freebayes →
1.3.5-3 →
armhf → 2021-10-09 06:09:59
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| freebayes 1.3.5-3 (armhf) Sat, 09 Oct 2021 05:37:25 +0000 |
+==============================================================================+
Package: freebayes
Version: 1.3.5-3
Source Version: 1.3.5-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-529cddcf-10c2-44bf-81c2-797bd7df3d77' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.8 MB in 26s (1006 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 bookworm-staging/main freebayes 1.3.5-3 (dsc) [2221 B]
Get:2 http://172.17.0.1/private bookworm-staging/main freebayes 1.3.5-3 (tar) [2890 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main freebayes 1.3.5-3 (diff) [11.4 kB]
Fetched 2904 kB in 0s (6167 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/freebayes-JTmnZ6/freebayes-1.3.5' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/freebayes-JTmnZ6' 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-eCMa42/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-eCMa42/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-eCMa42/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-eCMa42/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2870 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (21.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 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, 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
Filtered Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools
dpkg-deb: building package 'sbuild-build-depends-freebayes-dummy' in '/<<BUILDDIR>>/resolver-eCMa42/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-eCMa42/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Sources [605 B]
Get:5 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ Packages [674 B]
Fetched 2612 B in 1s (3392 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates
debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gcc-11-base gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libasan6 libatomic1
libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev
libcairo2 libcc1-0 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1
libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0
libelf1 libexpat1 libfastahack-dev libfastahack0 libffi8
libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1
libfreetype6 libfribidi0 libgcc-s1 libgfortran5 libglib2.0-0 libgomp1
libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 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
libstdc++6 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6
libthai-data libthai0 libtiff5 libtk8.6 libtool libubsan1 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-distutils python3-lib2to3 python3-minimal python3-pkg-resources
python3.9 python3.9-minimal r-base-core r-cran-cli r-cran-colorspace
r-cran-crayon r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-farver
r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband
r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler
r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell
r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr
r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-scales
r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr
samtools sensible-utils 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
ash csh fish ksh tcsh zsh 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-callr
r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-prettycode
r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rstudioapi r-cran-shiny
r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shinyjs
r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer
r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr
r-cran-magick r-cran-sf r-cran-getopt r-cran-bit64 r-cran-formattable
r-cran-stringi r-cran-survival r-cran-units r-cran-testthat
r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools
r-cran-inline r-cran-dichromat r-cran-bench r-cran-blob r-cran-brio
r-cran-evaluate r-cran-hms r-cran-htmltools r-cran-pkgbuild r-cran-pkgload
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-testthat r-cran-mockery
r-cran-covr r-cran-ragg r-cran-dplyr r-cran-hexbin r-cran-hmisc
r-cran-interp r-cran-knitr r-cran-mapproj r-cran-maps r-cran-maptools
r-cran-multcomp r-cran-quantreg r-cran-rmarkdown r-cran-rpart r-cran-sf
r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-lubridate r-cran-domc
r-cran-abind r-cran-bit64 r-cran-hms r-cran-data.table r-cran-rsqlite
r-cran-mockr r-cran-generics r-cran-waldo r-cran-dbi systemd | cron
| cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
x11-utils x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdextrautils ca-certificates
debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.1
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 libffi8 libfile-stripnondeterminism-perl libfml-dev libfml0
libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 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-distutils
python3-lib2to3 python3-minimal python3-pkg-resources python3.9
python3.9-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-crayon
r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-farver r-cran-ggplot2
r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling
r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass
r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar
r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer
r-cran-rcpp r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8
r-cran-vctrs r-cran-viridislite r-cran-withr samtools
sbuild-build-depends-freebayes-dummy sensible-utils sysstat ucf unzip
x11-common xdg-utils zip zlib1g-dev
The following packages will be upgraded:
gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-s1 libgomp1 libstdc++6
libubsan1
8 upgraded, 185 newly installed, 0 to remove and 14 not upgraded.
Need to get 110 MB of archives.
After this operation, 248 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-eCMa42/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [960 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-7+rpi1 [1944 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-7+rpi1 [797 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-7+rpi1 [88.1 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-7+rpi1 [205 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-7+rpi1 [36.2 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-7+rpi1 [37.7 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-7+rpi1 [8188 B]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-7+rpi1 [465 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.7-4+rpi1 [794 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-2 [80.3 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.7-4+rpi1 [1632 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libffi8 armhf 3.4.2-2 [21.2 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.7-4+rpi1 [1618 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf python3.9 armhf 3.9.7-4+rpi1 [480 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libncurses6 armhf 6.2+20201114-4 [79.7 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf bc armhf 1.07.1-3 [101 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf openssl armhf 1.1.1l-1 [815 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:50 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:51 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:52 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:53 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:54 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:55 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:56 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:57 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:58 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:59 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:60 http://172.17.0.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:61 http://172.17.0.1/private bookworm-staging/main armhf libfreetype6 armhf 2.10.4+dfsg-1 [353 kB]
Get:62 http://172.17.0.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:63 http://172.17.0.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:64 http://172.17.0.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:65 http://172.17.0.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:66 http://172.17.0.1/private bookworm-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-9 [135 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-9 [179 kB]
Get:68 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:69 http://172.17.0.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:70 http://172.17.0.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:71 http://172.17.0.1/private bookworm-staging/main armhf libbwa-dev armhf 0.7.17-6 [137 kB]
Get:72 http://172.17.0.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:73 http://172.17.0.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:74 http://172.17.0.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:75 http://172.17.0.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:76 http://172.17.0.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:77 http://172.17.0.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:78 http://172.17.0.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:79 http://172.17.0.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:80 http://172.17.0.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:81 http://172.17.0.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:82 http://172.17.0.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:83 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:84 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:85 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:86 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:87 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:88 http://172.17.0.1/private bookworm-staging/main armhf libcurl4 armhf 7.74.0-1.3 [305 kB]
Get:89 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:90 http://172.17.0.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-1+b1 [39.7 kB]
Get:91 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.7-2 [44.1 kB]
Get:92 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.7-2 [40.5 kB]
Get:93 http://172.17.0.1/private bookworm-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-3 [4780 B]
