Build log for freebayes (1.3.5-1) on armhf

freebayes → 1.3.5-1 → armhf → 2021-05-09 00:28:48

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02

+==============================================================================+
| freebayes 1.3.5-1 (armhf)                    Sat, 08 May 2021 23:53:57 +0000 |
+==============================================================================+

Package: freebayes
Version: 1.3.5-1
Source Version: 1.3.5-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-cadb4131-8aff-4e20-b925-31998732c57d' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.5 MB in 25s (1011 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| 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 2904 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main freebayes 1.3.5-1 (dsc) [2253 B]
Get:2 http://172.17.0.1/private bullseye-staging/main freebayes 1.3.5-1 (tar) [2890 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main freebayes 1.3.5-1 (diff) [11.2 kB]
Fetched 2904 kB in 1s (5118 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/freebayes-KkHzeb/freebayes-1.3.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/freebayes-KkHzeb' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-doya6o/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-doya6o/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-doya6o/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2741 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core 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:
  bsdextrautils libnss-nis libnss-nisplus libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12585 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, python3, 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 (>= 1.0.0~rc1+dfsg1-6)
Filtered Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, python3, 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 (>= 1.0.0~rc1+dfsg1-6)
dpkg-deb: building package 'sbuild-build-depends-freebayes-dummy' in '/<<BUILDDIR>>/resolver-doya6o/apt_archive/sbuild-build-depends-freebayes-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-freebayes-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Sources [620 B]
Get:5 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ Packages [691 B]
Fetched 2644 B in 1s (3616 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install freebayes 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:
  libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bc 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 libbamtools2.5.1 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 libice6 libicu67 libjbig0 libjpeg62-turbo
  libjsoncpp-dev libjsoncpp24 liblapack3 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
  libpython3.9-minimal libpython3.9-stdlib librtmp1 libsensors-config
  libsensors5 libseqlib-dev libseqlib2 libsigsegv2 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 libwebp6
  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-minimal python3-pkg-resources python3.9 python3.9-minimal
  r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli
  r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest
  r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2
  r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-jsonlite
  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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten
  r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx
  r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rematch2
  r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales
  r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite
  r-cran-waldo r-cran-withr samtools sysstat ucf unzip x11-common xdg-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 liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran
  | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser
  libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools
  python3.9-venv python3.9-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf
  r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr
  r-cran-rmarkdown r-cran-prettycode 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-hmisc
  r-cran-maps r-cran-maptools r-cran-multcomp r-cran-rpart r-cran-sf
  r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats
  r-cran-stringr r-cran-magick r-cran-httr r-cran-curl r-cran-getopt
  r-cran-bit64 r-cran-cpp11 r-cran-bitops r-cran-doparallel r-cran-foreach
  r-cran-iterators r-cran-itertools r-cran-inline r-cran-dichromat
  r-cran-mockery r-cran-usethis r-cran-bench r-cran-blob r-cran-formattable
  r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr 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-cliapp r-cran-mockery r-cran-sp
  r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-quantreg r-cran-xml2
  r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl
  r-cran-rmarkdown r-cran-mockr r-cran-bit64 r-cran-hms r-cran-data.table
  r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-generics 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 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 libbamtools2.5.1 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 libice6 libicu67 libjbig0 libjpeg62-turbo
  libjsoncpp-dev libjsoncpp24 liblapack3 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
  libpython3.9-minimal libpython3.9-stdlib librtmp1 libsensors-config
  libsensors5 libseqlib-dev libseqlib2 libsigsegv2 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 libwebp6
  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-minimal python3-pkg-resources python3.9 python3.9-minimal
  r-base-core r-cran-assertthat r-cran-brio r-cran-callr r-cran-cli
  r-cran-colorspace r-cran-crayon r-cran-desc r-cran-diffobj r-cran-digest
  r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2
  r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-jsonlite
  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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten
  r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx
  r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rematch2
  r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales
  r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite
  r-cran-waldo r-cran-withr samtools sbuild-build-depends-freebayes-dummy
  sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev
0 upgraded, 197 newly installed, 0 to remove and 0 not upgraded.
Need to get 107 MB of archives.
After this operation, 251 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-doya6o/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [972 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.2-1+rpi1 [791 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.2-1+rpi1 [1625 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmpdec3 armhf 2.5.1-1+rpi1 [73.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.2-1+rpi1 [1616 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.2-1+rpi1 [466 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf bc armhf 1.07.1-2+b1 [101 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1k-1 [814 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.4 [1049 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [353 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-9 [135 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-9 [179 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libbwa-dev armhf 0.7.17-6 [137 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.7.0-2 [310 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.7.0-2 [706 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.2 [302 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.74.0-1.2 [305 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.2 [375 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.13-1+b1 [39.7 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.7-1 [40.3 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-2 [4612 B]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-2 [4276 B]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-7 [23.9 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-7 [26.5 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libfml0 armhf 0.1+git20190320.b499514-1+rpi1 [68.7 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libfml-dev armhf 0.1+git20190320.b499514-1+rpi1 [80.8 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.8-1 [1183 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+22 [252 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp-dev armhf 1.9.4-4 [25.4 