OiAhJZ/freebayes-1.3.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/freebayes-OiAhJZ' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged 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, libvcflib-tools, debhelper, build-essential, fakeroot
Filtered 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, libvcflib-tools, debhelper, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [481 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [554 B]
Fetched 1992 B in 0s (53.1 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap libperl5.34 perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates
debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.2
libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcurl3-gnutls libcurl4
libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0
libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev
libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0
libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 libice6
libicu71 libjbig0 libjpeg62-turbo libjsoncpp-dev libjsoncpp25 liblapack3
liblerc4 liblzma-dev liblzma5 libmagic-mgc libmagic1 libmd0 libmpdec3
libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0
libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librtmp1 libsensors-config libsensors5 libseqlib-dev
libseqlib2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh2-1
libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6
libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libvcflib-dev
libvcflib-tools libvcflib1 libwebp7 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxrender1 libxss1 libxt6 littler m4 man-db media-types meson ninja-build
openssl parallel pkg-config po-debconf procps python3 python3-distutils
python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools
python3.10 python3.10-minimal r-base-core r-cran-cli r-cran-colorspace
r-cran-digest r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue
r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice
r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix
r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig
r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs
r-cran-viridislite r-cran-withr samtools sysstat ucf unzip x11-common
xdg-utils xz-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libbamtools-doc libcurl4-doc
libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev low-memory-monitor liblzma-doc lm-sensors tcl8.6 tk8.6
libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc
apparmor less www-browser ash csh fish ksh tcsh zsh libmail-box-perl
python3-doc python3-tk python3-venv python-setuptools-doc python3.10-venv
python3.10-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib
r-base-html r-cran-callr r-cran-covr r-cran-htmltools r-cran-htmlwidgets
r-cran-knitr r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot
r-cran-rstudioapi r-cran-whoami r-cran-kernsmooth r-cran-kernlab
r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr
r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-crayon
r-cran-dbi r-cran-forcats r-cran-r.utils r-cran-rsqlite r-cran-stringr
r-cran-waldo r-cran-profvis r-cran-magick r-cran-sf r-cran-lintr
r-cran-tidyverse r-cran-getopt r-cran-bit64 r-cran-formattable
r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival
r-cran-units r-cran-vdiffr r-cran-testthat r-cran-doparallel r-cran-foreach
r-cran-iterators r-cran-itertools r-cran-inline r-cran-fs r-cran-usethis
r-cran-dichromat r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate
r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr
r-cran-pkgdown r-cran-zeallot cwltool isag
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libgpm2 publicsuffix libltdl-dev libmail-sendmail-perl psmisc
r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery
r-cran-covr r-cran-ragg r-cran-dplyr r-cran-hexbin r-cran-hmisc
r-cran-interp r-cran-knitr r-cran-mapproj r-cran-maps r-cran-maptools
r-cran-multcomp r-cran-quantreg r-cran-rmarkdown r-cran-rpart r-cran-sf
r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-crayon r-cran-lubridate
r-cran-domc r-cran-abind r-cran-bit64 r-cran-hms r-cran-stringi
r-cran-data.table r-cran-rsqlite r-cran-mockr r-cran-formattable
r-cran-generics r-cran-waldo r-cran-dbi systemd | cron | cron-daemon
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates
debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.2
libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcurl3-gnutls libcurl4
libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0
libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev
libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0
libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 libice6
libicu71 libjbig0 libjpeg62-turbo libjsoncpp-dev libjsoncpp25 liblapack3
liblerc4 liblzma-dev libmagic-mgc libmagic1 libmd0 libmpdec3 libncurses6
libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libprocps8
libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib
librtmp1 libsensors-config libsensors5 libseqlib-dev libseqlib2 libsm6
libsmithwaterman-dev libsmithwaterman0 libssh2-1 libssw-dev libssw0
libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data
libthai0 libtiff5 libtk8.6 libtool libuchardet0 libvcflib-dev
libvcflib-tools libvcflib1 libwebp7 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxrender1 libxss1 libxt6 littler m4 man-db media-types meson ninja-build
openssl parallel pkg-config po-debconf procps python3 python3-distutils
python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools
python3.10 python3.10-minimal r-base-core r-cran-cli r-cran-colorspace
r-cran-digest r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue
r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice
r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix
r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig
r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp
r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs
r-cran-viridislite r-cran-withr samtools sbuild-build-depends-main-dummy
sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev
The following packages will be upgraded:
liblzma5 xz-utils
2 upgraded, 182 newly installed, 0 to remove and 32 not upgraded.
Need to get 110 MB of archives.