Get:94 http://172.17.0.1/private bookworm-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-3 [4412 B]
Get:95 http://172.17.0.1/private bookworm-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-8 [24.0 kB]
Get:96 http://172.17.0.1/private bookworm-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-8 [26.7 kB]
Get:97 http://172.17.0.1/private bookworm-staging/main armhf libfml0 armhf 0.1+git20190320.b499514-1+rpi1 [68.7 kB]
Get:98 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:99 http://172.17.0.1/private bookworm-staging/main armhf libfml-dev armhf 0.1+git20190320.b499514-1+rpi1 [80.8 kB]
Get:100 http://172.17.0.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:101 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-7+rpi1 [235 kB]
Get:102 http://172.17.0.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.0-1 [1208 kB]
Get:103 http://172.17.0.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:104 http://172.17.0.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:105 http://172.17.0.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:106 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:107 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:108 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
Get:109 http://172.17.0.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:110 http://172.17.0.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:111 http://172.17.0.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:112 http://172.17.0.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [122 kB]
Get:113 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp24 armhf 1.9.4-5 [67.4 kB]
Get:114 http://172.17.0.1/private bookworm-staging/main armhf libjsoncpp-dev armhf 1.9.4-5 [25.5 kB]
Get:115 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:116 http://172.17.0.1/private bookworm-staging/main armhf libthai-data all 0.1.28-4.1 [171 kB]
Get:117 http://172.17.0.1/private bookworm-staging/main armhf libthai0 armhf 0.1.28-4.1 [51.4 kB]
Get:118 http://172.17.0.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.48.10+ds1-1 [184 kB]
Get:119 http://172.17.0.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.48.10+ds1-1 [66.6 kB]
Get:120 http://172.17.0.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.48.10+ds1-1 [56.8 kB]
Get:121 http://172.17.0.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:122 http://172.17.0.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:123 http://172.17.0.1/private bookworm-staging/main armhf libsensors-config all 1:3.6.0-7 [32.3 kB]
Get:124 http://172.17.0.1/private bookworm-staging/main armhf libsensors5 armhf 1:3.6.0-7 [49.6 kB]
Get:125 http://172.17.0.1/private bookworm-staging/main armhf libssw0 armhf 1.1-13 [21.0 kB]
Get:126 http://172.17.0.1/private bookworm-staging/main armhf libseqlib2 armhf 1.2.0+dfsg-6 [139 kB]
Get:127 http://172.17.0.1/private bookworm-staging/main armhf libssw-dev armhf 1.1-13 [24.0 kB]
Get:128 http://172.17.0.1/private bookworm-staging/main armhf libseqlib-dev armhf 1.2.0+dfsg-6 [197 kB]
Get:129 http://172.17.0.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:130 http://172.17.0.1/private bookworm-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-11 [33.1 kB]
Get:131 http://172.17.0.1/private bookworm-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-11 [36.6 kB]
Get:132 http://172.17.0.1/private bookworm-staging/main armhf libtabixpp0 armhf 1.1.0-4 [8604 B]
Get:133 http://172.17.0.1/private bookworm-staging/main armhf libtabixpp-dev armhf 1.1.0-4 [8156 B]
Get:134 http://172.17.0.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.11+dfsg-1 [894 kB]
Get:135 http://172.17.0.1/private bookworm-staging/main armhf libwebp6 armhf 0.6.1-2.1 [225 kB]
Get:136 http://172.17.0.1/private bookworm-staging/main armhf libtiff5 armhf 4.3.0-2 [272 kB]
Get:137 http://172.17.0.1/private bookworm-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:138 http://172.17.0.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:139 http://172.17.0.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.11.1-1 [681 kB]
Get:140 http://172.17.0.1/private bookworm-staging/main armhf libvcflib1 armhf 1.0.2+dfsg-2+b2 [127 kB]
Get:141 http://172.17.0.1/private bookworm-staging/main armhf libvcflib-dev armhf 1.0.2+dfsg-2+b2 [85.2 kB]
Get:142 http://172.17.0.1/private bookworm-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:143 http://172.17.0.1/private bookworm-staging/main armhf unzip armhf 6.0-26 [151 kB]
Get:144 http://172.17.0.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:145 http://172.17.0.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:146 http://172.17.0.1/private bookworm-staging/main armhf r-base-core armhf 4.1.1-2 [25.3 MB]
Get:147 http://172.17.0.1/private bookworm-staging/main armhf r-cran-littler armhf 0.3.13-2 [94.5 kB]
Get:148 http://172.17.0.1/private bookworm-staging/main armhf littler all 0.3.13-2 [16.4 kB]
Get:149 http://172.17.0.1/private bookworm-staging/main armhf r-cran-pkgkitten all 0.2.2-2 [27.0 kB]
Get:150 http://172.17.0.1/private bookworm-staging/main armhf r-cran-rcpp armhf 1.0.7-2 [1997 kB]
Get:151 http://172.17.0.1/private bookworm-staging/main armhf r-cran-plyr armhf 1.8.6-2 [830 kB]
Get:152 http://172.17.0.1/private bookworm-staging/main armhf r-cran-digest armhf 0.6.28-1 [187 kB]
Get:153 http://172.17.0.1/private bookworm-staging/main armhf r-cran-glue armhf 1.4.2-1 [139 kB]
Get:154 http://172.17.0.1/private bookworm-staging/main armhf r-cran-gtable all 0.3.0+dfsg-2 [163 kB]
Get:155 http://172.17.0.1/private bookworm-staging/main armhf r-cran-isoband armhf 0.2.5-1 [1756 kB]
Get:156 http://172.17.0.1/private bookworm-staging/main armhf r-cran-mass armhf 7.3-54-2 [1117 kB]
Get:157 http://172.17.0.1/private bookworm-staging/main armhf r-cran-lattice armhf 0.20-45-1 [1176 kB]
Get:158 http://172.17.0.1/private bookworm-staging/main armhf r-cran-nlme armhf 3.1.153-1 [2266 kB]
Get:159 http://172.17.0.1/private bookworm-staging/main armhf r-cran-matrix armhf 1.3-4-2 [3573 kB]
Get:160 http://172.17.0.1/private bookworm-staging/main armhf r-cran-mgcv armhf 1.8-37-1 [2980 kB]
Get:161 http://172.17.0.1/private bookworm-staging/main armhf r-cran-rlang armhf 0.4.11-1 [1186 kB]
Get:162 http://172.17.0.1/private bookworm-staging/main armhf r-cran-farver armhf 2.1.0-1 [1394 kB]
Get:163 http://172.17.0.1/private bookworm-staging/main armhf r-cran-labeling all 0.4.2-1 [62.7 kB]
Get:164 http://172.17.0.1/private bookworm-staging/main armhf r-cran-lifecycle all 1.0.0-1 [91.2 kB]
Get:165 http://172.17.0.1/private bookworm-staging/main armhf r-cran-colorspace armhf 2.0-2+dfsg-1 [1690 kB]
Get:166 http://172.17.0.1/private bookworm-staging/main armhf r-cran-munsell all 0.5.0-2 [236 kB]
Get:167 http://172.17.0.1/private bookworm-staging/main armhf r-cran-r6 all 2.5.1-1 [105 kB]
Get:168 http://172.17.0.1/private bookworm-staging/main armhf r-cran-rcolorbrewer all 1.1-2-3 [54.4 kB]
Get:169 http://172.17.0.1/private bookworm-staging/main armhf r-cran-viridislite all 0.4.0-2 [1298 kB]
Get:170 http://172.17.0.1/private bookworm-staging/main armhf r-cran-scales all 1.1.1-1 [557 kB]
Get:171 http://172.17.0.1/private bookworm-staging/main armhf r-cran-ellipsis armhf 0.3.2-2 [35.1 kB]
Get:172 http://172.17.0.1/private bookworm-staging/main armhf r-cran-fansi armhf 0.5.0-1 [379 kB]
Get:173 http://172.17.0.1/private bookworm-staging/main armhf r-cran-magrittr armhf 2.0.1-1 [197 kB]
Get:174 http://172.17.0.1/private bookworm-staging/main armhf r-cran-cli armhf 3.0.1-1 [735 kB]
Get:175 http://172.17.0.1/private bookworm-staging/main armhf r-cran-crayon all 1.4.1-1 [145 kB]
Get:176 http://172.17.0.1/private bookworm-staging/main armhf r-cran-utf8 armhf 1.2.2-1 [129 kB]
Get:177 http://172.17.0.1/private bookworm-staging/main armhf r-cran-vctrs armhf 0.3.8-1 [1099 kB]
Get:178 http://172.17.0.1/private bookworm-staging/main armhf r-cran-pillar all 1.6.3+dfsg-1 [410 kB]
Get:179 http://172.17.0.1/private bookworm-staging/main armhf r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get:180 http://172.17.0.1/private bookworm-staging/main armhf r-cran-tibble armhf 3.1.4+dfsg-2 [458 kB]
Get:181 http://172.17.0.1/private bookworm-staging/main armhf r-cran-withr all 2.4.2-1 [213 kB]
Get:182 http://172.17.0.1/private bookworm-staging/main armhf r-cran-ggplot2 all 3.3.5+dfsg-2 [3215 kB]
Get:183 http://172.17.0.1/private bookworm-staging/main armhf r-cran-gridbase all 0.4-7-5 [163 kB]
Get:184 http://172.17.0.1/private bookworm-staging/main armhf libvcflib-tools armhf 1.0.2+dfsg-2+b2 [622 kB]
Get:185 http://172.17.0.1/private bookworm-staging/main armhf ninja-build armhf 1.10.1-1 [92.5 kB]
Get:186 http://172.17.0.1/private bookworm-staging/main armhf python3-pkg-resources all 52.0.0-4 [190 kB]
Get:187 http://172.17.0.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.7-1 [79.4 kB]
Get:188 http://172.17.0.1/private bookworm-staging/main armhf python3-distutils all 3.9.7-1 [146 kB]
Get:189 http://172.17.0.1/private bookworm-staging/main armhf meson all 0.59.2-1 [496 kB]
Get:190 http://172.17.0.1/private bookworm-staging/main armhf sysstat armhf 12.5.2-2 [542 kB]
Get:191 http://172.17.0.1/private bookworm-staging/main armhf parallel all 20210822+ds-2 [1970 kB]
Get:192 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:193 http://172.17.0.1/private bookworm-staging/main armhf samtools armhf 1.13-2 [525 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 110 MB in 11s (10.1 MB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../bsdextrautils_2.37.2-1_armhf.deb ...
Unpacking bsdextrautils (2.37.2-1) ...
Preparing to unpack .../libasan6_11.2.0-7+rpi1_armhf.deb ...
Unpacking libasan6:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libubsan1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libubsan1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libgomp1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../gcc-11-base_11.2.0-7+rpi1_armhf.deb ...
Unpacking gcc-11-base:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Setting up gcc-11-base:armhf (11.2.0-7+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libgcc-s1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libgcc-s1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Setting up libgcc-s1:armhf (11.2.0-7+rpi1) ...
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../libcc1-0_11.2.0-7+rpi1_armhf.deb ...
Unpacking libcc1-0:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libatomic1_11.2.0-7+rpi1_armhf.deb ...