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.46.2-3 [172 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.46.2-3 [55.7 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.46.2-3 [46.7 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libsensors-config all 1:3.6.0-7 [32.3 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libsensors5 armhf 1:3.6.0-7 [49.6 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libssw0 armhf 1.1-13 [21.0 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libseqlib2 armhf 1.2.0+dfsg-4 [139 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libssw-dev armhf 1.1-13 [24.0 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libseqlib-dev armhf 1.2.0+dfsg-4 [197 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-11 [33.1 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-11 [36.6 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libtabixpp0 armhf 1.1.0-4 [8604 B]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libtabixpp-dev armhf 1.1.0-4 [8156 B]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.11+dfsg-1 [894 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.2.0-1 [268 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.11-2 [681 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libvcflib1 armhf 1.0.2+dfsg-2 [126 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libvcflib-dev armhf 1.0.2+dfsg-2 [84.9 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-26 [151 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 4.0.4-1 [24.8 MB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf r-cran-littler armhf 0.3.12-1 [92.4 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf littler all 0.3.12-1 [15.6 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pkgkitten all 0.2.1-1 [26.5 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcpp armhf 1.0.6-1 [1998 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf r-cran-plyr armhf 1.8.6-2 [830 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf r-cran-digest armhf 0.6.27-1 [186 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf r-cran-glue armhf 1.4.2-1 [139 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf r-cran-gtable all 0.3.0+dfsg-2 [163 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf r-cran-brio armhf 1.1.1-1 [31.4 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf r-cran-ps armhf 1.5.0-1 [274 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf r-cran-r6 all 2.5.0-1 [104 kB]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf r-cran-processx armhf 3.4.5-1 [292 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf r-cran-callr all 3.5.1-1 [386 kB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf r-cran-assertthat all 0.2.1-2 [56.5 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf r-cran-cli all 2.3.0-1 [480 kB]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf r-cran-crayon all 1.4.0-1 [143 kB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rprojroot all 2.0.2-1 [114 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf r-cran-desc all 1.2.0-3 [301 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rlang armhf 0.4.10-1 [1182 kB]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf r-cran-ellipsis armhf 0.3.1-1 [31.5 kB]
Get:155 http://172.17.0.1/private bullseye-staging/main armhf r-cran-evaluate all 0.14-2 [81.1 kB]
Get:156 http://172.17.0.1/private bullseye-staging/main armhf r-cran-jsonlite armhf 1.7.2+dfsg-1 [442 kB]
Get:157 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lifecycle all 0.2.0-2 [93.2 kB]
Get:158 http://172.17.0.1/private bullseye-staging/main armhf r-cran-magrittr armhf 2.0.1-1 [197 kB]
Get:159 http://172.17.0.1/private bullseye-staging/main armhf r-cran-prettyunits all 1.1.1-2 [39.1 kB]
Get:160 http://172.17.0.1/private bullseye-staging/main armhf r-cran-withr all 2.4.1-1 [210 kB]
Get:161 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pkgbuild all 1.2.0-1 [146 kB]
Get:162 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rstudioapi all 0.13-1 [262 kB]
Get:163 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pkgload armhf 1.1.0-1 [170 kB]
Get:164 http://172.17.0.1/private bullseye-staging/main armhf r-cran-praise all 1.0.0-4 [20.1 kB]
Get:165 http://172.17.0.1/private bullseye-staging/main armhf r-cran-diffobj armhf 0.3.2-1 [1084 kB]
Get:166 http://172.17.0.1/private bullseye-staging/main armhf r-cran-fansi armhf 0.4.2-1 [337 kB]
Get:167 http://172.17.0.1/private bullseye-staging/main armhf r-cran-utf8 armhf 1.1.4-2 [128 kB]
Get:168 http://172.17.0.1/private bullseye-staging/main armhf r-cran-vctrs armhf 0.3.6-1 [1085 kB]
Get:169 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pillar all 1.4.7-1 [227 kB]
Get:170 http://172.17.0.1/private bullseye-staging/main armhf r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get:171 http://172.17.0.1/private bullseye-staging/main armhf r-cran-tibble armhf 3.0.6+dfsg-1 [417 kB]
Get:172 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rematch2 all 2.1.2-2 [46.3 kB]
Get:173 http://172.17.0.1/private bullseye-staging/main armhf r-cran-waldo all 0.2.3-2 [79.3 kB]
Get:174 http://172.17.0.1/private bullseye-staging/main armhf r-cran-testthat armhf 3.0.1-1 [1442 kB]
Get:175 http://172.17.0.1/private bullseye-staging/main armhf r-cran-isoband armhf 0.2.3-2 [2047 kB]
Get:176 http://172.17.0.1/private bullseye-staging/main armhf r-cran-mass armhf 7.3-53.1-1 [1113 kB]
Get:177 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lattice armhf 0.20-41-1+b1 [1167 kB]
Get:178 http://172.17.0.1/private bullseye-staging/main armhf r-cran-nlme armhf 3.1.152-1 [2246 kB]
Get:179 http://172.17.0.1/private bullseye-staging/main armhf r-cran-matrix armhf 1.3-2-1 [3565 kB]
Get:180 http://172.17.0.1/private bullseye-staging/main armhf r-cran-mgcv armhf 1.8-34-1 [2972 kB]
Get:181 http://172.17.0.1/private bullseye-staging/main armhf r-cran-farver armhf 2.0.3-1+b1 [1381 kB]
Get:182 http://172.17.0.1/private bullseye-staging/main armhf r-cran-labeling all 0.4.2-1 [62.7 kB]
Get:183 http://172.17.0.1/private bullseye-staging/main armhf r-cran-colorspace armhf 2.0-0+dfsg-1 [1677 kB]
Get:184 http://172.17.0.1/private bullseye-staging/main armhf r-cran-munsell all 0.5.0-2 [236 kB]
Get:185 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB]
Get:186 http://172.17.0.1/private bullseye-staging/main armhf r-cran-viridislite all 0.3.0-4 [59.2 kB]
Get:187 http://172.17.0.1/private bullseye-staging/main armhf r-cran-scales all 1.1.1-1 [557 kB]
Get:188 http://172.17.0.1/private bullseye-staging/main armhf r-cran-ggplot2 all 3.3.3+dfsg-1 [3158 kB]
Get:189 http://172.17.0.1/private bullseye-staging/main armhf r-cran-gridbase all 0.4-7-5 [163 kB]
Get:190 http://172.17.0.1/private bullseye-staging/main armhf libvcflib-tools armhf 1.0.2+dfsg-2 [623 kB]
Get:191 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.10.1-1 [92.5 kB]
Get:192 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 52.0.0-3 [189 kB]
Get:193 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.56.2-1 [437 kB]
Get:194 http://172.17.0.1/private bullseye-staging/main armhf sysstat armhf 12.5.2-2 [542 kB]
Get:195 http://172.17.0.1/private bullseye-staging/main armhf parallel all 20161222-1.1 [306 kB]
Get:196 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:197 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.11-1 [502 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 107 MB in 31s (3392 kB/s)
Selecting previously unselected package libuchardet0:armhf.
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Unpacking man-db (2.9.4-2) ...
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Unpacking libexpat1:armhf (2.2.10-2) ...
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Unpacking python3.9-minimal (3.9.2-1+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1+rpi1) ...
Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.9.2-3) ...
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Unpacking media-types (4.0.0) ...
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Unpacking libmpdec3:armhf (2.5.1-1+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../3-libpython3.9-stdlib_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../4-python3.9_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.2-1+rpi1) ...
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Preparing to unpack .../5-libpython3-stdlib_3.9.2-3_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.2-3) ...
Setting up python3-minimal (3.9.2-3) ...
Selecting previously unselected package python3.
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Creating config file /etc/papersize with new version