After this operation, 275 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.8-1 [768 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.8-1 [1476 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf liblzma5 armhf 5.2.7-0.1 [170 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.8-1 [1597 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.8-1 [505 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7.1 [41.9 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7.1 [457 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf bc armhf 1.07.1-3 [101 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 3.0.5-4 [1346 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20211016 [156 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf xz-utils armhf 5.2.7-0.1 [328 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.38-2 [273 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.12.1+dfsg-3 [352 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config armhf 2.13.1-4.5 [281 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.5 [330 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.5 [416 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.2 armhf 2.5.2+dfsg-2 [127 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.2+dfsg-2 [183 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-2 [28.6 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.7-1 [112 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libbwa-dev armhf 0.7.17-7 [150 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.8.1-2 [308 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.8.1-2 [704 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-6 [496 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.85.0-1 [320 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.85.0-1 [325 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.85.0-1 [397 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4 [4856 B]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4 [4484 B]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-10 [23.9 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-10 [26.3 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libfml0 armhf 0.1+git20190320.b499514-1+rpi1 [68.7 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libfml-dev armhf 0.1+git20190320.b499514-1+rpi1 [80.8 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2.1 [63.7 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.2.0-3+rpi1 [238 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.1-1 [1214 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 5.2.0-2 [1835 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-4 [59.5 kB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-3 [367 kB]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.7-0.1 [228 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.16+ds-3 [1479 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp-dev armhf 1.9.5-4 [26.4 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.1-2 [1587 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf liblerc4 armhf 4.0.0+ds-2 [133 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.50.10+ds-1 [214 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.50.10+ds-1 [68.6 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.50.10+ds-1 [58.3 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7.1 [31.6 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf libssw0 armhf 1.1-13 [21.0 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf libseqlib2 armhf 1.2.0+dfsg-9 [132 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libssw-dev armhf 1.1-13 [24.0 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libseqlib-dev armhf 1.2.0+dfsg-9 [194 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [32.4 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12 [36.7 kB]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libtabixpp0 armhf 1.1.1-1 [8960 B]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libtabixpp-dev armhf 1.1.1-1 [8532 B]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.12+dfsg-1 [906 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libwebp7 armhf 1.2.2-2 [237 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.4.0-5 [277 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.12-1 [680 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libvcflib1 armhf 1.0.3+dfsg-2 [126 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libvcflib-dev armhf 1.0.3+dfsg-2 [85.2 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf unzip armhf 6.0-27 [152 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.1-1 [159 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf r-base-core armhf 4.2.1-3 [27.7 MB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf r-cran-littler armhf 0.3.16-1 [95.4 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf littler all 0.3.17-1 [14.4 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf r-cran-pkgkitten all 0.2.2-2 [27.0 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rcpp armhf 1.0.9-1 [2036 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf r-cran-plyr armhf 1.8.7-1 [833 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf r-cran-digest armhf 0.6.30-2 [177 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf r-cran-glue armhf 1.6.2-1 [152 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf r-cran-gtable all 0.3.1+dfsg-1 [165 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf r-cran-isoband armhf 0.2.6-1 [1759 kB]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf r-cran-mass armhf 7.3-58.1-1 [1126 kB]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf r-cran-lattice armhf 0.20-45-3 [1176 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf r-cran-nlme armhf 3.1.160-1 [2241 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf r-cran-matrix armhf 1.5-1-1 [3685 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf r-cran-mgcv armhf 1.8-41-1 [3132 kB]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rlang armhf 1.0.6-1 [1621 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf r-cran-farver armhf 2.1.1-1 [1390 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf r-cran-labeling all 0.4.2-1 [62.7 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf r-cran-cli armhf 3.4.1-1 [1242 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf r-cran-colorspace armhf 2.0-3+dfsg-1 [1697 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf r-cran-munsell all 0.5.0-2 [236 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf r-cran-r6 all 2.5.1-1 [105 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf r-cran-viridislite all 0.4.1-1 [1299 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf r-cran-scales all 1.2.1-1 [614 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf r-cran-fansi armhf 1.0.3-1 [611 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf r-cran-magrittr armhf 2.0.3-1 [200 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf r-cran-utf8 armhf 1.2.2-1 [129 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf r-cran-vctrs armhf 0.4.2-1 [1240 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf r-cran-pillar all 1.8.1+dfsg-1 [463 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf r-cran-tibble armhf 3.1.8+dfsg-1 [516 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf r-cran-withr all 2.5.0-1 [236 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf r-cran-ggplot2 all 3.3.6+dfsg-1 [3213 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf r-cran-gridbase all 0.4-7-5 [163 kB]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libvcflib-tools armhf 1.0.3+dfsg-2 [645 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf ninja-build armhf 1.11.1-1 [114 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 65.5.0-1 [278 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.8-1 [77.3 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.8-1 [139 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 65.5.0-1 [519 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf meson all 0.63.3-1 [536 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf sysstat armhf 12.5.6-1 [555 kB]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf parallel all 20220722+ds-1 [1849 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.16.1-1 [559 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpython3.10-minimal:armhf (3.10.8-1) ...
Setting up libexpat1:armhf (2.5.0-1) ...
Setting up python3.10-minimal (3.10.8-1) ...
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Unpacking python3-minimal (3.10.6-1) ...
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Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel'
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Setting up libhtscodecs2:armhf (1.3.0-4) ...
Setting up media-types (8.0.0) ...
Setting up libpipeline1:armhf (1.5.6-3) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-4) ...
Setting up libpixman-1-0:armhf (0.40.0-1) ...
Setting up libicu71:armhf (71.1-3) ...
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Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up liblerc4:armhf (4.0.0+ds-2) ...
Setting up bsdextrautils (2.38.1-1.1) ...
Setting up libdatrie1:armhf (0.2.13-2+b2) ...
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Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.74.1-1) ...
No schema files found: doing nothing.
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Setting up libbrotli1:armhf (1.0.9-2+b2) ...
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invoke-rc.d: could not determine current runlevel
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Setting up libsensors-config (1:3.6.0-7.1) ...
Setting up libsmithwaterman0:armhf (0.0+git20160702.2610e25-12) ...
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Setting up libblas3:armhf (3.10.1-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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Setting up sysstat (12.5.6-1) ...
Creating config file /etc/default/sysstat with new version
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update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Creating config file /etc/papersize with new version
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Updating certificates in /etc/ssl/certs...
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Setting up libfreetype6:armhf (2.12.1+dfsg-3) ...
Setting up libbamtools-dev:armhf (2.5.2+dfsg-2) ...
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Setting up dh-strip-nondeterminism (1.13.0-1) ...
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Setting up groff-base (1.22.4-8) ...
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Setting up libcurl4:armhf (7.85.0-1) ...
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Setting up libharfbuzz0b:armhf (5.2.0-2) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libpython3-stdlib:armhf (3.10.6-1) ...
Setting up libhts3:armhf (1.16+ds-3) ...
Setting up python3.10 (3.10.8-1) ...
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Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libhts-dev:armhf (1.16+ds-3) ...