Unpacking libatomic1:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Preparing to unpack .../libstdc++6_11.2.0-7+rpi1_armhf.deb ...
Unpacking libstdc++6:armhf (11.2.0-7+rpi1) over (11.2.0-4+rpi1) ...
Setting up libstdc++6:armhf (11.2.0-7+rpi1) ...
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12515 files and directories currently installed.)
Preparing to unpack .../0-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../1-groff-base_1.22.4-7_armhf.deb ...
Unpacking groff-base (1.22.4-7) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../2-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../3-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../4-libpython3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../5-libexpat1_2.4.1-2_armhf.deb ...
Unpacking libexpat1:armhf (2.4.1-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../6-python3.9-minimal_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.7-4+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.7-4+rpi1) ...
Setting up libexpat1:armhf (2.4.1-2) ...
Setting up python3.9-minimal (3.9.7-4+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13351 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.2-3_armhf.deb ...
Unpacking python3-minimal (3.9.2-3) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libffi8:armhf.
Preparing to unpack .../2-libffi8_3.4.2-2_armhf.deb ...
Unpacking libffi8:armhf (3.4.2-2) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../3-libmpdec3_2.5.1-2+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-2+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../4-libpython3.9-stdlib_3.9.7-4+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../5-python3.9_3.9.7-4+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.7-4+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../6-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.
(Reading database ... 13754 files and directories currently installed.)
Preparing to unpack .../000-python3_3.9.2-3_armhf.deb ...
Unpacking python3 (3.9.2-3) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../001-libncurses6_6.2+20201114-4_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-4) ...
Selecting previously unselected package libprocps8:armhf.
Preparing to unpack .../002-libprocps8_2%3a3.3.17-5_armhf.deb ...
Unpacking libprocps8:armhf (2:3.3.17-5) ...
Selecting previously unselected package procps.
Preparing to unpack .../003-procps_2%3a3.3.17-5_armhf.deb ...
Unpacking procps (2:3.3.17-5) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../004-sensible-utils_0.0.17_all.deb ...
Unpacking sensible-utils (0.0.17) ...
Selecting previously unselected package bc.
Preparing to unpack .../005-bc_1.07.1-3_armhf.deb ...
Unpacking bc (1.07.1-3) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../006-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../007-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../008-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../009-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package ucf.
Preparing to unpack .../010-ucf_3.0043_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../011-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../012-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../013-autoconf_2.71-2_all.deb ...
Unpacking autoconf (2.71-2) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../014-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../015-automake_1%3a1.16.4-2_all.deb ...
Unpacking automake (1:1.16.4-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../016-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package openssl.
Preparing to unpack .../017-openssl_1.1.1l-1_armhf.deb ...
Unpacking openssl (1.1.1l-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../018-ca-certificates_20210119_all.deb ...
Unpacking ca-certificates (20210119) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../019-libdebhelper-perl_13.5.2_all.deb ...
Unpacking libdebhelper-perl (13.5.2) ...
Selecting previously unselected package libtool.
Preparing to unpack .../020-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../021-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../023-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../025-dh-strip-nondeterminism_1.12.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.12.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../026-libelf1_0.185-2_armhf.deb ...
Unpacking libelf1:armhf (0.185-2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../027-dwz_0.14-1_armhf.deb ...
Unpacking dwz (0.14-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../028-libicu67_67.1-7_armhf.deb ...
Unpacking libicu67:armhf (67.1-7) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../029-libxml2_2.9.12+dfsg-5_armhf.deb ...
Unpacking libxml2:armhf (2.9.12+dfsg-5) ...
Selecting previously unselected package gettext.
Preparing to unpack .../030-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../031-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../033-debhelper_13.5.2_all.deb ...
Unpacking debhelper (13.5.2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../034-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../035-libpng16-16_1.6.37-3_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.37-3) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../036-libfreetype6_2.10.4+dfsg-1_armhf.deb ...
Unpacking libfreetype6:armhf (2.10.4+dfsg-1) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../037-fonts-dejavu-core_2.37-2_all.deb ...
Unpacking fonts-dejavu-core (2.37-2) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../038-fontconfig-config_2.13.1-4.2_all.deb ...
Unpacking fontconfig-config (2.13.1-4.2) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../039-libfontconfig1_2.13.1-4.2_armhf.deb ...
Unpacking libfontconfig1:armhf (2.13.1-4.2) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../040-fontconfig_2.13.1-4.2_armhf.deb ...
Unpacking fontconfig (2.13.1-4.2) ...
Selecting previously unselected package libbamtools2.5.1:armhf.
Preparing to unpack .../041-libbamtools2.5.1_2.5.1+dfsg-9_armhf.deb ...
Unpacking libbamtools2.5.1:armhf (2.5.1+dfsg-9) ...
Selecting previously unselected package libbamtools-dev:armhf.
Preparing to unpack .../042-libbamtools-dev_2.5.1+dfsg-9_armhf.deb ...
Unpacking libbamtools-dev:armhf (2.5.1+dfsg-9) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../043-libblas3_3.9.0-3_armhf.deb ...
Unpacking libblas3:armhf (3.9.0-3) ...
Selecting previously unselected package libmd0:armhf.
Preparing to unpack .../044-libmd0_1.0.4-1_armhf.deb ...
Unpacking libmd0:armhf (1.0.4-1) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../045-libbsd0_0.11.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.3-1) ...
Selecting previously unselected package libbwa-dev.
Preparing to unpack .../046-libbwa-dev_0.7.17-6_armhf.deb ...
Unpacking libbwa-dev (0.7.17-6) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../047-libpixman-1-0_0.40.0-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.40.0-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../048-libxau6_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../049-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../050-libxcb1_1.14-3_armhf.deb ...
Unpacking libxcb1:armhf (1.14-3) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../051-libx11-data_2%3a1.7.2-2_all.deb ...
Unpacking libx11-data (2:1.7.2-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../052-libx11-6_2%3a1.7.2-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.7.2-2) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../053-libxcb-render0_1.14-3_armhf.deb ...
Unpacking libxcb-render0:armhf (1.14-3) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../054-libxcb-shm0_1.14-3_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.14-3) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../055-libxext6_2%3a1.3.4-1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../056-libxrender1_1%3a0.9.10-1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../057-libcairo2_1.16.0-5_armhf.deb ...
Unpacking libcairo2:armhf (1.16.0-5) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../058-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../059-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../060-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../061-libssh2-1_1.10.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.10.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../062-libcurl3-gnutls_7.74.0-1.3_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.3) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../063-libcurl4_7.74.0-1.3_armhf.deb ...
Unpacking libcurl4:armhf (7.74.0-1.3) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../064-libcurl4-gnutls-dev_7.74.0-1.3_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Selecting previously unselected package libdatrie1:armhf.
Preparing to unpack .../065-libdatrie1_0.2.13-1+b1_armhf.deb ...
Unpacking libdatrie1:armhf (0.2.13-1+b1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../066-libdeflate0_1.7-2_armhf.deb ...
Unpacking libdeflate0:armhf (1.7-2) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../067-libdeflate-dev_1.7-2_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.7-2) ...
Selecting previously unselected package libdisorder0:armhf.
Preparing to unpack .../068-libdisorder0_0.0.2+git20130809.8062ee1-3_armhf.deb ...
Unpacking libdisorder0:armhf (0.0.2+git20130809.8062ee1-3) ...
Selecting previously unselected package libdisorder-dev:armhf.
Preparing to unpack .../069-libdisorder-dev_0.0.2+git20130809.8062ee1-3_armhf.deb ...
Unpacking libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-3) ...
Selecting previously unselected package libfastahack0:armhf.
Preparing to unpack .../070-libfastahack0_1.0.0+dfsg-8_armhf.deb ...
Unpacking libfastahack0:armhf (1.0.0+dfsg-8) ...
Selecting previously unselected package libfastahack-dev:armhf.
Preparing to unpack .../071-libfastahack-dev_1.0.0+dfsg-8_armhf.deb ...
Unpacking libfastahack-dev:armhf (1.0.0+dfsg-8) ...
Selecting previously unselected package libfml0:armhf.
Preparing to unpack .../072-libfml0_0.1+git20190320.b499514-1+rpi1_armhf.deb ...
Unpacking libfml0:armhf (0.1+git20190320.b499514-1+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../073-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libfml-dev:armhf.
Preparing to unpack .../074-libfml-dev_0.1+git20190320.b499514-1+rpi1_armhf.deb ...
Unpacking libfml-dev:armhf (0.1+git20190320.b499514-1+rpi1) ...
Selecting previously unselected package libfribidi0:armhf.
Preparing to unpack .../075-libfribidi0_1.0.8-2_armhf.deb ...