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Not building database; man-db/auto-update is not 'true'.
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Creating config file /etc/R/Renviron with new version
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Setting up r-cran-gridbase (0.4-7-5) ...
Setting up r-cran-assertthat (0.2.1-2) ...
Setting up littler (0.3.12-1) ...
Setting up r-cran-withr (2.4.1-1) ...
Setting up r-cran-processx (3.4.5-1) ...
Setting up r-cran-praise (1.0.0-4) ...
Setting up r-cran-digest (0.6.27-1) ...
Setting up r-cran-evaluate (0.14-2) ...
Setting up r-cran-prettyunits (1.1.1-2) ...
Setting up r-cran-fansi (0.4.2-1) ...
Setting up r-cran-mass (7.3-53.1-1) ...
Setting up r-cran-glue (1.4.2-1) ...
Setting up r-cran-cli (2.3.0-1) ...
Setting up r-cran-lifecycle (0.2.0-2) ...
Setting up r-cran-rprojroot (2.0.2-1) ...
Setting up r-cran-jsonlite (1.7.2+dfsg-1) ...
Setting up r-cran-rstudioapi (0.13-1) ...
Setting up r-cran-pkgconfig (2.0.3-2) ...
Setting up r-cran-utf8 (1.1.4-2) ...
Setting up r-cran-colorspace (2.0-0+dfsg-1) ...
Setting up r-cran-plyr (1.8.6-2) ...
Setting up r-cran-rcolorbrewer (1.1-2-3) ...
Setting up r-cran-matrix (1.3-2-1) ...
Setting up r-cran-mgcv (1.8-34-1) ...
Setting up r-cran-ellipsis (0.3.1-1) ...
Setting up r-cran-callr (3.5.1-1) ...
Setting up r-cran-desc (1.2.0-3) ...
Setting up r-cran-munsell (0.5.0-2) ...
Setting up r-cran-scales (1.1.1-1) ...
Setting up r-cran-pkgbuild (1.2.0-1) ...
Setting up r-cran-vctrs (0.3.6-1) ...
Setting up r-cran-pillar (1.4.7-1) ...
Setting up r-cran-pkgload (1.1.0-1) ...
Setting up r-cran-tibble (3.0.6+dfsg-1) ...
Setting up r-cran-rematch2 (2.1.2-2) ...
Setting up r-cran-waldo (0.2.3-2) ...
Setting up r-cran-testthat (3.0.1-1) ...
Setting up r-cran-isoband (0.2.3-2) ...
Setting up r-cran-ggplot2 (3.3.3+dfsg-1) ...
Setting up libvcflib-tools (1.0.2+dfsg-2) ...
Setting up sbuild-build-depends-freebayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-11+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-11+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.28-1+rpi1
Package versions: adduser_3.118 apt_2.2.3 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.49 bash_5.1-2 bc_1.07.1-2+b1 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-7 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.75 debhelper_13.3.4 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.46.2-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-7 file_1:5.39-3 findutils_4.8.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20210202-1 libacl1_2.2.53-10 libapt-pkg6.0_2.2.3 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbamtools-dev_2.5.1+dfsg-9 libbamtools2.5.1_2.5.1+dfsg-9 libbinutils_2.35.2-2+rpi1 libblas3_3.9.0-3 libblkid1_2.36.1-7 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbwa-dev_0.7.17-6 libbz2-1.0_1.0.8-4 libc-bin_2.31-11+rpi1 libc-dev-bin_2.31-11+rpi1 libc6_2.31-11+rpi1 libc6-dev_2.31-11+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-1 libcrypt-dev_1:4.4.18-2 libcrypt1_1:4.4.18-2 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.2 libcurl4_7.74.0-1.2 libcurl4-gnutls-dev_7.74.0-1.2 libdatrie1_0.2.13-1+b1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.257 libdebhelper-perl_13.3.4 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdisorder-dev_0.0.2+git20130809.8062ee1-2 libdisorder0_0.0.2+git20130809.8062ee1-2 libdpkg-perl_1.20.9+rpi1 libelf1_0.183-1 libexpat1_2.2.10-2 libext2fs2_1.46.2-1 libfakeroot_1.25.3-1.1 libfastahack-dev_1.0.0+dfsg-7 libfastahack0_1.0.0+dfsg-7 libfdisk1_2.36.1-7 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.11.0-1 libfml-dev_0.1+git20190320.b499514-1+rpi1 libfml0_0.1+git20190320.b499514-1+rpi1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.4+dfsg-1 libfribidi0_1.0.8-2 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-3 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6+rpi1 libglib2.0-0_2.66.8-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-3 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.18.3-5 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.2-3 libhts-dev_1.11-4 libhts3_1.11-4 libice6_2:1.0.10-1 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:2.0.6-4 libjsoncpp-dev_1.9.4-4 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-5 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-5 libkrb5support0_1.18.3-5 libksba8_1.5.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.57+dfsg-2 libldap-common_2.4.57+dfsg-2 liblz4-1_1.9.3-1+rpi1 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.36.1-7 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.7.2-3 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-7 libpam-modules-bin_1.4.0-7 libpam-runtime_1.4.0-7 libpam0g_1.4.0-7 libpango-1.0-0_1.46.2-3 libpangocairo-1.0-0_1.46.2-3 libpangoft2-1.0-0_1.46.2-3 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4 libpipeline1_1.5.3-1 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.2-1+rpi1 libpython3.9-stdlib_3.9.2-1+rpi1 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsensors-config_1:3.6.0-7 libsensors5_1:3.6.0-7 libsepol1_3.1-1 libseqlib-dev_1.2.0+dfsg-4 libseqlib2_1.2.0+dfsg-4 libsigsegv2_2.13-1 libsm6_2:1.2.3-1 libsmartcols1_2.36.1-7 libsmithwaterman-dev_0.0+git20160702.2610e25-11 libsmithwaterman0_0.0+git20160702.2610e25-11 libsqlite3-0_3.34.1-3 libss2_1.46.2-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1k-1 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-5+rpi1 libtabixpp-dev_1.1.0-4 libtabixpp0_1.1.0-4 libtasn1-6_4.16.0-2 libtcl8.6_8.6.11+dfsg-1 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.2.0-1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtk8.6_8.6.11-2 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-7 libvcflib-dev_1.0.2+dfsg-2 libvcflib-tools_1.0.2+dfsg-2 libvcflib1_1.0.2+dfsg-2 libwebp6_0.6.1-2 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libxau6_1:1.0.9-1 libxcb-render0_1.14-3 libxcb-shm0_1.14-3 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxft2_2.3.2-2 libxml2_2.9.10+dfsg-6.3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.28-1+rpi1 littler_0.3.12-1 login_1:4.8.1-1 logsave_1.46.2-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 meson_0.56.2-1 mount_2.36.1-7 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 ninja-build_1.10.1-1 openssl_1.1.1k-1 parallel_20161222-1.1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4 perl-base_5.32.1-4 perl-modules-5.32_5.32.1-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.2-3 python3-minimal_3.9.2-3 python3-pkg-resources_52.0.0-3 python3.9_3.9.2-1+rpi1 python3.9-minimal_3.9.2-1+rpi1 r-base-core_4.0.4-1 r-cran-assertthat_0.2.1-2 r-cran-brio_1.1.1-1 r-cran-callr_3.5.1-1 r-cran-cli_2.3.0-1 r-cran-colorspace_2.0-0+dfsg-1 r-cran-crayon_1.4.0-1 r-cran-desc_1.2.0-3 r-cran-diffobj_0.3.2-1 r-cran-digest_0.6.27-1 r-cran-ellipsis_0.3.1-1 r-cran-evaluate_0.14-2 r-cran-fansi_0.4.2-1 r-cran-farver_2.0.3-1+b1 r-cran-ggplot2_3.3.3+dfsg-1 r-cran-glue_1.4.2-1 r-cran-gridbase_0.4-7-5 r-cran-gtable_0.3.0+dfsg-2 r-cran-isoband_0.2.3-2 r-cran-jsonlite_1.7.2+dfsg-1 r-cran-labeling_0.4.2-1 r-cran-lattice_0.20-41-1+b1 r-cran-lifecycle_0.2.0-2 r-cran-littler_0.3.12-1 r-cran-magrittr_2.0.1-1 r-cran-mass_7.3-53.1-1 r-cran-matrix_1.3-2-1 r-cran-mgcv_1.8-34-1 r-cran-munsell_0.5.0-2 r-cran-nlme_3.1.152-1 r-cran-pillar_1.4.7-1 r-cran-pkgbuild_1.2.0-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.1-1 r-cran-pkgload_1.1.0-1 r-cran-plyr_1.8.6-2 r-cran-praise_1.0.0-4 r-cran-prettyunits_1.1.1-2 r-cran-processx_3.4.5-1 r-cran-ps_1.5.0-1 r-cran-r6_2.5.0-1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.6-1 r-cran-rematch2_2.1.2-2 r-cran-rlang_0.4.10-1 r-cran-rprojroot_2.0.2-1 r-cran-rstudioapi_0.13-1 r-cran-scales_1.1.1-1 r-cran-testthat_3.0.1-1 r-cran-tibble_3.0.6+dfsg-1 r-cran-utf8_1.1.4-2 r-cran-vctrs_0.3.6-1 r-cran-viridislite_0.3.0-4 r-cran-waldo_0.2.3-2 r-cran-withr_2.4.1-1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-freebayes-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysstat_12.5.2-2 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 ucf_3.0043 unzip_6.0-26 util-linux_2.36.1-7 x11-common_1:7.7+22 xdg-utils_1.1.3-4.1 xz-utils_5.2.5-2 zip_3.0-12 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.qAw878S_/trustedkeys.kbx': General error
gpgv: Signature made Wed Feb 10 10:31:15 2021 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./freebayes_1.3.5-1.dsc
dpkg-source: info: extracting freebayes in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking freebayes_1.3.5.orig.tar.gz
dpkg-source: info: unpacking freebayes_1.3.5-1.debian.tar.xz