Setting up python3 (3.10.6-1) ...
Setting up man-db (2.11.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.16.1-1) ...
Setting up libxt6:armhf (1:1.2.1-1) ...
Setting up parallel (20220722+ds-1) ...
Setting up libtabixpp0:armhf (1.1.1-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up python3-lib2to3 (3.10.8-1) ...
Setting up libseqlib2:armhf (1.2.0+dfsg-9) ...
Setting up python3-pkg-resources (65.5.0-1) ...
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Setting up libseqlib-dev:armhf (1.2.0+dfsg-9) ...
Setting up meson (0.63.3-1) ...
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Setting up libtabixpp-dev:armhf (1.1.1-1) ...
Setting up libvcflib-dev:armhf (1.0.3+dfsg-2) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
Processing triggers for sgml-base (1.31) ...
Setting up libfontconfig1:armhf (2.13.1-4.5) ...
Setting up fontconfig (2.13.1-4.5) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.6-1) ...
Setting up libtk8.6:armhf (8.6.12-1) ...
Setting up libpango-1.0-0:armhf (1.50.10+ds-1) ...
Setting up libcairo2:armhf (1.16.0-6) ...
Setting up libpangoft2-1.0-0:armhf (1.50.10+ds-1) ...
Setting up libpangocairo-1.0-0:armhf (1.50.10+ds-1) ...
Setting up r-base-core (4.2.1-3) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-gtable (0.3.1+dfsg-1) ...
Setting up r-cran-labeling (0.4.2-1) ...
Setting up r-cran-lattice (0.20-45-3) ...
Setting up r-cran-nlme (3.1.160-1) ...
Setting up r-cran-farver (2.1.1-1) ...
Setting up r-cran-viridislite (0.4.1-1) ...
Setting up r-cran-r6 (2.5.1-1) ...
Setting up r-cran-pkgkitten (0.2.2-2) ...
Setting up r-cran-magrittr (2.0.3-1) ...
Setting up r-cran-littler (0.3.16-1) ...
Setting up r-cran-rcpp (1.0.9-1) ...
Setting up r-cran-rlang (1.0.6-1) ...
Setting up r-cran-gridbase (0.4-7-5) ...
Setting up littler (0.3.17-1) ...
Setting up r-cran-withr (2.5.0-1) ...
Setting up r-cran-digest (0.6.30-2) ...
Setting up r-cran-fansi (1.0.3-1) ...
Setting up r-cran-mass (7.3-58.1-1) ...
Setting up r-cran-glue (1.6.2-1) ...
Setting up r-cran-cli (3.4.1-1) ...
Setting up r-cran-lifecycle (1.0.3+dfsg-1) ...
Setting up r-cran-pkgconfig (2.0.3-2) ...
Setting up r-cran-utf8 (1.2.2-1) ...
Setting up r-cran-colorspace (2.0-3+dfsg-1) ...
Setting up r-cran-plyr (1.8.7-1) ...
Setting up r-cran-rcolorbrewer (1.1-3-1) ...
Setting up r-cran-isoband (0.2.6-1) ...
Setting up r-cran-matrix (1.5-1-1) ...
Setting up r-cran-mgcv (1.8-41-1) ...
Setting up r-cran-vctrs (0.4.2-1) ...
Setting up r-cran-pillar (1.8.1+dfsg-1) ...
Setting up r-cran-munsell (0.5.0-2) ...
Setting up r-cran-tibble (3.1.8+dfsg-1) ...
Setting up r-cran-scales (1.2.1-1) ...
Setting up r-cran-ggplot2 (3.3.6+dfsg-1) ...
Setting up libvcflib-tools (1.0.3+dfsg-2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20211016) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for libc-bin (2.35-2+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 bc_1.07.1-3 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20211016 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 fontconfig_2.13.1-4.5 fontconfig-config_2.13.1-4.5 fonts-dejavu-core_2.37-2 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.39-6+rpi1 libblas3_3.10.1-2 libblkid1_2.38.1-1.1 libbrotli1_1.0.9-2+b2 libbsd0_0.11.7-1 libbwa-dev_0.7.17-7 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcairo2_1.16.0-6 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl3-gnutls_7.85.0-1 libcurl4_7.85.0-1 libcurl4-gnutls-dev_7.85.0-1 libdatrie1_0.2.13-2+b2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10.1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdisorder-dev_0.0.2+git20130809.8062ee1-4 libdisorder0_0.0.2+git20130809.8062ee1-4 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexpat1_2.5.0-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libfastahack-dev_1.0.0+dfsg-10 libfastahack0_1.0.0+dfsg-10 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfml-dev_0.1+git20190320.b499514-1+rpi1 libfml0_0.1+git20190320.b499514-1+rpi1 libfontconfig1_2.13.1-4.5 libfreetype6_2.12.1+dfsg-3 libfribidi0_1.0.8-2.1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-3+rpi1 libglib2.0-0_2.74.1-1 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.20-1 libharfbuzz0b_5.2.0-2 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libice6_2:1.0.10-1 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:2.1.2-1 libjsoncpp-dev_1.9.5-4 libjsoncpp25_1.9.5-4 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 liblapack3_3.10.1-2 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblerc4_4.0.0+ds-2 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.2.7-0.1 liblzma5_5.2.7-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpango-1.0-0_1.50.10+ds-1 libpangocairo-1.0-0_1.50.10+ds-1 libpangoft2-1.0-0_1.50.10+ds-1 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libpixman-1-0_0.40.0-1 libpng16-16_1.6.38-2 libprocps8_2:3.3.17-7.1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.8-1 libpython3.10-stdlib_3.10.8-1 libreadline8_8.