Unpacking libfribidi0:armhf (1.0.8-2) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../076-libgfortran5_11.2.0-7+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (11.2.0-7+rpi1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../077-libglib2.0-0_2.70.0-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.70.0-1) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../078-libgraphite2-3_1.3.14-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.14-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../079-libharfbuzz0b_2.7.4-1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (2.7.4-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../080-libhtscodecs2_1.1.1-3_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.1.1-3) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../081-libhts3_1.13+ds-2_armhf.deb ...
Unpacking libhts3:armhf (1.13+ds-2) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../082-liblzma-dev_5.2.5-2_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-2) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../083-libhts-dev_1.13+ds-2_armhf.deb ...
Unpacking libhts-dev:armhf (1.13+ds-2) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../084-x11-common_1%3a7.7+23_all.deb ...
Unpacking x11-common (1:7.7+23) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../085-libice6_2%3a1.0.10-1_armhf.deb ...
Unpacking libice6:armhf (2:1.0.10-1) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../086-libjbig0_2.1-3.1+b2_armhf.deb ...
Unpacking libjbig0:armhf (2.1-3.1+b2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../087-libjpeg62-turbo_1%3a2.0.6-4_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.0.6-4) ...
Selecting previously unselected package libjsoncpp24:armhf.
Preparing to unpack .../088-libjsoncpp24_1.9.4-5_armhf.deb ...
Unpacking libjsoncpp24:armhf (1.9.4-5) ...
Selecting previously unselected package libjsoncpp-dev:armhf.
Preparing to unpack .../089-libjsoncpp-dev_1.9.4-5_armhf.deb ...
Unpacking libjsoncpp-dev:armhf (1.9.4-5) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../090-liblapack3_3.9.0-3_armhf.deb ...
Unpacking liblapack3:armhf (3.9.0-3) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../091-libthai-data_0.1.28-4.1_all.deb ...
Unpacking libthai-data (0.1.28-4.1) ...
Selecting previously unselected package libthai0:armhf.
Preparing to unpack .../092-libthai0_0.1.28-4.1_armhf.deb ...
Unpacking libthai0:armhf (0.1.28-4.1) ...
Selecting previously unselected package libpango-1.0-0:armhf.
Preparing to unpack .../093-libpango-1.0-0_1.48.10+ds1-1_armhf.deb ...
Unpacking libpango-1.0-0:armhf (1.48.10+ds1-1) ...
Selecting previously unselected package libpangoft2-1.0-0:armhf.
Preparing to unpack .../094-libpangoft2-1.0-0_1.48.10+ds1-1_armhf.deb ...
Unpacking libpangoft2-1.0-0:armhf (1.48.10+ds1-1) ...
Selecting previously unselected package libpangocairo-1.0-0:armhf.
Preparing to unpack .../095-libpangocairo-1.0-0_1.48.10+ds1-1_armhf.deb ...
Unpacking libpangocairo-1.0-0:armhf (1.48.10+ds1-1) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../096-libpaper1_1.1.28_armhf.deb ...
Unpacking libpaper1:armhf (1.1.28) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../097-libpaper-utils_1.1.28_armhf.deb ...
Unpacking libpaper-utils (1.1.28) ...
Selecting previously unselected package libsensors-config.
Preparing to unpack .../098-libsensors-config_1%3a3.6.0-7_all.deb ...
Unpacking libsensors-config (1:3.6.0-7) ...
Selecting previously unselected package libsensors5:armhf.
Preparing to unpack .../099-libsensors5_1%3a3.6.0-7_armhf.deb ...
Unpacking libsensors5:armhf (1:3.6.0-7) ...
Selecting previously unselected package libssw0:armhf.
Preparing to unpack .../100-libssw0_1.1-13_armhf.deb ...
Unpacking libssw0:armhf (1.1-13) ...
Selecting previously unselected package libseqlib2:armhf.
Preparing to unpack .../101-libseqlib2_1.2.0+dfsg-6_armhf.deb ...
Unpacking libseqlib2:armhf (1.2.0+dfsg-6) ...
Selecting previously unselected package libssw-dev:armhf.
Preparing to unpack .../102-libssw-dev_1.1-13_armhf.deb ...
Unpacking libssw-dev:armhf (1.1-13) ...
Selecting previously unselected package libseqlib-dev:armhf.
Preparing to unpack .../103-libseqlib-dev_1.2.0+dfsg-6_armhf.deb ...
Unpacking libseqlib-dev:armhf (1.2.0+dfsg-6) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../104-libsm6_2%3a1.2.3-1_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.3-1) ...
Selecting previously unselected package libsmithwaterman0.
Preparing to unpack .../105-libsmithwaterman0_0.0+git20160702.2610e25-11_armhf.deb ...
Unpacking libsmithwaterman0 (0.0+git20160702.2610e25-11) ...
Selecting previously unselected package libsmithwaterman-dev.
Preparing to unpack .../106-libsmithwaterman-dev_0.0+git20160702.2610e25-11_armhf.deb ...
Unpacking libsmithwaterman-dev (0.0+git20160702.2610e25-11) ...
Selecting previously unselected package libtabixpp0:armhf.
Preparing to unpack .../107-libtabixpp0_1.1.0-4_armhf.deb ...
Unpacking libtabixpp0:armhf (1.1.0-4) ...
Selecting previously unselected package libtabixpp-dev:armhf.
Preparing to unpack .../108-libtabixpp-dev_1.1.0-4_armhf.deb ...
Unpacking libtabixpp-dev:armhf (1.1.0-4) ...
Selecting previously unselected package libtcl8.6:armhf.
Preparing to unpack .../109-libtcl8.6_8.6.11+dfsg-1_armhf.deb ...
Unpacking libtcl8.6:armhf (8.6.11+dfsg-1) ...
Selecting previously unselected package libwebp6:armhf.
Preparing to unpack .../110-libwebp6_0.6.1-2.1_armhf.deb ...
Unpacking libwebp6:armhf (0.6.1-2.1) ...
Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../111-libtiff5_4.3.0-2_armhf.deb ...
Unpacking libtiff5:armhf (4.3.0-2) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../112-libxft2_2.3.2-2_armhf.deb ...
Unpacking libxft2:armhf (2.3.2-2) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../113-libxss1_1%3a1.2.3-1_armhf.deb ...
Unpacking libxss1:armhf (1:1.2.3-1) ...
Selecting previously unselected package libtk8.6:armhf.
Preparing to unpack .../114-libtk8.6_8.6.11.1-1_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.11.1-1) ...
Selecting previously unselected package libvcflib1:armhf.
Preparing to unpack .../115-libvcflib1_1.0.2+dfsg-2+b2_armhf.deb ...
Unpacking libvcflib1:armhf (1.0.2+dfsg-2+b2) ...
Selecting previously unselected package libvcflib-dev:armhf.
Preparing to unpack .../116-libvcflib-dev_1.0.2+dfsg-2+b2_armhf.deb ...
Unpacking libvcflib-dev:armhf (1.0.2+dfsg-2+b2) ...
Selecting previously unselected package zip.
Preparing to unpack .../117-zip_3.0-12_armhf.deb ...
Unpacking zip (3.0-12) ...
Selecting previously unselected package unzip.
Preparing to unpack .../118-unzip_6.0-26_armhf.deb ...
Unpacking unzip (6.0-26) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../119-xdg-utils_1.1.3-4.1_all.deb ...
Unpacking xdg-utils (1.1.3-4.1) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../120-libxt6_1%3a1.2.0-1_armhf.deb ...
Unpacking libxt6:armhf (1:1.2.0-1) ...
Selecting previously unselected package r-base-core.
Preparing to unpack .../121-r-base-core_4.1.1-2_armhf.deb ...
Unpacking r-base-core (4.1.1-2) ...
Selecting previously unselected package r-cran-littler.
Preparing to unpack .../122-r-cran-littler_0.3.13-2_armhf.deb ...
Unpacking r-cran-littler (0.3.13-2) ...
Selecting previously unselected package littler.
Preparing to unpack .../123-littler_0.3.13-2_all.deb ...
Unpacking littler (0.3.13-2) ...
Selecting previously unselected package r-cran-pkgkitten.
Preparing to unpack .../124-r-cran-pkgkitten_0.2.2-2_all.deb ...
Unpacking r-cran-pkgkitten (0.2.2-2) ...
Selecting previously unselected package r-cran-rcpp.
Preparing to unpack .../125-r-cran-rcpp_1.0.7-2_armhf.deb ...
Unpacking r-cran-rcpp (1.0.7-2) ...
Selecting previously unselected package r-cran-plyr.
Preparing to unpack .../126-r-cran-plyr_1.8.6-2_armhf.deb ...
Unpacking r-cran-plyr (1.8.6-2) ...
Selecting previously unselected package r-cran-digest.