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-cadb4131-8aff-4e20-b925-31998732c57d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package freebayes
dpkg-buildpackage: info: source version 1.3.5-1
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: 0.56.2
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/build
Build type: native build
Project name: freebayes
Project version: 1.3.4
Using 'CFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2'
C compiler for the host machine: cc (gcc 10.2.1 "cc (Raspbian 10.2.1-6+rpi1) 10.2.1 20210110")
C linker for the host machine: cc ld.bfd 2.35.2
Using 'CXXFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2'
C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Raspbian 10.2.1-6+rpi1) 10.2.1 20210110")
C++ linker for the host machine: c++ ld.bfd 2.35.2
Using 'CFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2'
Using 'CXXFLAGS' from environment with value: '-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2'
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 5.2.5
Run-time dependency threads found: YES
Run-time dependency htslib found: YES 1.11-4
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

Option optimization is: 0 [default: 3]
Found ninja-1.10.1 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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/vector:72,
                 from ../src/Bias.h:8,
                 from ../src/Bias.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Bias.h:8,
                 from ../src/Bias.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void Bias::open(std::string&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/vector:72,
                 from ../src/Dirichlet.h:4,
                 from ../src/Dirichlet.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘long double dirichletln(const std::vector<long double>&, const std::vector<int>&, long double)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘long double dirichlet(const std::vector<long double>&, const std::vector<int>&, long double)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/vector:72,
                 from ../src/Allele.h:8,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Allele.h:8,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::vector<Allele>&, bool (*)(Allele&, Allele&))’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::vector<Allele>&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector<std::vector<Allele> > groupAlleles_copy(std::__cxx11::list<Allele>&, bool (*)(Allele&, Allele&))’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector<Allele> alleleUnion(std::vector<Allele>&, std::vector<Allele>&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/Allele.h:8,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<Allele> genotypeAllelesFromAlleleGroups(std::vector<std::vector<Allele*> >&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<Allele> genotypeAllelesFromAlleles(std::vector<Allele>&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<Allele> genotypeAllelesFromAlleles(std::vector<Allele*>&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<Allele> genotypeAllelesFromAlleleGroups(std::vector<std::vector<Allele> >&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
                 from ../src/Allele.h:10,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Allele.h:10,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In function ‘std::map<Allele, int> countAlleles(std::vector<Allele*>&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h: In function ‘std::map<Allele, int> countAlleles(std::__cxx11::list<Allele*>&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Allele.h:8,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector<Allele> uniqueAlleles(std::__cxx11::list<Allele*>&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Allele.h:10,
                 from ../src/Allele.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In function ‘std::map<Allele, int> countAlleles(std::vector<Allele>&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 /usr/include/c++/10/vector:72,
                 from ../src/DataLikelihood.h:5,
                 from ../src/DataLikelihood.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<std::pair<Genotype*, long double> >::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SampleDataLikelihood}; _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SampleDataLikelihood>::iterator’ changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function ‘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&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘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> > >&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
  121 |    _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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/bits/stl_algobase.h:71,
                 from /usr/include/c++/10/bits/stl_tree.h:63,
                 from /usr/include/c++/10/map:60,
                 from ../src/FBFasta.h:12,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/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++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
  155 |         operator()(_Iterator1 __it1, _Iterator2 __it2)
      |         ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:155:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
                 from ../src/FBFasta.h:15,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FB::FastaIndexEntry&}; _Tp = FB::FastaIndexEntry; _Alloc = std::allocator<FB::FastaIndexEntry>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<FB::FastaIndexEntry>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
                 from ../src/FBFasta.h:12,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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++/10/bits/stl_tree.h:2193:5: 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
 2193 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2458:7: 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
In file included from /usr/include/c++/10/map:61,
                 from ../src/FBFasta.h:12,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_map.h: In member function ‘std::string FB::FastaReference::sequenceNameStartingWith(std::string)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/FBFasta.h:18,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_algo.h:79:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
   79 |     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:79:5: 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++/10/bits/stl_algo.h:82:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
   82 |       if (__comp(__a, __b))
      |           ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:84:14: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
   84 |    if (__comp(__b, __c))
      |        ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:86:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
   86 |    else if (__comp(__a, __c))
      |             ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:91:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
   91 |       else if (__comp(__a, __c))
      |                ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:93:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
   93 |       else if (__comp(__b, __c))
      |                ~~~~~~^~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/FBFasta.h:18,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Distance = int; _Tp = FB::FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_val<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_heap.h:134:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
  134 |     __push_heap(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Distance = int; _Tp = FB::FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/FBFasta.h:18,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1662 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: 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++/10/bits/stl_algo.h:1662:5: 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++/10/bits/stl_algo.h:1668:12: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1668 |  if (__comp(__i, __first))
      |      ~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(FB::FastaIndexEntry, FB::FastaIndexEntry)>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1924:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1924 |       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1925 |       __comp);
      |       ~~~~~~~                     
/usr/include/c++/10/bits/stl_algo.h:1924:34: 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++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1937 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/FBFasta.h:12,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_map.h: In function ‘std::ostream& FB::operator<<(std::ostream&, FB::FastaIndex&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/vector:67,
                 from ../src/FBFasta.h:15,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/FBFasta.h:18,
                 from ../src/FBFasta.cpp:9:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
 1891 |  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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/vector:72,
                 from ../src/Utility.h:7,
                 from ../src/Multinomial.h:4,
                 from ../src/Multinomial.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘long double multinomialSamplingProb(const std::vector<long double>&, const std::vector<int>&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘long double multinomialSamplingProbLn(const std::vector<long double>&, const std::vector<int>&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 /usr/include/c++/10/vector:72,
                 from ../src/Marginals.h:4,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
                 from ../src/Marginals.h:5,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Marginals.h:5,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In function ‘long double marginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Marginals.h:4,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Marginals.h:5,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Marginals.h:4,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In function ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Marginals.h:5,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Marginals.h:4,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Marginals.h:5,
                 from ../src/Marginals.cpp:1:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/set:60,
                 from ../src/NonCall.h:6,
                 from ../src/NonCall.cpp:1:
/usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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++/10/bits/stl_tree.h:2193:5: 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
 2193 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2458:7: 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
In file included from /usr/include/c++/10/map:61,
                 from ../src/NonCall.h:7,
                 from ../src/NonCall.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In member function ‘void NonCalls::aggregatePerSample(std::map<std::__cxx11::basic_string<char>, NonCall>&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h: In member function ‘void NonCalls::record(const string&, long int, const Samples&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/algorithm:62,
                 from ../src/Result.h:6,
                 from ../src/Result.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Result.h:6,
                 from ../src/Result.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Result.h:6,
                 from ../src/Result.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1662 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1937 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function ‘void Result::sortDataLikelihoods()’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1891 |  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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Distance = int; _Tp = std::pair<Allele, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: 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
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  253 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  339 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: 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++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: 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
