Raspbian Package Auto-Building

Build log for vt (0.57721+ds-2) on armhf

vt0.57721+ds-2armhf → 2020-07-15 13:30:50

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

+==============================================================================+
| vt 0.57721+ds-2 (armhf)                      Wed, 15 Jul 2020 12:52:48 +0000 |
+==============================================================================+

Package: vt
Version: 0.57721+ds-2
Source Version: 0.57721+ds-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-2e24e5a5-1a0a-4d2c-bbd2-f9547dfaa99e' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.6 MB in 24s (1013 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: 'vt' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/vt.git
Please use:
git clone https://salsa.debian.org/med-team/vt.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 18.6 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main vt 0.57721+ds-2 (dsc) [2163 B]
Get:2 http://172.17.0.1/private bullseye-staging/main vt 0.57721+ds-2 (tar) [18.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main vt 0.57721+ds-2 (diff) [7152 B]
Fetched 18.6 MB in 2s (7707 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/vt-9AZTFx/vt-0.57721+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/vt-9AZTFx' 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-G96TBd/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-G96TBd/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-G96TBd/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-G96TBd/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2729 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  bsdextrautils libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 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-G96TBd/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 (22.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12348 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 all)

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


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

Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libcurl4-openssl-dev, libssl-dev, libdeflate-dev, libhts-dev, libpcre2-dev, libsvm-dev, libtclap-dev, r-mathlib, r-base-core
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libbz2-dev, liblzma-dev, libcurl4-openssl-dev, libssl-dev, libdeflate-dev, libhts-dev, libpcre2-dev, libsvm-dev, libtclap-dev, r-mathlib, r-base-core
dpkg-deb: building package 'sbuild-build-depends-vt-dummy' in '/<<BUILDDIR>>/resolver-G96TBd/apt_archive/sbuild-build-depends-vt-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-vt-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-G96TBd/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Sources [558 B]
Get:5 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ Packages [641 B]
Fetched 2532 B in 1s (3239 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install vt build dependencies (apt-based resolver)
--------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev 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 libblas3 libbrotli1 libbsd0 libbz2-dev libcairo2
  libcroco3 libcurl3-gnutls libcurl4 libcurl4-openssl-dev libdatrie1
  libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
  libhts-dev libhts3 libice6 libicu67 libjbig0 libjpeg62-turbo libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblzma-dev libmagic-mgc
  libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
  libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
  libpcre2-posix2 libpipeline1 libpixman-1-0 libpng16-16 libpsl5 librtmp1
  libsigsegv2 libsm6 libssh2-1 libssl-dev libsub-override-perl libsvm-dev
  libsvm3 libtcl8.6 libtclap-dev libthai-data libthai0 libtiff5 libtk8.6
  libtool libuchardet0 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0
  libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1
  libxt6 m4 man-db openssl po-debconf r-base-core r-mathlib sensible-utils 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 libcurl4-doc libidn11-dev libkrb5-dev
  libldap2-dev librtmp-dev libssh2-1-dev pkg-config krb5-doc krb5-user
  liblzma-doc libssl-doc tcl8.6 tk8.6 libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-base-html
Recommended packages:
  curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs krb5-locales publicsuffix libltdl-dev
  libmail-sendmail-perl r-recommended r-base-dev r-doc-html
  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 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 libblas3 libbrotli1 libbsd0 libbz2-dev libcairo2
  libcroco3 libcurl3-gnutls libcurl4 libcurl4-openssl-dev libdatrie1
  libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
  libhts-dev libhts3 libice6 libicu67 libjbig0 libjpeg62-turbo libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblzma-dev libmagic-mgc
  libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
  libpaper-utils libpaper1 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
  libpcre2-posix2 libpipeline1 libpixman-1-0 libpng16-16 libpsl5 librtmp1
  libsigsegv2 libsm6 libssh2-1 libssl-dev libsub-override-perl libsvm-dev
  libsvm3 libtcl8.6 libtclap-dev libthai-data libthai0 libtiff5 libtk8.6
  libtool libuchardet0 libwebp6 libx11-6 libx11-data libxau6 libxcb-render0
  libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1
  libxt6 m4 man-db openssl po-debconf r-base-core r-mathlib
  sbuild-build-depends-vt-dummy sensible-utils ucf unzip x11-common xdg-utils
  zip zlib1g-dev
0 upgraded, 114 newly installed, 0 to remove and 3 not upgraded.
Need to get 69.3 MB of archives.
After this operation, 168 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-G96TBd/apt_archive ./ sbuild-build-depends-vt-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1g-1 [811 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20200601 [158 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-2 [1158 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-2 [8286 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.2+dfsg-2 [346 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-3 [28.0 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-2 [110 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-2 [101 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10 [61.7 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10 [112 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10 [320 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10 [135 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-2 [61.2 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1 [286 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-openssl-dev armhf 7.68.0-1 [360 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-3+b3 [36.4 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-4+rpi1 [231 