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsensors-config_1:3.6.0-7.1 libsensors5_1:3.6.0-7.1 libsepol1_3.1-1 libsepol2_3.4-2 libseqlib-dev_1.2.0+dfsg-9 libseqlib2_1.2.0+dfsg-9 libsm6_2:1.2.3-1 libsmartcols1_2.38.1-1.1 libsmithwaterman-dev_0.0+git20160702.2610e25-12 libsmithwaterman0_0.0+git20160702.2610e25-12 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.5-4 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtabixpp-dev_1.1.1-1 libtabixpp0_1.1.1-1 libtasn1-6_4.19.0-2 libtcl8.6_8.6.12+dfsg-1 libthai-data_0.1.29-1 libthai0_0.1.29-1 libtiff5_4.4.0-5 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtk8.6_8.6.12-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libvcflib-dev_1.0.3+dfsg-2 libvcflib-tools_1.0.3+dfsg-2 libvcflib1_1.0.3+dfsg-2 libwebp7_1.2.2-2 libx11-6_2:1.8.1-2 libx11-data_2:1.8.1-2 libxau6_1:1.0.9-1 libxcb-render0_1.15-1 libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxft2_2.3.6-1 libxml2_2.9.14+dfsg-1 libxrender1_1:0.9.10-1.1 libxss1_1:1.2.3-1 libxt6_1:1.2.1-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 littler_0.3.17-1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 meson_0.63.3-1 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ninja-build_1.11.1-1 openssl_3.0.5-4 parallel_20220722+ds-1 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7.1 python3_3.10.6-1 python3-distutils_3.10.8-1 python3-lib2to3_3.10.8-1 python3-minimal_3.10.6-1 python3-pkg-resources_65.5.0-1 python3-setuptools_65.5.0-1 python3.10_3.10.8-1 python3.10-minimal_3.10.8-1 r-base-core_4.2.1-3 r-cran-cli_3.4.1-1 r-cran-colorspace_2.0-3+dfsg-1 r-cran-digest_0.6.30-2 r-cran-fansi_1.0.3-1 r-cran-farver_2.1.1-1 r-cran-ggplot2_3.3.6+dfsg-1 r-cran-glue_1.6.2-1 r-cran-gridbase_0.4-7-5 r-cran-gtable_0.3.1+dfsg-1 r-cran-isoband_0.2.6-1 r-cran-labeling_0.4.2-1 r-cran-lattice_0.20-45-3 r-cran-lifecycle_1.0.3+dfsg-1 r-cran-littler_0.3.16-1 r-cran-magrittr_2.0.3-1 r-cran-mass_7.3-58.1-1 r-cran-matrix_1.5-1-1 r-cran-mgcv_1.8-41-1 r-cran-munsell_0.5.0-2 r-cran-nlme_3.1.160-1 r-cran-pillar_1.8.1+dfsg-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.2-2 r-cran-plyr_1.8.7-1 r-cran-r6_2.5.1-1 r-cran-rcolorbrewer_1.1-3-1 r-cran-rcpp_1.0.9-1 r-cran-rlang_1.0.6-1 r-cran-scales_1.2.1-1 r-cran-tibble_3.1.8+dfsg-1 r-cran-utf8_1.2.2-1 r-cran-vctrs_0.4.2-1 r-cran-viridislite_0.4.1-1 r-cran-withr_2.5.0-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysstat_12.5.6-1 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 ucf_3.0043 unzip_6.0-27 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xz-utils_5.2.7-0.1 zip_3.0-12 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----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
Checksums-Sha256:
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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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.H0Wsl9T3/trustedkeys.kbx': General error
gpgv: Signature made Tue Nov 1 13:45:15 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./freebayes_1.3.6-2.dsc
dpkg-source: info: extracting freebayes in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking freebayes_1.3.6.orig.tar.gz
dpkg-source: info: unpacking freebayes_1.3.6-2.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=79d111ecf76d4d72929efb4c6c309344
JOURNAL_STREAM=8:26624
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-0bdffe15-6dd9-4898-89a5-577fcf48fff8
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c163355
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package freebayes
dpkg-buildpackage: info: source version 1.3.6-2
dpkg-buildpackage: info: source distribution unstable
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-arch
dh binary-arch --buildsystem=meson --builddir=build
dh_update_autotools_config -a -O--buildsystem=meson -O--builddir=build
dh_autoreconf -a -O--buildsystem=meson -O--builddir=build
dh_auto_configure -a -O--buildsystem=meson -O--builddir=build
cd build && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf
The Meson build system
Version: 0.63.3
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/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 (Raspbian 12.2.0-3+rpi1) 12.2.0")
C linker for the host machine: cc ld.bfd 2.39
C++ compiler for the host machine: c++ (gcc 12.2.0 "c++ (Raspbian 12.2.0-3+rpi1) 12.2.0")
C++ linker for the host machine: c++ ld.bfd 2.39
Host machine cpu family: arm
Host machine cpu: armv7l
Found pkg-config: /usr/bin/pkg-config (0.29.2)
Run-time dependency zlib found: YES 1.2.11
Run-time dependency liblzma found: YES 5.2.7
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 -a -O--buildsystem=meson -O--builddir=build
cd build && LC_ALL=C.UTF-8 ninja -j4 -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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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<>());
| ~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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<>());
| ~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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<>());
| ~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++ -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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
[23/27] 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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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<>());
| ~~~~~~~~~~~~~~~
[24/27] 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
[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=/<<PKGBUILDDIR>>=. -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 -Wnon-virtual-dtor -std=c++14 -O0 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>'
mkdir -p test/bash-tap/
ln -s -t test/bash-tap /<<PKGBUILDDIR>>/debian/bash-tap/*
mkdir -p test/test-simple-bash
ln -s -t test/test-simple-bash /<<PKGBUILDDIR>>/debian/test-simple-bash/*
dh_auto_test -- -v --timeout-multiplier 100
cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test -v --timeout-multiplier 100
ninja: Entering directory `/<<PKGBUILDDIR>>/build'
ninja: no work to do.