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/vector:72,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘std::vector<Allele> Genotype::alternateAlleles(std::string&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {GenotypeElement}; _Tp = GenotypeElement; _Alloc = std::allocator<GenotypeElement>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<GenotypeElement>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function ‘long double GenotypeCombo::hweExpectedFrequencyln(Genotype*)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<long double> Genotype::alleleProbabilities()’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<long double> GenotypeCombo::alleleProbs()’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<long double> Genotype::alleleProbabilities(Bias&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In function ‘std::vector<std::vector<ValueType> > multichoose(int, std::vector<ValueType>&) [with T = Allele]’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator<Genotype>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Genotype>::iterator’ changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<std::pair<Allele, int> >::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: 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++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/list:63,
                 from ../src/Allele.h:9,
                 from ../src/Genotype.h:15,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GenotypeCombo&}; _Tp = GenotypeCombo; _Alloc = std::allocator<GenotypeCombo>]’:
/usr/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type ‘std::__cxx11::list<GenotypeCombo>::iterator’ changed in GCC 7.1
 1909 |        _M_insert(iterator __position, _Args&&... __args)
      |        ^~~~~~~~~
/usr/include/c++/10/bits/stl_list.h: In function ‘void allLocalGenotypeCombinations(std::__cxx11::list<GenotypeCombo>&, GenotypeCombo&, SampleDataLikelihoods&, Samples&, std::map<std::__cxx11::basic_string<char>, int>&, long double, bool, bool, bool, bool, bool, bool, long double, bool)’:
/usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator<GenotypeCombo>’ changed in GCC 7.1
 1212 |       { this->_M_insert(end(), __x); }
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_list.h: In function ‘bool bandedGenotypeCombinations(std::__cxx11::list<GenotypeCombo>&, GenotypeCombo&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::map<std::__cxx11::basic_string<char>, int>&, int, int, long double, bool, bool, bool, bool, bool, bool, long double, bool)’:
/usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator<GenotypeCombo>’ changed in GCC 7.1
 1212 |       { this->_M_insert(end(), __x); }
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
                 from ../src/Genotype.h:10,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Genotype.h:10,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In function ‘void addAllHomozygousCombos(std::__cxx11::list<GenotypeCombo>&, SampleDataLikelihoods&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::vector<Allele>&, long double, bool, bool, bool, bool, bool, bool, long double)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/map:60,
                 from ../src/Genotype.h:10,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/10/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1662 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1662 |     __heap_select(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: 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++/10/map:61,
                 from ../src/Genotype.h:10,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In function ‘void combinePopulationCombos(std::__cxx11::list<GenotypeCombo>&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::list<GenotypeCombo> >&)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:339:5: 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
  339 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: 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++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:253:5: 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
  253 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: 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++/10/bits/stl_heap.h:253:5: 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 file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  424 |    std::__pop_heap(__first, __last, __last, __comp);
      |    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1666 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In constructor ‘Genotype::Genotype(std::vector<Allele>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<GenotypeElement*, std::vector<GenotypeElement> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘std::vector<Genotype> allPossibleGenotypes(int, std::vector<Allele>&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Genotype*, std::vector<Genotype> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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 file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_heap.h:424:19: 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
  424 |    std::__pop_heap(__first, __last, __last, __comp);
      |    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1959:25: 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
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: 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
 1666 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
                 from ../src/Genotype.h:10,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_map.h: In function ‘std::vector<std::pair<Allele, int> > alternateAlleles(GenotypeCombo&, std::string)’:
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
/usr/include/c++/10/bits/stl_map.h:501:37: 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
  501 |    __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |          std::tuple<const key_type&>(__k),
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |          std::tuple<>());
      |          ~~~~~~~~~~~~~~~             
In file included from /usr/include/c++/10/vector:72,
                 from ../src/Genotype.h:5,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/vector.tcc:121:21: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: 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
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1937 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsScaledByMarginals(std::vector<SampleDataLikelihood>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1937 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginals(std::vector<SampleDataLikelihood>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleDataLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1937 |       std::__heap_select(__first, __middle, __last, __comp);
      |       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void sortSampleDataLikelihoods(std::vector<SampleDataLikelihood>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/Genotype.h:7,
                 from ../src/Genotype.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<SampleMarginalAndObsCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginalsAndObs(std::vector<SampleDataLikelihood>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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
In file included from /usr/include/c++/10/map:60,
                 from ../src/Sample.h:6,
                 from ../src/Sample.cpp:1:
/usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, long double>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long double> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long double> >]’:
/usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long double>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long double> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long double> > >::const_iterator’ changed in GCC 7.1
 2193 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Distance = int; _Tp = std::pair<Allele, int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: 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
  223 |     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
      |     ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: 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++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1819:5: 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
 1819 |     __unguarded_linear_insert(_RandomAccessIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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
 1839 |     __insertion_sort(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: 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++/10/vector:72,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Predicate = __gnu_cxx::__ops::_Iter_pred<bool (*)(const Allele&)>]’:
/usr/include/c++/10/bits/stl_algo.h:833:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  833 |     __remove_if(_ForwardIterator __first, _ForwardIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:833:5: 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++/10/vector:72,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
  184 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In member function ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’:
/usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  914 |       return std::__remove_if(__first, __last,
      |              ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
  915 |          __gnu_cxx::__ops::__pred_iter(__pred));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1461 |  return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  914 |       return std::__remove_if(__first, __last,
      |              ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
  915 |          __gnu_cxx::__ops::__pred_iter(__pred));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1461 |  return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  914 |       return std::__remove_if(__first, __last,
      |              ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
  915 |          __gnu_cxx::__ops::__pred_iter(__pred));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1461 |  return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<Allele, int>}; _Tp = std::pair<Allele, int>; _Alloc = std::allocator<std::pair<Allele, int> >]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<std::pair<Allele, int> >::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:340:5: note: parameter passing for argument of type ‘std::vector<Allele>::const_iterator’ changed in GCC 7.1
  340 |     vector<_Tp, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:356:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  356 |  _M_realloc_insert(begin() + __n, std::move(__v));
      |  ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  339 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  253 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:339:5: 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
  339 |     __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: 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++/10/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_heap.h:253:5: 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
  253 |     __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
      |     ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: 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++/10/bits/stl_heap.h:253:5: 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 file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePositionCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  424 |    std::__pop_heap(__first, __last, __last, __comp);
      |    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1666 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’:
/usr/include/c++/10/bits/stl_algo.h:914:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  914 |       return std::__remove_if(__first, __last,
      |              ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
  915 |          __gnu_cxx::__ops::__pred_iter(__pred));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1461:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1461 |  return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