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.4-1+rpi1+b1 [1309 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-4 [318 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-4 [4796 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-2 [1602 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.44.7-4 [165 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.44.7-4 [52.6 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.44.7-4 [44.9 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.34-7 [190 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.34-7 [181 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix2 armhf 10.34-7 [44.7 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.34-7 [614 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1g-1 [1573 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libsvm3 armhf 3.24+ds-4 [38.5 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libsvm-dev armhf 3.24+ds-4 [59.0 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.10+dfsg-1 [886 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libtclap-dev armhf 1.2.2-1 [139 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0+git191117-2 [250 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.10-1 [678 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1+b3 [156 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-25 [152 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-2 [74.6 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 4.0.2-1 [24.7 MB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf r-mathlib armhf 4.0.2-1 [2017 kB]
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Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../103-libtiff5_4.1.0+git191117-2_armhf.deb ...
Unpacking libtiff5:armhf (4.1.0+git191117-2) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../104-libxft2_2.3.2-2_armhf.deb ...
Unpacking libxft2:armhf (2.3.2-2) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../105-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 .../106-libtk8.6_8.6.10-1_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.10-1) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../107-libxt6_1%3a1.1.5-1+b3_armhf.deb ...
Unpacking libxt6:armhf (1:1.1.5-1+b3) ...
Selecting previously unselected package zip.
Preparing to unpack .../108-zip_3.0-11_armhf.deb ...
Unpacking zip (3.0-11) ...
Selecting previously unselected package unzip.
Preparing to unpack .../109-unzip_6.0-25_armhf.deb ...
Unpacking unzip (6.0-25) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../110-xdg-utils_1.1.3-2_all.deb ...
Unpacking xdg-utils (1.1.3-2) ...
Selecting previously unselected package r-base-core.
Preparing to unpack .../111-r-base-core_4.0.2-1_armhf.deb ...
Unpacking r-base-core (4.0.2-1) ...
Selecting previously unselected package r-mathlib.
Preparing to unpack .../112-r-mathlib_4.0.2-1_armhf.deb ...
Unpacking r-mathlib (4.0.2-1) ...
Selecting previously unselected package sbuild-build-depends-vt-dummy.
Preparing to unpack .../113-sbuild-build-depends-vt-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-vt-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.9-1) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up libpixman-1-0:armhf (0.36.0-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libicu67:armhf (67.1-2) ...
Setting up libdatrie1:armhf (0.2.12-3+b3) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.3-2) ...
No schema files found: doing nothing.
Setting up unzip (6.0-25) ...
Setting up libdebhelper-perl (13.2) ...
Setting up libbrotli1:armhf (1.0.7-6.1) ...
Setting up x11-common (1:7.7+20) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
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 libnghttp2-14:armhf (1.41.0-2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libpcre2-16-0:armhf (10.34-7) ...
Setting up libkrb5support0:armhf (1.17-10) ...
Setting up zip (3.0-11) ...
Setting up autotools-dev (20180224.1) ...
Setting up libpcre2-32-0:armhf (10.34-7) ...
Setting up libblas3:armhf (3.9.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libx11-data (2:1.6.9-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libfribidi0:armhf (1.0.8-2) ...
Setting up libssl-dev:armhf (1.1.1g-1) ...
Setting up libpng16-16:armhf (1.6.37-2) ...
Setting up libtcl8.6:armhf (8.6.10+dfsg-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libwebp6:armhf (0.6.1-2) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libpcre2-posix2:armhf (10.34-7) ...
Setting up libk5crypto3:armhf (1.17-10) ...
Setting up libgfortran5:armhf (10.1.0-4+rpi1) ...
Setting up libtclap-dev (1.2.2-1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up r-mathlib (4.0.2-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-3) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-10) ...
Setting up libtiff5:armhf (4.1.0+git191117-2) ...
Setting up openssl (1.1.1g-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libdeflate-dev:armhf (1.6-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up xdg-utils (1.1.3-2) ...
Setting up libsvm3 (3.24+ds-4) ...
Setting up libbz2-dev:armhf (1.0.8-3) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.9.0-2) ...
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 (1.14-2) ...
Setting up libpcre2-dev:armhf (10.34-7) ...
Setting up libtool (2.4.6-14) ...
Setting up libxcb-render0:armhf (1.14-2) ...
Setting up m4 (1.4.18-4) ...
Setting up libxcb-shm0:armhf (1.14-2) ...
Setting up libthai0:armhf (0.1.28-3) ...
Setting up ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
126 added, 0 removed; done.
Setting up libfreetype6:armhf (2.10.2+dfsg-2) ...
Setting up libsvm-dev (3.24+ds-4) ...
Setting up libgssapi-krb5-2:armhf (1.17-10) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0043) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up libcurl4:armhf (7.68.0-1) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
Setting up libharfbuzz0b:armhf (2.6.4-1+rpi1+b1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up automake (1:1.16.2-3) ...
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 gettext (0.19.8.1-10) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up fontconfig-config (2.13.1-4.2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libcurl3-gnutls:armhf (7.68.0-1) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libcurl4-openssl-dev:armhf (7.68.0-1) ...
Setting up libxt6:armhf (1:1.1.5-1+b3) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libhts3:armhf (1.10.2-4) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:armhf (8.6.10-1) ...
Setting up libpango-1.0-0:armhf (1.44.7-4) ...
Setting up libhts-dev:armhf (1.10.2-4) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up libpangoft2-1.0-0:armhf (1.44.7-4) ...
Setting up libpangocairo-1.0-0:armhf (1.44.7-4) ...
Setting up r-base-core (4.0.2-1) ...