1/5 T00 RUNNING
>>> MALLOC_PERTURB_=104 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t
2/5 T01 RUNNING
>>> MALLOC_PERTURB_=160 /usr/bin/prove -e bash -v t/01_call_variants.t
3/5 T01b RUNNING
>>> MALLOC_PERTURB_=190 /usr/bin/prove -e bash -v t/01b_call_variants.t
4/5 T02 RUNNING
>>> MALLOC_PERTURB_=182 /usr/bin/prove -e bash -v t/02_multi_bam.t
1/5 T00 OK 1.57s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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, 1 wallclock secs ( 0.12 usr 0.01 sys + 0.40 cusr 0.39 csys = 0.92 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
5/5 T03 RUNNING
>>> MALLOC_PERTURB_=200 /usr/bin/prove -e bash -v t/03_reference_bases.t
5/5 T03 OK 1.22s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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 ( 0.11 usr 0.00 sys + 0.15 cusr 0.11 csys = 0.37 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
4/5 T02 OK 2.95s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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, 2 wallclock secs ( 0.11 usr 0.01 sys + 0.43 cusr 0.46 csys = 1.01 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
3/5 T01b OK 21.22s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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, 20 wallclock secs ( 0.09 usr 0.03 sys + 21.71 cusr 2.07 csys = 23.90 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
2/5 T01 OK 59.76s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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, 59 wallclock secs ( 0.12 usr 0.01 sys + 33.71 cusr 54.92 csys = 88.76 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: 23851 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 /<<PKGBUILDDIR>>/build/meson-logs/testlog.txt
rm test/bash-tap/*
rm test/test-simple-bash/*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=meson -O--builddir=build
dh_prep -a -O--buildsystem=meson -O--builddir=build
dh_auto_install --destdir=debian/freebayes/ -a -O--buildsystem=meson -O--builddir=build
cd build && DESTDIR=/<<PKGBUILDDIR>>/debian/freebayes LC_ALL=C.UTF-8 ninja install
[0/1] Installing files.
Installing freebayes to /<<PKGBUILDDIR>>/debian/freebayes/usr/bin
Installing bamleftalign to /<<PKGBUILDDIR>>/debian/freebayes/usr/bin
dh_install -a -O--buildsystem=meson -O--builddir=build
dh_installdocs -a -O--buildsystem=meson -O--builddir=build
dh_installchangelogs -a -O--buildsystem=meson -O--builddir=build
dh_installexamples -a -O--buildsystem=meson -O--builddir=build
dh_installsystemduser -a -O--buildsystem=meson -O--builddir=build
dh_perl -a -O--buildsystem=meson -O--builddir=build
dh_link -a -O--buildsystem=meson -O--builddir=build
dh_strip_nondeterminism -a -O--buildsystem=meson -O--builddir=build
dh_compress -a -O--buildsystem=meson -O--builddir=build
dh_fixperms -a -O--buildsystem=meson -O--builddir=build
dh_missing -a -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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/freebayes/usr/bin/freebayes debian/freebayes/usr/bin/bamleftalign were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=meson -O--builddir=build
dh_gencontrol -a -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 -a -O--buildsystem=meson -O--builddir=build
dh_builddeb -a -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=any -O../freebayes_1.3.6-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../freebayes_1.3.6-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-11-04T04:32:40Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
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: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.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:
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298f71ef96ad03e9b516ebcce8a9d268ea395092 9838 freebayes_1.3.6-2_armhf.buildinfo
129776980494d1eda646f018aaec483e62c6123c 1410336 freebayes_1.3.6-2_armhf.deb
Checksums-Sha256:
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fe66657c1378b0d3438901ac34374f0d21e2d7fa0518e4da6a5ba761391a99f7 9838 freebayes_1.3.6-2_armhf.buildinfo
49abf687b88ff37ba9edf28922ba20cbdd0919674c92773da7fe6f4ecbe03d02 1410336 freebayes_1.3.6-2_armhf.deb
Files:
710aab4674919d1b7e1139b9fddfa9ed 6440360 debug optional freebayes-dbgsym_1.3.6-2_armhf.deb
ae922db96af3dcb9a974f0ed07ccc0ad 9838 science optional freebayes_1.3.6-2_armhf.buildinfo
b041283aedd8fcacc42d27a155a67698 1410336 science optional freebayes_1.3.6-2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: freebayes
Binary: freebayes freebayes-dbgsym