Preparing to unpack .../127-r-cran-digest_0.6.28-1_armhf.deb ...
Unpacking r-cran-digest (0.6.28-1) ...
Selecting previously unselected package r-cran-glue.
Preparing to unpack .../128-r-cran-glue_1.4.2-1_armhf.deb ...
Unpacking r-cran-glue (1.4.2-1) ...
Selecting previously unselected package r-cran-gtable.
Preparing to unpack .../129-r-cran-gtable_0.3.0+dfsg-2_all.deb ...
Unpacking r-cran-gtable (0.3.0+dfsg-2) ...
Selecting previously unselected package r-cran-isoband.
Preparing to unpack .../130-r-cran-isoband_0.2.5-1_armhf.deb ...
Unpacking r-cran-isoband (0.2.5-1) ...
Selecting previously unselected package r-cran-mass.
Preparing to unpack .../131-r-cran-mass_7.3-54-2_armhf.deb ...
Unpacking r-cran-mass (7.3-54-2) ...
Selecting previously unselected package r-cran-lattice.
Preparing to unpack .../132-r-cran-lattice_0.20-45-1_armhf.deb ...
Unpacking r-cran-lattice (0.20-45-1) ...
Selecting previously unselected package r-cran-nlme.
Preparing to unpack .../133-r-cran-nlme_3.1.153-1_armhf.deb ...
Unpacking r-cran-nlme (3.1.153-1) ...
Selecting previously unselected package r-cran-matrix.
Preparing to unpack .../134-r-cran-matrix_1.3-4-2_armhf.deb ...
Unpacking r-cran-matrix (1.3-4-2) ...
Selecting previously unselected package r-cran-mgcv.
Preparing to unpack .../135-r-cran-mgcv_1.8-37-1_armhf.deb ...
Unpacking r-cran-mgcv (1.8-37-1) ...
Selecting previously unselected package r-cran-rlang.
Preparing to unpack .../136-r-cran-rlang_0.4.11-1_armhf.deb ...
Unpacking r-cran-rlang (0.4.11-1) ...
Selecting previously unselected package r-cran-farver.
Preparing to unpack .../137-r-cran-farver_2.1.0-1_armhf.deb ...
Unpacking r-cran-farver (2.1.0-1) ...
Selecting previously unselected package r-cran-labeling.
Preparing to unpack .../138-r-cran-labeling_0.4.2-1_all.deb ...
Unpacking r-cran-labeling (0.4.2-1) ...
Selecting previously unselected package r-cran-lifecycle.
Preparing to unpack .../139-r-cran-lifecycle_1.0.0-1_all.deb ...
Unpacking r-cran-lifecycle (1.0.0-1) ...
Selecting previously unselected package r-cran-colorspace.
Preparing to unpack .../140-r-cran-colorspace_2.0-2+dfsg-1_armhf.deb ...
Unpacking r-cran-colorspace (2.0-2+dfsg-1) ...
Selecting previously unselected package r-cran-munsell.
Preparing to unpack .../141-r-cran-munsell_0.5.0-2_all.deb ...
Unpacking r-cran-munsell (0.5.0-2) ...
Selecting previously unselected package r-cran-r6.
Preparing to unpack .../142-r-cran-r6_2.5.1-1_all.deb ...
Unpacking r-cran-r6 (2.5.1-1) ...
Selecting previously unselected package r-cran-rcolorbrewer.
Preparing to unpack .../143-r-cran-rcolorbrewer_1.1-2-3_all.deb ...
Unpacking r-cran-rcolorbrewer (1.1-2-3) ...
Selecting previously unselected package r-cran-viridislite.
Preparing to unpack .../144-r-cran-viridislite_0.4.0-2_all.deb ...
Unpacking r-cran-viridislite (0.4.0-2) ...
Selecting previously unselected package r-cran-scales.
Preparing to unpack .../145-r-cran-scales_1.1.1-1_all.deb ...
Unpacking r-cran-scales (1.1.1-1) ...
Selecting previously unselected package r-cran-ellipsis.
Preparing to unpack .../146-r-cran-ellipsis_0.3.2-2_armhf.deb ...
Unpacking r-cran-ellipsis (0.3.2-2) ...
Selecting previously unselected package r-cran-fansi.
Preparing to unpack .../147-r-cran-fansi_0.5.0-1_armhf.deb ...
Unpacking r-cran-fansi (0.5.0-1) ...
Selecting previously unselected package r-cran-magrittr.
Preparing to unpack .../148-r-cran-magrittr_2.0.1-1_armhf.deb ...
Unpacking r-cran-magrittr (2.0.1-1) ...
Selecting previously unselected package r-cran-cli.
Preparing to unpack .../149-r-cran-cli_3.0.1-1_armhf.deb ...
Unpacking r-cran-cli (3.0.1-1) ...
Selecting previously unselected package r-cran-crayon.
Preparing to unpack .../150-r-cran-crayon_1.4.1-1_all.deb ...
Unpacking r-cran-crayon (1.4.1-1) ...
Selecting previously unselected package r-cran-utf8.
Preparing to unpack .../151-r-cran-utf8_1.2.2-1_armhf.deb ...
Unpacking r-cran-utf8 (1.2.2-1) ...
Selecting previously unselected package r-cran-vctrs.
Preparing to unpack .../152-r-cran-vctrs_0.3.8-1_armhf.deb ...
Unpacking r-cran-vctrs (0.3.8-1) ...
Selecting previously unselected package r-cran-pillar.
Preparing to unpack .../153-r-cran-pillar_1.6.3+dfsg-1_all.deb ...
Unpacking r-cran-pillar (1.6.3+dfsg-1) ...
Selecting previously unselected package r-cran-pkgconfig.
Preparing to unpack .../154-r-cran-pkgconfig_2.0.3-2_all.deb ...
Unpacking r-cran-pkgconfig (2.0.3-2) ...
Selecting previously unselected package r-cran-tibble.
Preparing to unpack .../155-r-cran-tibble_3.1.4+dfsg-2_armhf.deb ...
Unpacking r-cran-tibble (3.1.4+dfsg-2) ...
Selecting previously unselected package r-cran-withr.
Preparing to unpack .../156-r-cran-withr_2.4.2-1_all.deb ...
Unpacking r-cran-withr (2.4.2-1) ...
Selecting previously unselected package r-cran-ggplot2.
Preparing to unpack .../157-r-cran-ggplot2_3.3.5+dfsg-2_all.deb ...
Unpacking r-cran-ggplot2 (3.3.5+dfsg-2) ...
Selecting previously unselected package r-cran-gridbase.
Preparing to unpack .../158-r-cran-gridbase_0.4-7-5_all.deb ...
Unpacking r-cran-gridbase (0.4-7-5) ...
Selecting previously unselected package libvcflib-tools.
Preparing to unpack .../159-libvcflib-tools_1.0.2+dfsg-2+b2_armhf.deb ...
Unpacking libvcflib-tools (1.0.2+dfsg-2+b2) ...
Selecting previously unselected package ninja-build.
Preparing to unpack .../160-ninja-build_1.10.1-1_armhf.deb ...
Unpacking ninja-build (1.10.1-1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../161-python3-pkg-resources_52.0.0-4_all.deb ...
Unpacking python3-pkg-resources (52.0.0-4) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../162-python3-lib2to3_3.9.7-1_all.deb ...
Unpacking python3-lib2to3 (3.9.7-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../163-python3-distutils_3.9.7-1_all.deb ...
Unpacking python3-distutils (3.9.7-1) ...
Selecting previously unselected package meson.
Preparing to unpack .../164-meson_0.59.2-1_all.deb ...
Unpacking meson (0.59.2-1) ...
Selecting previously unselected package sysstat.
Preparing to unpack .../165-sysstat_12.5.2-2_armhf.deb ...
Unpacking sysstat (12.5.2-2) ...
Selecting previously unselected package parallel.
Preparing to unpack .../166-parallel_20210822+ds-2_all.deb ...
Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel'
Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel'
Unpacking parallel (20210822+ds-2) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../167-pkg-config_0.29.2-1_armhf.deb ...
Unpacking pkg-config (0.29.2-1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../168-samtools_1.13-2_armhf.deb ...
Unpacking samtools (1.13-2) ...
Selecting previously unselected package sbuild-build-depends-freebayes-dummy.
Preparing to unpack .../169-sbuild-build-depends-freebayes-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-freebayes-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.1.1-3) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-3) ...
Setting up libpixman-1-0:armhf (0.40.0-1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libdatrie1:armhf (0.2.13-1+b1) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up unzip (6.0-26) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: WARNING: No init system and policy-rc.d missing! Defaulting to block.
Setting up libsensors-config (1:3.6.0-7) ...
Setting up libsmithwaterman0 (0.0+git20160702.2610e25-11) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-2) ...