Creating config file /etc/R/Renviron with new version
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Setting up sbuild-build-depends-vt-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
Processing triggers for ca-certificates (20200601) ...
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_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.6 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdextrautils_2.35.2-6 bsdutils_1:2.35.2-6 build-essential_12.8 bzip2_1.0.8-3 ca-certificates_20200601 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-6 file_1:5.38-5 findutils_4.7.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblas3_3.9.0-2 libblkid1_2.35.2-6 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libbz2-dev_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libcurl3-gnutls_7.68.0-1 libcurl4_7.68.0-1 libcurl4-openssl-dev_7.68.0-1 libdatrie1_0.2.12-3+b3 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.2 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-6 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.2+dfsg-2 libfribidi0_1.0.8-2 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10.1.0-4+rpi1 libglib2.0-0_2.64.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.17-10 libharfbuzz0b_2.6.4-1+rpi1+b1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-4 libhts3_1.10.2-4 libice6_2:1.0.9-2 libicu67_67.1-2 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjbig0_2.1-3.1+b2 libjpeg62-turbo_1:1.5.2-2+b1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libksba8_1.4.0-2 liblapack3_3.9.0-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-6 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.44.7-4 libpangocairo-1.0-0_1.44.7-4 libpangoft2-1.0-0_1.44.7-4 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-16-0_10.34-7 libpcre2-32-0_10.34-7 libpcre2-8-0_10.34-7 libpcre2-dev_10.34-7 libpcre2-posix2_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.37-2 libpsl5_0.21.0-1.1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.35.2-6 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1g-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsvm-dev_3.24+ds-4 libsvm3_3.24+ds-4 libsystemd0_245.6-2+rpi1 libtasn1-6_4.16.0-2 libtcl8.6_8.6.10+dfsg-1 libtclap-dev_1.2.2-1 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git191117-2 libtinfo6_6.2-1 libtk8.6_8.6.10-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.35.2-6 libwebp6_0.6.1-2 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.10+dfsg-5+b1 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1+b3 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-6 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 r-base-core_4.0.2-1 r-mathlib_4.0.2-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-vt-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0043 unzip_6.0-25 util-linux_2.35.2-6 x11-common_1:7.7+20 xdg-utils_1.1.3-2 xz-utils_5.2.4-1 zip_3.0-11 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 '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul 13 13:06:13 2020 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 ./vt_0.57721+ds-2.dsc
dpkg-source: info: extracting vt in /<<BUILDDIR>>/vt-0.57721+ds
dpkg-source: info: unpacking vt_0.57721+ds.orig.tar.xz
dpkg-source: info: unpacking vt_0.57721+ds-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying makefile
dpkg-source: info: applying fix-spelling
dpkg-source: info: applying test-fail-on-error