      |         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<Allele, int>*, std::vector<std::pair<Allele, int> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<AllelePairIntCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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
 1945 |     __introsort_loop(_RandomAccessIterator __first,
      |     ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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 file included from /usr/include/c++/10/bits/stl_algo.h:61,
                 from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_heap.h:424:19: 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
  424 |    std::__pop_heap(__first, __last, __last, __comp);
      |    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1959:25: 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
 1959 |    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: 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
 1666 |       std::__make_heap(__first, __middle, __comp);
      |       ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<Allele> AlleleParser::genotypeAlleles(std::map<std::__cxx11::basic_string<char>, std::vector<Allele*> >&, Samples&, bool, int)’:
/usr/include/c++/10/bits/vector.tcc:121:21: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type ‘std::vector<Allele>::const_iterator’ changed in GCC 7.1
 1294 |       { return _M_insert_rval(__position, std::move(__x)); }
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/vector.tcc:121:21: 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
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
                 from ../src/AlleleParser.h:11,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
 1974 |    std::__introsort_loop(__first, __last,
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
 1975 |     std::__lg(__last - __first) * 2,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 1976 |     __comp);
      |     ~~~~~~~              
/usr/include/c++/10/bits/stl_algo.h:1886:25: 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
 1886 |    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
      |    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
 1891 |  std::__insertion_sort(__first, __last, __comp);
      |  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/AlleleParser.h:7,
                 from ../src/AlleleParser.cpp:1:
/usr/include/c++/10/bits/stl_vector.h:1294:30: note: parameter passing for argument of type ‘std::vector<Allele>::const_iterator’ changed in GCC 7.1
 1294 |       { return _M_insert_rval(__position, std::move(__x)); }
      |                ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void AlleleParser::getInputVariantsInRegion(std::string&, long int, long int)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void AlleleParser::updateInputVariants(long int, int)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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++/10/vector:72,
                 from ../src/Utility.h:7,
                 from ../src/Utility.cpp:3:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘long double jointQuality(const std::vector<short int>&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function ‘double entropy(const string&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
  121 |    _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,
                 from ../src/Utility.cpp:3:
../ttmath/ttmathuint.h: In function ‘BigFloat big_exp(long double)’:
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& x)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2740 |    table[i] = p.table[i];
      |               ~~~~~~~^
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& x)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from ../ttmath/ttmathbig.h:46,
                 from ../ttmath/ttmath.h:58,
                 from ../src/Utility.h:18,
                 from ../src/Utility.cpp:3:
../ttmath/ttmathint.h:652:40: warning: ‘x.ttmath::UInt<8>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  652 |    UInt<value_size>::table[i] = p.table[i];
      |                                 ~~~~~~~^
In file included from ../ttmath/ttmathint.h:48,
                 from ../ttmath/ttmathbig.h:46,
                 from ../ttmath/ttmath.h:58,
                 from ../src/Utility.h:18,
                 from ../src/Utility.cpp:3:
../ttmath/ttmathuint.h: In function ‘long double logsumexp_probs(const std::vector<long double>&)’:
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& maxNb)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2740 |    table[i] = p.table[i];
      |               ~~~~~~~^
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& maxNb)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from ../ttmath/ttmathbig.h:46,
                 from ../ttmath/ttmath.h:58,
                 from ../src/Utility.h:18,
                 from ../src/Utility.cpp:3:
../ttmath/ttmathint.h:652:40: warning: ‘maxNb.ttmath::UInt<8>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  652 |    UInt<value_size>::table[i] = p.table[i];
      |                                 ~~~~~~~^
In file included from /usr/include/c++/10/vector:72,
                 from ../src/Utility.h:7,
                 from ../src/Utility.cpp:3:
/usr/include/c++/10/bits/vector.tcc: In function ‘long double poissonPvalLn(int, int)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
  121 |    _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,
                 from ../src/Utility.cpp:3:
../ttmath/ttmathuint.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
 2740 |    table[i] = p.table[i];
      |               ~~~~~~~^
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
../ttmath/ttmathuint.h:2740:22: warning: ‘*((void*)(& result)+32).ttmath::UInt<2>::table[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized]
[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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 /usr/include/c++/10/vector:72,
                 from ../src/ResultData.h:4,
                 from ../src/ResultData.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
                 from ../src/Genotype.h:10,
                 from ../src/ResultData.h:7,
                 from ../src/ResultData.cpp:1:
/usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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++/10/bits/stl_tree.h:2193:5: 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
 2193 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/ResultData.h:4,
                 from ../src/ResultData.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘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*)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[24/27] rm -f libfreebayes_common.a && gcc-ar csrD 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 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -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/10/../../../arm-linux-gnueabihf/libvcflib.so /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libsmithwaterman.so /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libdisorder.so /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libfastahack.so /usr/lib/arm-linux-gnueabihf/libseqlib.so /usr/lib/libbwa.a -ltabixpp -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 -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 /usr/include/c++/10/vector:72,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SampleDataLikelihood&}; _Tp = SampleDataLikelihood; _Alloc = std::allocator<SampleDataLikelihood>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SampleDataLikelihood>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator<long double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long double>::iterator’ changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator<Allele>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<Allele>::iterator’ changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void Results::update(SampleDataLikelihoods&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
                 from ../src/freebayes.cpp:13:
/usr/include/c++/10/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _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++/10/bits/stl_tree.h:2193:5: 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
 2193 |     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/list:63,
                 from ../src/Utility.h:8,
                 from ../src/Parameters.h:14,
                 from ../src/freebayes.cpp:26:
/usr/include/c++/10/bits/stl_list.h: In member function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_insert(std::__cxx11::list<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const GenotypeCombo&}; _Tp = GenotypeCombo; _Alloc = std::allocator<GenotypeCombo>]’:
/usr/include/c++/10/bits/stl_list.h:1909:8: note: parameter passing for argument of type ‘std::__cxx11::list<GenotypeCombo>::iterator’ changed in GCC 7.1
 1909 |        _M_insert(iterator __position, _Args&&... __args)
      |        ^~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/bits/vector.tcc: In function ‘int main(int, char**)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/list:63,
                 from ../src/Utility.h:8,
                 from ../src/Parameters.h:14,
                 from ../src/freebayes.cpp:26:
/usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator<GenotypeCombo>’ changed in GCC 7.1
 1212 |       { this->_M_insert(end(), __x); }
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
                 from ../src/freebayes.cpp:12:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long double*, std::vector<long double> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
 1198 |    _M_realloc_insert(end(), __x);
      |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/list:63,
                 from ../src/Utility.h:8,
                 from ../src/Parameters.h:14,
                 from ../src/freebayes.cpp:26:
/usr/include/c++/10/bits/stl_list.h:1212:24: note: parameter passing for argument of type ‘std::_List_iterator<GenotypeCombo>’ changed in GCC 7.1
 1212 |       { this->_M_insert(end(), __x); }
      |         ~~~~~~~~~~~~~~~^~~~~~~~~~~~
[27/27] c++  -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -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 -ltabixpp /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libvcflib.so /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libsmithwaterman.so /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libdisorder.so /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/libfastahack.so /usr/lib/arm-linux-gnueabihf/libseqlib.so /usr/lib/libbwa.a -ltabixpp -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.
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,  3 wallclock secs ( 0.25 usr  0.04 sys +  0.56 cusr  0.59 csys =  1.44 CPU)
Result: PASS
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,  5 wallclock secs ( 0.26 usr  0.01 sys +  0.51 cusr  0.89 csys =  1.67 CPU)
Result: PASS
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 ( 0.27 usr  0.02 sys +  0.17 cusr  0.28 csys =  0.74 CPU)
Result: PASS
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, 48 wallclock secs ( 0.24 usr  0.04 sys + 47.83 cusr  3.27 csys = 51.38 CPU)
Result: PASS
[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: 14191 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
t/01_call_variants.t .. 
1..16
ok 1 - variant calling recovers most of the GiAB variants in a test region
ok 2 - freebayes produces the same number of calls if targeted per site or called without targets
ok 3 - a targets bed file can be used with the same effect as running by region
ok 4 - reading from stdin or not makes no difference
ok 5 - freebayes processes all alignments in BAM input
ok 6 - freebayes processes all alignments in CRAM input
ok 7 - freebayes correctly handles variant input
ok 8 - freebayes puts required variants in output
ok 9 - freebayes limits calls to input variants correctly
ok 10 - freebayes reports all input variants even when there is no input data
ok 11 - freebayes handles region and variant input
ok 12 - freebayes limits to variant input correctly when region is given
ok 13 - freebayes handles variant input and reading from stdin
ok 14 - freebayes limits to variant input when reading from stdin
ok 15 - freebayes handles region, stdin, and variant input
ok 16 - !
ok
All tests successful.
Files=1, Tests=16, 91 wallclock secs ( 0.26 usr  0.02 sys + 71.76 cusr 31.81 csys = 103.85 CPU)
Result: PASS
1/5 T00  OK             3.78s
2/5 T01  OK             91.66s
3/5 T01b OK             49.11s
4/5 T02  OK             5.88s
5/5 T03  OK             2.35s