Setting up bc (1.07.1-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libgomp1:armhf (11.2.0-7+rpi1) ...
Setting up libfastahack0:armhf (1.0.0+dfsg-8) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up ninja-build (1.10.1-1) ...
Setting up libasan6:armhf (11.2.0-7+rpi1) ...
Setting up libfastahack-dev:armhf (1.0.0+dfsg-8) ...
Setting up zip (3.0-12) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libjpeg62-turbo:armhf (1:2.0.6-4) ...
Setting up libx11-data (2:1.7.2-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-4) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libfribidi0:armhf (1.0.8-2) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-9) ...
Setting up libpng16-16:armhf (1.6.37-3) ...
Setting up libatomic1:armhf (11.2.0-7+rpi1) ...
Setting up libtcl8.6:armhf (8.6.11+dfsg-1) ...
Setting up autopoint (0.21-4) ...
Setting up libwebp6:armhf (0.6.1-2.1) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libsensors5:armhf (1:3.6.0-7) ...
Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-3) ...
Setting up libgfortran5:armhf (11.2.0-7+rpi1) ...
Setting up libbwa-dev (0.7.17-6) ...
Setting up libjsoncpp24:armhf (1.9.4-5) ...
Setting up liblzma-dev:armhf (5.2.5-2) ...
Setting up libubsan1:armhf (11.2.0-7+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libffi8:armhf (3.4.2-2) ...
Setting up libmd0:armhf (1.0.4-1) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-4.1) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up libtiff5:armhf (4.3.0-2) ...
Setting up openssl (1.1.1l-1) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up libdeflate-dev:armhf (1.7-2) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libssw0:armhf (1.1-13) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libcc1-0:armhf (11.2.0-7+rpi1) ...
Setting up libprocps8:armhf (2:3.3.17-5) ...
Setting up libpython3.9-stdlib:armhf (3.9.7-4+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-3) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libjsoncpp-dev:armhf (1.9.4-5) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libssw-dev:armhf (1.1-13) ...
Setting up libtool (2.4.6-15) ...
Setting up libxcb-render0:armhf (1.14-3) ...
Setting up libglib2.0-0:armhf (2.70.0-1) ...
No schema files found: doing nothing.
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.3) ...
Setting up libxcb-shm0:armhf (1.14-3) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3) ...
Setting up libfml0:armhf (0.1+git20190320.b499514-1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libthai0:armhf (0.1.28-4.1) ...
Setting up ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
Setting up libfreetype6:armhf (2.10.4+dfsg-1) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-9) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-11) ...
Setting up ucf (3.0043) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.74.0-1.3) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libharfbuzz0b:armhf (2.7.4-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up sysstat (12.5.2-2) ...
Creating config file /etc/default/sysstat with new version
update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode
Setting up python3.9 (3.9.7-4+rpi1) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpaper1:armhf (1.1.28) ...
Creating config file /etc/papersize with new version
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up libfml-dev:armhf (0.1+git20190320.b499514-1+rpi1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up fontconfig-config (2.13.1-4.2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libhts-dev:armhf (1.13+ds-2) ...
Setting up python3 (3.9.2-3) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.13-2) ...
Setting up dh-autoreconf (20) ...
Setting up libxt6:armhf (1:1.2.0-1) ...
Setting up parallel (20210822+ds-2) ...
Setting up libtabixpp0:armhf (1.1.0-4) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up python3-lib2to3 (3.9.7-1) ...
Setting up libseqlib2:armhf (1.2.0+dfsg-6) ...
Setting up python3-pkg-resources (52.0.0-4) ...
Setting up python3-distutils (3.9.7-1) ...
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libtk8.6:armhf (8.6.11.1-1) ...
Setting up libpango-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up libseqlib-dev:armhf (1.2.0+dfsg-6) ...
Setting up meson (0.59.2-1) ...
Setting up debhelper (13.5.2) ...
Setting up libcairo2:armhf (1.16.0-5) ...
Setting up libvcflib1:armhf (1.0.2+dfsg-2+b2) ...
Setting up libtabixpp-dev:armhf (1.1.0-4) ...
Setting up libpangoft2-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up libvcflib-dev:armhf (1.0.2+dfsg-2+b2) ...
Setting up r-base-core (4.1.1-2) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.4.1-1) ...
Setting up r-cran-gtable (0.3.0+dfsg-2) ...
Setting up r-cran-labeling (0.4.2-1) ...
Setting up r-cran-lattice (0.20-45-1) ...
Setting up r-cran-nlme (3.1.153-1) ...
Setting up r-cran-farver (2.1.0-1) ...
Setting up r-cran-viridislite (0.4.0-2) ...
Setting up r-cran-r6 (2.5.1-1) ...
Setting up r-cran-pkgkitten (0.2.2-2) ...
Setting up r-cran-magrittr (2.0.1-1) ...
Setting up r-cran-littler (0.3.13-2) ...
Setting up r-cran-rcpp (1.0.7-2) ...
Setting up r-cran-rlang (0.4.11-1) ...
Setting up r-cran-gridbase (0.4-7-5) ...
Setting up littler (0.3.13-2) ...
Setting up r-cran-withr (2.4.2-1) ...
Setting up r-cran-digest (0.6.28-1) ...
Setting up r-cran-fansi (0.5.0-1) ...
Setting up r-cran-mass (7.3-54-2) ...
Setting up r-cran-glue (1.4.2-1) ...
Setting up r-cran-cli (3.0.1-1) ...
Setting up r-cran-lifecycle (1.0.0-1) ...
Setting up r-cran-pkgconfig (2.0.3-2) ...
Setting up r-cran-utf8 (1.2.2-1) ...
Setting up r-cran-colorspace (2.0-2+dfsg-1) ...
Setting up r-cran-plyr (1.8.6-2) ...
Setting up r-cran-rcolorbrewer (1.1-2-3) ...
Setting up r-cran-isoband (0.2.5-1) ...
Setting up r-cran-matrix (1.3-4-2) ...
Setting up r-cran-mgcv (1.8-37-1) ...
Setting up r-cran-ellipsis (0.3.2-2) ...
Setting up r-cran-munsell (0.5.0-2) ...
Setting up r-cran-scales (1.1.1-1) ...
Setting up r-cran-vctrs (0.3.8-1) ...
Setting up r-cran-pillar (1.6.3+dfsg-1) ...
Setting up r-cran-tibble (3.1.4+dfsg-2) ...
Setting up r-cran-ggplot2 (3.3.5+dfsg-2) ...
Setting up libvcflib-tools (1.0.2+dfsg-2+b2) ...