Architecture: armhf
Version: 1.3.6-2
Checksums-Md5:
710aab4674919d1b7e1139b9fddfa9ed 6440360 freebayes-dbgsym_1.3.6-2_armhf.deb
b041283aedd8fcacc42d27a155a67698 1410336 freebayes_1.3.6-2_armhf.deb
Checksums-Sha1:
6d3373abf24db55fea8260a755fe753f894f3925 6440360 freebayes-dbgsym_1.3.6-2_armhf.deb
129776980494d1eda646f018aaec483e62c6123c 1410336 freebayes_1.3.6-2_armhf.deb
Checksums-Sha256:
ac6f633c4e7e3698e3e7c197d5543710c580273262c4d72504036afb078ba572 6440360 freebayes-dbgsym_1.3.6-2_armhf.deb
49abf687b88ff37ba9edf28922ba20cbdd0919674c92773da7fe6f4ecbe03d02 1410336 freebayes_1.3.6-2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Fri, 04 Nov 2022 04:32:38 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-9),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2~rc2-2),
bc (= 1.07.1-3),
binutils (= 2.39-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.39-6+rpi1),
binutils-common (= 2.39-6+rpi1),
bsdextrautils (= 2.38.1-1.1),
bsdutils (= 1:2.38.1-1.1),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
ca-certificates (= 20211016),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-3+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.79),
debhelper (= 13.10.1),
debianutils (= 5.7-0.3),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14+20220924-2),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
fontconfig (= 2.13.1-4.5),
fontconfig-config (= 2.13.1-4.5),
fonts-dejavu-core (= 2.37-2),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-3+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-3+rpi1),
gcc-12-base (= 12.2.0-3+rpi1),
gettext (= 0.21-9),
gettext-base (= 0.21-9),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.12-1),
hostname (= 3.23),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-3+rpi1),
libatomic1 (= 12.2.0-3+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbamtools-dev (= 2.5.2+dfsg-2),
libbamtools2.5.2 (= 2.5.2+dfsg-2),
libbinutils (= 2.39-6+rpi1),
libblas3 (= 3.10.1-2),
libblkid1 (= 2.38.1-1.1),
libbrotli1 (= 1.0.9-2+b2),
libbsd0 (= 0.11.7-1),
libbwa-dev (= 0.7.17-7),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.35-2+rpi1),
libc-dev-bin (= 2.35-2+rpi1),
libc6 (= 2.35-2+rpi1),
libc6-dev (= 2.35-2+rpi1),
libcairo2 (= 1.16.0-6),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 12.2.0-3+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.28-2),
libcrypt1 (= 1:4.4.28-2),
libctf-nobfd0 (= 2.39-6+rpi1),
libctf0 (= 2.39-6+rpi1),
libcurl3-gnutls (= 7.85.0-1),
libcurl4 (= 7.85.0-1),
libcurl4-gnutls-dev (= 7.85.0-1),
libdatrie1 (= 0.2.13-2+b2),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.264),
libdebhelper-perl (= 13.10.1),
libdeflate-dev (= 1.14-1),
libdeflate0 (= 1.14-1),
libdisorder-dev (= 0.0.2+git20130809.8062ee1-4),
libdisorder0 (= 0.0.2+git20130809.8062ee1-4),
libdpkg-perl (= 1.21.9+rpi1),
libelf1 (= 0.187-2+rpi2),
libexpat1 (= 2.5.0-1),
libfastahack-dev (= 1.0.0+dfsg-10),
libfastahack0 (= 1.0.0+dfsg-10),
libffi8 (= 3.4.2-4),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libfml-dev (= 0.1+git20190320.b499514-1+rpi1),
libfml0 (= 0.1+git20190320.b499514-1+rpi1),
libfontconfig1 (= 2.13.1-4.5),
libfreetype6 (= 2.12.1+dfsg-3),
libfribidi0 (= 1.0.8-2.1),
libgcc-12-dev (= 12.2.0-3+rpi1),
libgcc-s1 (= 12.2.0-3+rpi1),
libgcrypt20 (= 1.10.1-2+b2),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran5 (= 12.2.0-3+rpi1),
libglib2.0-0 (= 2.74.1-1),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgnutls30 (= 3.7.8-2),
libgomp1 (= 12.2.0-3+rpi1),
libgpg-error0 (= 1.45-2),
libgraphite2-3 (= 1.3.14-1),
libgssapi-krb5-2 (= 1.20-1),
libharfbuzz0b (= 5.2.0-2),
libhogweed6 (= 3.8.1-2),
libhts-dev (= 1.16+ds-3),
libhts3 (= 1.16+ds-3),
libhtscodecs2 (= 1.3.0-4),
libice6 (= 2:1.0.10-1),
libicu71 (= 71.1-3),
libidn2-0 (= 2.3.3-1),
libisl23 (= 0.25-1),
libjbig0 (= 2.1-3.1+b2),
libjpeg62-turbo (= 1:2.1.2-1),
libjsoncpp-dev (= 1.9.5-4),
libjsoncpp25 (= 1.9.5-4),
libk5crypto3 (= 1.20-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20-1),
libkrb5support0 (= 1.20-1),
liblapack3 (= 3.10.1-2),
libldap-2.5-0 (= 2.5.13+dfsg-2+rpi1),
liblerc4 (= 4.0.0+ds-2),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma-dev (= 5.2.7-0.1),
liblzma5 (= 5.2.7-0.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmd0 (= 1.0.4-2),
libmount1 (= 2.38.1-1.1),
libmpc3 (= 1.2.1-2),
libmpdec3 (= 2.5.1-2+rpi1),
libmpfr6 (= 4.1.0-3),
libncurses6 (= 6.3+20220423-2),
libncursesw6 (= 6.3+20220423-2),
libnettle8 (= 3.8.1-2),
libnghttp2-14 (= 1.50.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.24.1-1),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpango-1.0-0 (= 1.50.10+ds-1),