Ok:                 5   
Expected Fail:      0   
Fail:               0   
Unexpected Pass:    0   
Skipped:            0   
Timeout:            0   

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 -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_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 -a -O--buildsystem=meson -O--builddir=build
   dh_strip -a -a -O--buildsystem=meson -O--builddir=build
   dh_makeshlibs -a -a -O--buildsystem=meson -O--builddir=build
   dh_shlibdeps -a -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
   dh_md5sums -a -O--buildsystem=meson -O--builddir=build
   dh_builddeb -a -O--buildsystem=meson -O--builddir=build
dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.5-1_armhf.deb'.
dpkg-deb: building package 'freebayes' in '../freebayes_1.3.5-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../freebayes_1.3.5-1_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 2021-05-09T00:28:36Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


freebayes_1.3.5-1_armhf.changes:
--------------------------------

Format: 1.8
Date: Wed, 10 Feb 2021 11:28:21 +0100
Source: freebayes
Binary: freebayes freebayes-dbgsym
Architecture: armhf
Version: 1.3.5-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 freebayes  - Bayesian haplotype-based polymorphism discovery and genotyping
Changes:
 freebayes (1.3.5-1) unstable; urgency=medium
 .
   * New upstream version
   * watch file standard 4 (routine-update)
Checksums-Sha1:
 b8ab5033ba1640b78000b0b54fd01d20fdd0ff33 6300884 freebayes-dbgsym_1.3.5-1_armhf.deb
 25bb83b2c43f7e0ed364574c496c2871cbac9df9 10109 freebayes_1.3.5-1_armhf.buildinfo
 37f936c4c58d227ccc20b31b589b57bea56c60cc 1401968 freebayes_1.3.5-1_armhf.deb
Checksums-Sha256:
 7f4ab49005b15a238ee858d077038a65452075d1401e7b33e58fffa557670135 6300884 freebayes-dbgsym_1.3.5-1_armhf.deb
 42bc202320776fa206191245b52bf40c17c8939c1f24be571d218a7375b80e91 10109 freebayes_1.3.5-1_armhf.buildinfo
 4e3fd6e81b043710b9b330ec43916642ca28c5c957fe74e12055e58e7351a29d 1401968 freebayes_1.3.5-1_armhf.deb
Files:
 3b17e097b70bbbf6426fd62796915d56 6300884 debug optional freebayes-dbgsym_1.3.5-1_armhf.deb
 9b8b80b781074b62d480eac18825d04c 10109 science optional freebayes_1.3.5-1_armhf.buildinfo
 2d10172b0f9080011e0ab822f784f922 1401968 science optional freebayes_1.3.5-1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