Setting up sbuild-build-depends-freebayes-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+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_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-7+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 bc_1.07.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.37.2-1 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_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 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_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-7+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 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_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-7+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-7+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbamtools-dev_2.5.1+dfsg-9 libbamtools2.5.1_2.5.1+dfsg-9 libbinutils_2.37-5+rpi1 libblas3_3.9.0-3 libblkid1_2.37.2-1 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_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-7+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdatrie1_0.2.13-1+b1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdisorder-dev_0.0.2+git20130809.8062ee1-3 libdisorder0_0.0.2+git20130809.8062ee1-3 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libexpat1_2.4.1-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libfastahack-dev_1.0.0+dfsg-8 libfastahack0_1.0.0+dfsg-8 libffi7_3.3-6 libffi8_3.4.2-2 libfile-stripnondeterminism-perl_1.12.0-1 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_10.3.0-9+rpi1 libgcc-s1_11.2.0-7+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgfortran5_11.2.0-7+rpi1 libglib2.0-0_2.70.0-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-7+rpi1 libgpg-error0_1.42-3 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.18.3-7 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libice6_2:1.0.10-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:2.0.6-4 libjsoncpp-dev_1.9.4-5 libjsoncpp24_1.9.4-5 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack3_3.9.0-3 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.4-1 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-4 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpango-1.0-0_1.48.10+ds1-1 libpangocairo-1.0-0_1.48.10+ds1-1 libpangoft2-1.0-0_1.48.10+ds1-1 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 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_3.9.7-4+rpi1 libpython3.9-stdlib_3.9.7-4+rpi1 libreadline8_8.1-2 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-6 libseqlib2_1.2.0+dfsg-6 libsigsegv2_2.13-1 libsm6_2:1.2.3-1 libsmartcols1_2.37.2-1 libsmithwaterman-dev_0.0+git20160702.2610e25-11 libsmithwaterman0_0.0+git20160702.2610e25-11 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-7+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtabixpp-dev_1.1.0-4 libtabixpp0_1.1.0-4 libtasn1-6_4.17.0-2 libtcl8.6_8.6.11+dfsg-1 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libthai-data_0.1.28-4.1 libthai0_0.1.28-4.1 libtiff5_4.3.0-2 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtk8.6_8.6.11.1-1 libtool_2.4.6-15 libubsan1_11.2.0-7+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libvcflib-dev_1.0.2+dfsg-2+b2 libvcflib-tools_1.0.2+dfsg-2+b2 libvcflib1_1.0.2+dfsg-2+b2 libwebp6_0.6.1-2.1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 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_2:1.3.4-1 libxft2_2.3.2-2 libxml2_2.9.12+dfsg-5 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_5.10.46-4+rpi1 littler_0.3.13-2 login_1:4.8.1-1 logsave_1.46.4-1 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_0.59.2-1 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 ninja-build_1.10.1-1 openssl_1.1.1l-1 parallel_20210822+ds-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 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-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3-pkg-resources_52.0.0-4 python3.9_3.9.7-4+rpi1 python3.9-minimal_3.9.7-4+rpi1 r-base-core_4.1.1-2 r-cran-cli_3.0.1-1 r-cran-colorspace_2.0-2+dfsg-1 r-cran-crayon_1.4.1-1 r-cran-digest_0.6.28-1 r-cran-ellipsis_0.3.2-2 r-cran-fansi_0.5.0-1 r-cran-farver_2.1.0-1 r-cran-ggplot2_3.3.5+dfsg-2 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_0.2.5-1 r-cran-labeling_0.4.2-1 r-cran-lattice_0.20-45-1 r-cran-lifecycle_1.0.0-1 r-cran-littler_0.3.13-2 r-cran-magrittr_2.0.1-1 r-cran-mass_7.3-54-2 r-cran-matrix_1.3-4-2 r-cran-mgcv_1.8-37-1 r-cran-munsell_0.5.0-2 r-cran-nlme_3.1.153-1 r-cran-pillar_1.6.3+dfsg-1 r-cran-pkgconfig_2.0.3-2 r-cran-pkgkitten_0.2.2-2 r-cran-plyr_1.8.6-2 r-cran-r6_2.5.1-1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.7-2 r-cran-rlang_0.4.11-1 r-cran-scales_1.1.1-1 r-cran-tibble_3.1.4+dfsg-2 r-cran-utf8_1.2.2-1 r-cran-vctrs_0.3.8-1 r-cran-viridislite_0.4.0-2 r-cran-withr_2.4.2-1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 samtools_1.13-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-freebayes-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysstat_12.5.2-2 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 ucf_3.0043 unzip_6.0-26 util-linux_2.37.2-1 x11-common_1:7.7+23 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.SucG0aUb/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 7 06:28:14 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_1.3.5-3.dsc
dpkg-source: info: extracting freebayes in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking freebayes_1.3.5.orig.tar.gz
dpkg-source: info: unpacking freebayes_1.3.5-3.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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-529cddcf-10c2-44bf-81c2-797bd7df3d77
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package freebayes
dpkg-buildpackage: info: source version 1.3.5-3
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: 0.59.2
Source dir: /<<PKGBUILDDIR>>
Build dir: /<<PKGBUILDDIR>>/build
Build type: native build
Project name: freebayes
Project version: 1.3.4
C compiler for the host machine: cc (gcc 10.3.0 "cc (Raspbian 10.3.0-9+rpi1) 10.3.0")
C linker for the host machine: cc ld.bfd 2.37
C++ compiler for the host machine: c++ (gcc 10.3.0 "c++ (Raspbian 10.3.0-9+rpi1) 10.3.0")
C++ linker for the host machine: c++ ld.bfd 2.37
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 1.13+ds
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 -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 -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 -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 -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 -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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp
[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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:2460:7: 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
2460 | _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 -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 -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 -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:2195:5: 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
2195 | _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:2460:7: 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
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2460:7: 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:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1824 | __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:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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:1667:5: 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:1673:12: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1673 | 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1950:5: 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:1929:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1929 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1930 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1929:34: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<FB::FastaIndexEntry*, std::vector<FB::FastaIndexEntry> >’ changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp
[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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 -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:2460:7: 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
2460 | _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 -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:2195:5: 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
2195 | _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:2460:7: 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
2460 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2460:7: 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 -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:1824:5: 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
1824 | __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:1824:5: 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:1844:5: 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
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1844:5: 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:1844:5: 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:1844:5: 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:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1824 | __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<SampleLikelihoodCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1824 | __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<SampleMarginalCompare>]’:
/usr/include/c++/10/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1824 | __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:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:2460:7: 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
2460 | _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:2460:7: 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
2460 | _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:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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:1667:5: 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:1667:5: 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:1667:5: 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:1667:5: 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:1667:5: 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:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1824 | __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:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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:1667:5: 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:1667:5: 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1671 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1896 | 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:1950:5: 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
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: 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
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: 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
1671 | 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:1979:25: 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
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: 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
1896 | 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1896 | 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1896 | 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1896 | 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1964 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1896 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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:1824:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1824 | __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:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1844:5: 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:1667:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1667 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1667:5: 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:1667:5: 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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1942:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1942 | 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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SampleDataLikelihood*, std::vector<SampleDataLikelihood> >’ changed in GCC 7.1
1896 | 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 -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:2195:5: 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
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp
[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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
[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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:1824:5: 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
1824 | __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:1844:5: 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
1844 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1844:5: 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:1844:5: 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:1844:5: 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:1844:5: 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:838:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
838 | __remove_if(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:838:5: 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:919:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
919 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
920 | __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));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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:919:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
919 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
920 | __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:919:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
919 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
920 | __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:1950:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1671 | 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:919:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
919 | return std::__remove_if(__first, __last,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
920 | __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:1979:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Allele*, std::vector<Allele> >’ changed in GCC 7.1
1896 | 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:1950:5: 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
1950 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1950:5: 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:1964:25: 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
1964 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1671:23: 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
1671 | 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:1979:25: 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
1979 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1980 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1981 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:25: 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
1891 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1896:23: 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
1896 | 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++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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
[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -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]
[23/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -std=c++14 -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:2195:5: 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
2195 | _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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblzma.so -pthread /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/gcc/arm-linux-gnueabihf/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 -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/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 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:2195:5: 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
2195 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblzma.so -pthread /usr/lib/arm-linux-gnueabihf/libhts.so -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.
1/5 T00 RUNNING
>>> MALLOC_PERTURB_=172 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t
2/5 T01 RUNNING
>>> MALLOC_PERTURB_=223 /usr/bin/prove -e bash -v t/01_call_variants.t
3/5 T01b RUNNING
>>> MALLOC_PERTURB_=148 /usr/bin/prove -e bash -v t/01b_call_variants.t
4/5 T02 RUNNING
>>> MALLOC_PERTURB_=249 /usr/bin/prove -e bash -v t/02_multi_bam.t
1/5 T00 OK 3.39s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/00_region_and_target_handling.t ..
1..12
ok 1 - ref:4-5 ref:6-7 are empty
ok 2 - ref:4 ref:6 are empty
ok 3 - ref:5-6 ref:7-8
ok 4 - ref:5 ref:7
ok 5 - ref:5-
ok 6 - full output
ok 7 - --targets t/../00_region_and_target_handling.t.bed
ok 8 - --region ref
ok 9 - ref:1,0-
ok 10 - ref:1,0-1,1
ok 11 - ref:0-1
ok 12 - region outside of bounds error
ok
All tests successful.
Files=1, Tests=12, 2 wallclock secs ( 0.27 usr 0.03 sys + 0.60 cusr 0.62 csys = 1.52 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
5/5 T03 RUNNING
>>> MALLOC_PERTURB_=58 /usr/bin/prove -e bash -v t/03_reference_bases.t
4/5 T02 OK 5.61s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/02_multi_bam.t ..
1..7
ok 1 - freebayes calls from two identical BAMs
ok 2 - freebayes calls from two BAMs with different samples for different read groups
ok 3 - freebayes calls from two BAMs with different technologies for different read groups
ok 4 - freebayes rejects two BAMs with different samples for same read groups
ok 5 - freebayes rejects two BAMs with different technologies for same read groups
ok 6 - freebayes calls multiple alts from two different BAMs
ok 7 - freebayes rejects two BAMs with the same name
ok
All tests successful.
Files=1, Tests=7, 4 wallclock secs ( 0.25 usr 0.02 sys + 0.62 cusr 0.76 csys = 1.65 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
5/5 T03 OK 2.33s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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 0.03 sys + 0.20 cusr 0.26 csys = 0.76 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
3/5 T01b OK 49.67s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
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 ( 0.25 usr 0.03 sys + 48.84 cusr 3.94 csys = 53.06 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
2/5 T01 OK 95.84s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
stdout:
t/01_call_variants.t ..