libpangocairo-1.0-0 (= 1.50.10+ds-1),
libpangoft2-1.0-0 (= 1.50.10+ds-1),
libpaper-utils (= 1.1.28),
libpaper1 (= 1.1.28),
libpcre2-8-0 (= 10.40-1+b2),
libpcre3 (= 2:8.39-14),
libperl5.36 (= 5.36.0-4),
libpipeline1 (= 1.5.6-3),
libpixman-1-0 (= 0.40.0-1),
libpng16-16 (= 1.6.38-2),
libprocps8 (= 2:3.3.17-7.1),
libpsl5 (= 0.21.0-1.2),
libpython3-stdlib (= 3.10.6-1),
libpython3.10-minimal (= 3.10.8-1),
libpython3.10-stdlib (= 3.10.8-1),
libreadline8 (= 8.2-1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg-8),
libsasl2-modules-db (= 2.1.28+dfsg-8),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsensors-config (= 1:3.6.0-7.1),
libsensors5 (= 1:3.6.0-7.1),
libseqlib-dev (= 1.2.0+dfsg-9),
libseqlib2 (= 1.2.0+dfsg-9),
libsm6 (= 2:1.2.3-1),
libsmartcols1 (= 2.38.1-1.1),
libsmithwaterman-dev (= 0.0+git20160702.2610e25-12),
libsmithwaterman0 (= 0.0+git20160702.2610e25-12),
libsqlite3-0 (= 3.39.4-1),
libssh2-1 (= 1.10.0-3+b1),
libssl3 (= 3.0.5-4),
libssw-dev (= 1.1-13),
libssw0 (= 1.1-13),
libstdc++-12-dev (= 12.2.0-3+rpi1),
libstdc++6 (= 12.2.0-3+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 251.5-1+rpi1),
libtabixpp-dev (= 1.1.1-1),
libtabixpp0 (= 1.1.1-1),
libtasn1-6 (= 4.19.0-2),
libtcl8.6 (= 8.6.12+dfsg-1),
libthai-data (= 0.1.29-1),
libthai0 (= 0.1.29-1),
libtiff5 (= 4.4.0-5),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtk8.6 (= 8.6.12-1),
libtool (= 2.4.7-4),
libubsan1 (= 12.2.0-3+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 251.5-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-1.1),
libvcflib-dev (= 1.0.3+dfsg-2),
libvcflib-tools (= 1.0.3+dfsg-2),
libvcflib1 (= 1.0.3+dfsg-2),
libwebp7 (= 1.2.2-2),
libx11-6 (= 2:1.8.1-2),
libx11-data (= 2:1.8.1-2),
libxau6 (= 1:1.0.9-1),
libxcb-render0 (= 1.15-1),
libxcb-shm0 (= 1.15-1),
libxcb1 (= 1.15-1),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1),
libxft2 (= 2.3.6-1),
libxml2 (= 2.9.14+dfsg-1),
libxrender1 (= 1:0.9.10-1.1),
libxss1 (= 1:1.2.3-1),
libxt6 (= 1:1.2.1-1),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 5.19.6-1+rpi1),
littler (= 0.3.17-1),
login (= 1:4.12.3+dfsg1-1),
lsb-base (= 11.4+rpi1),
m4 (= 1.4.19-1),
make (= 4.3-4.1),
man-db (= 2.11.0-1),
mawk (= 1.3.4.20200120-3.1),
media-types (= 8.0.0),
meson (= 0.63.3-1),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
ninja-build (= 1.11.1-1),
openssl (= 3.0.5-4),
parallel (= 20220722+ds-1),
patch (= 2.7.6-7),
perl (= 5.36.0-4),
perl-base (= 5.36.0-4),
perl-modules-5.36 (= 5.36.0-4),
pkg-config (= 0.29.2-1),
po-debconf (= 1.0.21+nmu1),
procps (= 2:3.3.17-7.1),
python3 (= 3.10.6-1),
python3-distutils (= 3.10.8-1),
python3-lib2to3 (= 3.10.8-1),
python3-minimal (= 3.10.6-1),
python3-pkg-resources (= 65.5.0-1),
python3-setuptools (= 65.5.0-1),
python3.10 (= 3.10.8-1),
python3.10-minimal (= 3.10.8-1),
r-base-core (= 4.2.1-3),
r-cran-cli (= 3.4.1-1),
r-cran-colorspace (= 2.0-3+dfsg-1),
r-cran-digest (= 0.6.30-2),
r-cran-fansi (= 1.0.3-1),
r-cran-farver (= 2.1.1-1),
r-cran-ggplot2 (= 3.3.6+dfsg-1),
r-cran-glue (= 1.6.2-1),
r-cran-gridbase (= 0.4-7-5),
r-cran-gtable (= 0.3.1+dfsg-1),
r-cran-isoband (= 0.2.6-1),
r-cran-labeling (= 0.4.2-1),
r-cran-lattice (= 0.20-45-3),
r-cran-lifecycle (= 1.0.3+dfsg-1),
r-cran-littler (= 0.3.16-1),
r-cran-magrittr (= 2.0.3-1),
r-cran-mass (= 7.3-58.1-1),
r-cran-matrix (= 1.5-1-1),
r-cran-mgcv (= 1.8-41-1),
r-cran-munsell (= 0.5.0-2),
r-cran-nlme (= 3.1.160-1),
r-cran-pillar (= 1.8.1+dfsg-1),
r-cran-pkgconfig (= 2.0.3-2),
r-cran-pkgkitten (= 0.2.2-2),
r-cran-plyr (= 1.8.7-1),
r-cran-r6 (= 2.5.1-1),
r-cran-rcolorbrewer (= 1.1-3-1),
r-cran-rcpp (= 1.0.9-1),
r-cran-rlang (= 1.0.6-1),
r-cran-scales (= 1.2.1-1),
r-cran-tibble (= 3.1.8+dfsg-1),
r-cran-utf8 (= 1.2.2-1),
r-cran-vctrs (= 0.4.2-1),
r-cran-viridislite (= 0.4.1-1),
r-cran-withr (= 2.5.0-1),
readline-common (= 8.2-1),
rpcsvc-proto (= 1.4.2-4),
samtools (= 1.16.1-1),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.31),
sysstat (= 12.5.6-1),
sysvinit-utils (= 3.05-6),
tar (= 1.34+dfsg-1),
tzdata (= 2022d-1),
ucf (= 3.0043),
unzip (= 6.0-27),
util-linux (= 2.38.1-1.1),
util-linux-extra (= 2.38.1-1.1),
x11-common (= 1:7.7+23),
xdg-utils (= 1.1.3-4.1),
xz-utils (= 5.2.7-0.1),
zip (= 3.0-12),
zlib1g (= 1:1.2.11.dfsg-4.1),
zlib1g-dev (= 1:1.2.11.dfsg-4.1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1667309931"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
freebayes-dbgsym_1.3.6-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 6440360 bytes: control archive=648 bytes.