freebayes-dbgsym_1.3.5-1_armhf.deb
----------------------------------

 new Debian package, version 2.0.
 size 6300884 bytes: control archive=644 bytes.
     420 bytes,    12 lines      control              
     301 bytes,     3 lines      md5sums              
 Package: freebayes-dbgsym
 Source: freebayes
 Version: 1.3.5-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 6412
 Depends: freebayes (= 1.3.5-1)
 Section: debug
 Priority: optional
 Description: debug symbols for freebayes
 Build-Ids: 5df44f180375cfac7441218123592447b3cdf973 622129748a0ae5ab91e895f1898840daa05f93f2

drwxr-xr-x root/root         0 2021-02-10 10:28 ./
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/debug/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/debug/.build-id/5d/
-rw-r--r-- root/root   5662604 2021-02-10 10:28 ./usr/lib/debug/.build-id/5d/f44f180375cfac7441218123592447b3cdf973.debug
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/debug/.build-id/62/
-rw-r--r-- root/root    599856 2021-02-10 10:28 ./usr/lib/debug/.build-id/62/2129748a0ae5ab91e895f1898840daa05f93f2.debug
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root    289724 2021-02-10 10:28 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/freebayes.debug
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/
lrwxrwxrwx root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes-dbgsym -> freebayes


freebayes_1.3.5-1_armhf.deb
---------------------------

 new Debian package, version 2.0.
 size 1401968 bytes: control archive=2120 bytes.
     847 bytes,    17 lines      control              
    4378 bytes,    52 lines      md5sums              
 Package: freebayes
 Version: 1.3.5-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3769
 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libseqlib2 (>= 1.2.0), libstdc++6 (>= 5.2), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.2+dfsg), zlib1g (>= 1:1.1.4)
 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 2021-02-10 10:28 ./
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/bin/
-rwxr-xr-x root/root   1142020 2021-02-10 10:28 ./usr/bin/bamleftalign
-rwxr-xr-x root/root   1735828 2021-02-10 10:28 ./usr/bin/freebayes
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes/
-rw-r--r-- root/root      9562 2021-02-10 09:21 ./usr/share/doc/freebayes/README.md.gz
-rw-r--r-- root/root       278 2021-02-10 10:28 ./usr/share/doc/freebayes/README.test
-rw-r--r-- root/root        83 2021-02-10 10:28 ./usr/share/doc/freebayes/README.test_data
-rw-r--r-- root/root      2505 2021-02-10 09:21 ./usr/share/doc/freebayes/RELEASE-NOTES.md
-rw-r--r-- root/root      1628 2021-02-10 10:28 ./usr/share/doc/freebayes/changelog.Debian.gz
-rw-r--r-- root/root      3194 2021-02-10 10:28 ./usr/share/doc/freebayes/copyright
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/
-rw-r--r-- root/root        83 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/README.test_data
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/bash-tap/
-rw-r--r-- root/root       906 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/pipeline.sh
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/regression/
-rw-r--r-- root/root     73144 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/regression/NA12878.chr22.tiny.vcf
-rw-r--r-- root/root        94 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/regression/README.md
drwxr-xr-x root/root         0 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/splice/
-rw-r--r-- root/root     22589 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.bam
-rw-r--r-- root/root       288 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.bam.bai
-rw-r--r-- root/root      3801 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.fa
-rw-r--r-- root/root        15 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/splice/1:883884-887618.fa.fai
drwxr-xr-x root/root         0 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/t/
-rw-r--r-- root/root      3648 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/t/00_region_and_target_handling.t
-rw-r--r-- root/root      4908 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/t/01_call_variants.t
-rw-r--r-- root/root      2947 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/t/01b_call_variants.t
-rw-r--r-- root/root      2943 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/t/02_multi_bam.t
-rw-r--r-- root/root      1488 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/t/03_reference_bases.t
-rw-r--r-- root/root       246 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/targets.bed
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test-simple-bash/
-rw-r--r-- root/root        17 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.alt
-rw-r--r-- root/root       230 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.bam
-rw-r--r-- root/root        96 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.bam.bai
-rw-r--r-- root/root       112 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.bed
-rw-r--r-- root/root        17 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.ref
-rw-r--r-- root/root        15 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.ref.fai
-rw-r--r-- root/root       550 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/test.vcf
drwxr-xr-x root/root         0 2021-02-10 10:28 ./usr/share/doc/freebayes/examples/tiny/
-rw-r--r-- root/root       636 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/1read.bam
-rw-r--r-- root/root        96 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/1read.bam.bai
-rw-r--r-- root/root    287213 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam
-rw-r--r-- root/root        96 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.bam.bai
-rw-r--r-- root/root    155615 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.cram
-rw-r--r-- root/root     16307 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.giab.vcf
-rw-r--r-- root/root    287228 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam
-rw-r--r-- root/root        96 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/NA12878.chr22.tiny.hla.bam.bai
-rw-r--r-- root/root     12581 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/hla.fa
-rw-r--r-- root/root        33 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/hla.fa.fai
-rw-r--r-- root/root      2394 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/hla.vcf.gz
-rw-r--r-- root/root       120 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/hla.vcf.gz.tbi
-rw-r--r-- root/root     12565 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q with spaces.fa
-rw-r--r-- root/root        16 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q with spaces.fa.fai
-rw-r--r-- root/root        36 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q with spaces.regions
-rw-r--r-- root/root     12565 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q.fa
-rw-r--r-- root/root        16 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q.fa.fai
-rw-r--r-- root/root        36 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q.regions
-rw-r--r-- root/root      4168 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q.vcf.gz
-rw-r--r-- root/root       102 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q.vcf.gz.tbi
-rw-r--r-- root/root      2378 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q_spiked.vcf.gz
-rw-r--r-- root/root        91 2021-02-10 09:21 ./usr/share/doc/freebayes/examples/tiny/q_spiked.vcf.gz.tbi
-rw-r--r-- root/root       924 2021-02-10 10:28 ./usr/share/doc/freebayes/run-unit-test.gz


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 128956
Build-Time: 608
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1419
Job: freebayes_1.3.5-1
Machine Architecture: armhf
Package: freebayes
Package-Time: 2079
Source-Version: 1.3.5-1
Space: 128956
Status: successful
Version: 1.3.5-1
--------------------------------------------------------------------------------
Finished at 2021-05-09T00:28:36Z
Build needed 00:34:39, 128956k disc space
Raspbian Package Auto-Building

Build log for freebayes (1.3.5-1) on armhf