1..16
ok 1 - variant calling recovers most of the GiAB variants in a test region
ok 2 - freebayes produces the same number of calls if targeted per site or called without targets
ok 3 - a targets bed file can be used with the same effect as running by region
ok 4 - reading from stdin or not makes no difference
ok 5 - freebayes processes all alignments in BAM input
ok 6 - freebayes processes all alignments in CRAM input
ok 7 - freebayes correctly handles variant input
ok 8 - freebayes puts required variants in output
ok 9 - freebayes limits calls to input variants correctly
ok 10 - freebayes reports all input variants even when there is no input data
ok 11 - freebayes handles region and variant input
ok 12 - freebayes limits to variant input correctly when region is given
ok 13 - freebayes handles variant input and reading from stdin
ok 14 - freebayes limits to variant input when reading from stdin
ok 15 - freebayes handles region, stdin, and variant input
ok 16 - !
ok
All tests successful.
Files=1, Tests=16, 94 wallclock secs ( 0.23 usr 0.08 sys + 73.14 cusr 34.40 csys = 107.85 CPU)
Result: PASS
stderr:
[E::idx_find_and_load] Could not retrieve index file for '-'
Random access with SetRegion not available for STDIN reading (no index file)
ERROR(freebayes): Could not SetRegion to q:1..10000
t/01_call_variants.t: line 107: 5261 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
Ok: 5
Expected Fail: 0
Fail: 0
Unexpected Pass: 0
Skipped: 0
Timeout: 0
Full log written to /<<PKGBUILDDIR>>/build/meson-logs/testlog.txt
rm test/bash-tap/*
rm test/test-simple-bash/*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=meson -O--builddir=build
dh_prep -a -O--buildsystem=meson -O--builddir=build
dh_auto_install --destdir=debian/freebayes/ -a -O--buildsystem=meson -O--builddir=build
cd build && DESTDIR=/<<PKGBUILDDIR>>/debian/freebayes LC_ALL=C.UTF-8 ninja install
[0/1] Installing files.
Installing freebayes to /<<PKGBUILDDIR>>/debian/freebayes/usr/bin
Installing bamleftalign to /<<PKGBUILDDIR>>/debian/freebayes/usr/bin
dh_installdocs -a -O--buildsystem=meson -O--builddir=build
dh_installchangelogs -a -O--buildsystem=meson -O--builddir=build
dh_installexamples -a -O--buildsystem=meson -O--builddir=build
dh_installsystemduser -a -O--buildsystem=meson -O--builddir=build
dh_perl -a -O--buildsystem=meson -O--builddir=build
dh_link -a -O--buildsystem=meson -O--builddir=build
dh_strip_nondeterminism -a -O--buildsystem=meson -O--builddir=build
dh_compress -a -O--buildsystem=meson -O--builddir=build
dh_fixperms -a -O--buildsystem=meson -O--builddir=build
dh_missing -a -O--buildsystem=meson -O--builddir=build
dh_dwz -a -O--buildsystem=meson -O--builddir=build
dh_strip -a -O--buildsystem=meson -O--builddir=build
dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build
dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build
dpkg-shlibdeps: warning: debian/freebayes/usr/bin/freebayes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/freebayes/usr/bin/bamleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/freebayes/usr/bin/freebayes debian/freebayes/usr/bin/bamleftalign were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=meson -O--builddir=build
dh_gencontrol -a -O--buildsystem=meson -O--builddir=build
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_1.3.5-3_armhf.deb'.
dpkg-deb: building package 'freebayes' in '../freebayes_1.3.5-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../freebayes_1.3.5-3_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 2021-10-09T06:09:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
freebayes_1.3.5-3_armhf.changes:
--------------------------------
Format: 1.8
Date: Thu, 07 Oct 2021 08:09:27 +0200
Source: freebayes
Binary: freebayes freebayes-dbgsym
Architecture: armhf
Version: 1.3.5-3
Distribution: bookworm-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 (1.3.5-3) unstable; urgency=medium
.
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
* Remove constraints unnecessary since buster:
+ Build-Depends: Drop versioned constraint on libvcflib-tools.
Checksums-Sha1:
c86cf5b6db1a7483caaa66296afcd4aa0c58c0d6 6322776 freebayes-dbgsym_1.3.5-3_armhf.deb
b25dabf1f2506cd004939715e468b64d183a345f 9755 freebayes_1.3.5-3_armhf.buildinfo
99d9d1eb71ec07187417b16fbde6e6461600776b 1400892 freebayes_1.3.5-3_armhf.deb
Checksums-Sha256:
be26b8eb214d1ce29ece0714af7984c21d0b8535d0b226a48c6d7605b33cdb3f 6322776 freebayes-dbgsym_1.3.5-3_armhf.deb
9c3960653bb3a3a01b34871547549745cd5d34750c7e849b3b00255b1ec15c37 9755 freebayes_1.3.5-3_armhf.buildinfo
54f05be2376ba7d1f311cc3ba5b68299c9a9589c7e452ae470ba6b62f867e182 1400892 freebayes_1.3.5-3_armhf.deb
Files:
77de1bbfea58ba513e7307ecdc75d23d 6322776 debug optional freebayes-dbgsym_1.3.5-3_armhf.deb
3a9adf32d9d32053b1de658bcc7a8b55 9755 science optional freebayes_1.3.5-3_armhf.buildinfo
1314748c04728106ae938795eeda5353 1400892 science optional freebayes_1.3.5-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
freebayes-dbgsym_1.3.5-3_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 6322776 bytes: control archive=648 bytes.
420 bytes, 12 lines control
301 bytes, 3 lines md5sums
Package: freebayes-dbgsym
Source: freebayes
Version: 1.3.5-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6431
Depends: freebayes (= 1.3.5-3)
Section: debug
Priority: optional
Description: debug symbols for freebayes
Build-Ids: 7b1e85b9b5b6d130c8f64fc822e54ca10f565ad6 f2130e43cdd8bca88124fe8ae11094bf21c003bc
drwxr-xr-x root/root 0 2021-10-07 06:09 ./
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/debug/.build-id/7b/
-rw-r--r-- root/root 5680684 2021-10-07 06:09 ./usr/lib/debug/.build-id/7b/1e85b9b5b6d130c8f64fc822e54ca10f565ad6.debug
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/debug/.build-id/f2/
-rw-r--r-- root/root 603692 2021-10-07 06:09 ./usr/lib/debug/.build-id/f2/130e43cdd8bca88124fe8ae11094bf21c003bc.debug
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 286704 2021-10-07 06:09 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/freebayes.debug
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/share/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-07 06:09 ./usr/share/doc/freebayes-dbgsym -> freebayes
freebayes_1.3.5-3_armhf.deb
---------------------------
new Debian package, version 2.0.
size 1400892 bytes: control archive=2120 bytes.
847 bytes, 17 lines control
4378 bytes, 52 lines md5sums
Package: freebayes
Version: 1.3.5-3
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 2021-10-07 06:09 ./
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/bin/
-rwxr-xr-x root/root 1142020 2021-10-07 06:09 ./usr/bin/bamleftalign
-rwxr-xr-x root/root 1735828 2021-10-07 06:09 ./usr/bin/freebayes
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/share/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-07 06:09 ./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 2021-10-07 06:09 ./usr/share/doc/freebayes/README.test
-rw-r--r-- root/root 83 2021-10-07 06:09 ./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 1793 2021-10-07 06:09 ./usr/share/doc/freebayes/changelog.Debian.gz
-rw-r--r-- root/root 3194 2021-10-07 06:09 ./usr/share/doc/freebayes/copyright
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/
-rw-r--r-- root/root 83 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/README.test_data
drwxr-xr-x root/root 0 2021-10-07 06:09 ./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 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/regression/
-rw-r--r-- root/root 73144 2021-10-07 06:09 ./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 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/targets.bed
drwxr-xr-x root/root 0 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test-simple-bash/
-rw-r--r-- root/root 17 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.alt
-rw-r--r-- root/root 230 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.bam
-rw-r--r-- root/root 96 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.bam.bai
-rw-r--r-- root/root 112 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.bed
-rw-r--r-- root/root 17 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.ref
-rw-r--r-- root/root 15 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.ref.fai
-rw-r--r-- root/root 550 2021-10-07 06:09 ./usr/share/doc/freebayes/examples/test.vcf
drwxr-xr-x root/root 0 2021-10-07 06:09 ./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 2021-10-07 06:09 ./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: 128880
Build-Time: 600
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1294
Job: freebayes_1.3.5-3
Machine Architecture: armhf
Package: freebayes
Package-Time: 1945
Source-Version: 1.3.5-3
Space: 128880
Status: successful
Version: 1.3.5-3
--------------------------------------------------------------------------------
Finished at 2021-10-09T06:09:50Z
Build needed 00:32:25, 128880k disc space