420 bytes, 12 lines control
301 bytes, 3 lines md5sums
Package: freebayes-dbgsym
Source: freebayes
Version: 1.3.6-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6504
Depends: freebayes (= 1.3.6-2)
Section: debug
Priority: optional
Description: debug symbols for freebayes
Build-Ids: 0b8036d2109c1df3963465cb8abb9d7b7c04aab0 3f8d4c3bf8bbcb69d311884dbba5749245bfc7b4
drwxr-xr-x root/root 0 2022-11-01 13:38 ./
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 599304 2022-11-01 13:38 ./usr/lib/debug/.build-id/0b/8036d2109c1df3963465cb8abb9d7b7c04aab0.debug
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/.build-id/3f/
-rw-r--r-- root/root 5759596 2022-11-01 13:38 ./usr/lib/debug/.build-id/3f/8d4c3bf8bbcb69d311884dbba5749245bfc7b4.debug
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 285868 2022-11-01 13:38 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/freebayes.debug
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes-dbgsym -> freebayes
freebayes_1.3.6-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 1410336 bytes: control archive=2608 bytes.
860 bytes, 17 lines control
5646 bytes, 67 lines md5sums
Package: freebayes
Version: 1.3.6-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3903
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libseqlib2 (>= 1.2.0+dfsg), libstdc++6 (>= 11), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.3+dfsg), zlib1g (>= 1:1.1.4), python3
Recommends: parallel
Section: science
Priority: optional
Homepage: https://github.com/ekg/freebayes
Description: Bayesian haplotype-based polymorphism discovery and genotyping
FreeBayes is a Bayesian genetic variant detector designed to find
small polymorphisms, specifically SNPs (single-nucleotide
polymorphisms), indels (insertions and deletions), MNPs
(multi-nucleotide polymorphisms), and complex events (composite
insertion and substitution events) smaller than the length of a
short-read sequencing alignment.
drwxr-xr-x root/root 0 2022-11-01 13:38 ./
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/bin/
-rwxr-xr-x root/root 1195268 2022-11-01 13:38 ./usr/bin/bamleftalign
-rwxr-xr-x root/root 1784980 2022-11-01 13:38 ./usr/bin/freebayes
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes/
-rw-r--r-- root/root 10293 2022-01-21 09:38 ./usr/share/doc/freebayes/README.md.gz
-rw-r--r-- root/root 278 2022-11-01 13:38 ./usr/share/doc/freebayes/README.test
-rw-r--r-- root/root 83 2022-11-01 13:38 ./usr/share/doc/freebayes/README.test_data
-rw-r--r-- root/root 3317 2022-01-21 09:38 ./usr/share/doc/freebayes/RELEASE-NOTES.md
-rw-r--r-- root/root 1538 2022-11-01 13:38 ./usr/share/doc/freebayes/changelog.Debian.gz
-rw-r--r-- root/root 3194 2022-11-01 13:38 ./usr/share/doc/freebayes/copyright
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/
-rw-r--r-- root/root 83 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/README.test_data
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/bash-tap/
-rw-r--r-- root/root 109 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/freebayes-env.yaml
drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/performance/
-rw-r--r-- root/root 1652 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/performance/benchmark.md
-rw-r--r-- root/root 906 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/pipeline.sh
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/regression/
-rw-r--r-- root/root 73144 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/regression/NA12878.chr22.tiny.vcf
-rw-r--r-- root/root 94 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/regression/README.md
-rw-r--r-- root/root 287 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/runner.sh
-rw-r--r-- root/root 2743 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/snakemake-freebayes-parallel.smk
drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/
-rw-r--r-- root/root 22589 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.bam
-rw-r--r-- root/root 288 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.bam.bai
-rw-r--r-- root/root 3801 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.fa
-rw-r--r-- root/root 15 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.fa.fai
drwxr-xr-x root/root 0 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/
-rw-r--r-- root/root 3648 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/00_region_and_target_handling.t
-rw-r--r-- root/root 4908 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/01_call_variants.t
-rw-r--r-- root/root 2947 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/01b_call_variants.t
-rw-r--r-- root/root 2943 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/02_multi_bam.t
-rw-r--r-- root/root 1488 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/t/03_reference_bases.t
-rw-r--r-- root/root 246 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/targets.bed
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test-simple-bash/
-rw-r--r-- root/root 17 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.alt
-rw-r--r-- root/root 230 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.bam
-rw-r--r-- root/root 96 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.bam.bai
-rw-r--r-- root/root 112 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.bed
-rw-r--r-- root/root 17 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.ref
-rw-r--r-- root/root 15 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.ref.fai
-rw-r--r-- root/root 550 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/test.vcf
drwxr-xr-x root/root 0 2022-11-01 13:38 ./usr/share/doc/freebayes/examples/tiny/
-rw-r--r-- root/root 636 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/1read.bam
-rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/1read.bam.bai
-rw-r--r-- root/root 287213 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam
-rw-r--r-- root/root 96 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam.bai
-rw-r--r-- root/root 155615 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.cram
-rw-r--r-- root/root 16307 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.giab.vcf
-rw-r--r-- root/root 287228 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam
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-rw-r--r-- root/root 12565 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/q with spaces.fa
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-rw-r--r-- root/root 36 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/q with spaces.regions
-rw-r--r-- root/root 12565 2022-01-21 09:38 ./usr/share/doc/freebayes/examples/tiny/q.fa
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-rwxr-xr-x root/root 706 2022-01-21 09:38 ./usr/share/freebayes/scripts/generate_freebayes_region_scripts.sh
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-rwxr-xr-x root/root 839 2022-01-21 09:38 ./usr/share/freebayes/scripts/update_version.sh
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 84584
Build-Time: 274
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1296
Job: freebayes_1.3.6-2
Machine Architecture: armhf
Package: freebayes
Package-Time: 1601
Source-Version: 1.3.6-2
Space: 84584
Status: successful
Version: 1.3.6-2
--------------------------------------------------------------------------------
Finished at 2022-11-04T04:32:40Z
Build needed 00:26:41, 84584k disk space