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-2e24e5a5-1a0a-4d2c-bbd2-f9547dfaa99e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package vt
dpkg-buildpackage: info: source version 0.57721+ds-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_auto_clean
	make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/vt-0.57721+ds'
rm -rf vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o
make[1]: Leaving directory '/<<BUILDDIR>>/vt-0.57721+ds'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/vt-0.57721+ds'
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ahmm.o -c ahmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o align.o -c align.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o allele.o -c allele.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_1000g.o -c annotate_1000g.cpp
ahmm.cpp: In member function 'void AHMM::collect_statistics(int32_t, int32_t, int32_t)':
ahmm.cpp:687:35: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  687 |             rflank_start[MODEL] = NAN;
      |                                   ^~~
ahmm.cpp:688:34: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  688 |             rflank_start[READ] = NAN;
      |                                  ^~~
ahmm.cpp:689:33: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+Inff' to '2147483647' [-Woverflow]
  689 |             rflank_end[MODEL] = INFINITY;
      |                                 ^~~~~~~~
ahmm.cpp:690:32: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+Inff' to '2147483647' [-Woverflow]
  690 |             rflank_end[READ] = INFINITY;
      |                                ^~~~~~~~
ahmm.cpp: In member function 'void AHMM::clear_statistics()':
ahmm.cpp:737:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  737 |     lflank_start[MODEL] = NAN;
      |                           ^~~
ahmm.cpp:738:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  738 |     lflank_start[READ] = NAN;
      |                          ^~~
ahmm.cpp:739:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  739 |     lflank_end[MODEL] = NAN;
      |                         ^~~
ahmm.cpp:740:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  740 |     lflank_end[READ] = NAN;
      |                        ^~~
ahmm.cpp:741:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  741 |     motif_start[MODEL] = NAN;
      |                          ^~~
ahmm.cpp:742:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  742 |     motif_start[READ] = NAN;
      |                         ^~~
ahmm.cpp:743:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  743 |     motif_end[MODEL] = NAN;
      |                        ^~~
ahmm.cpp:744:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  744 |     motif_end[READ] = NAN;
      |                       ^~~
ahmm.cpp:745:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  745 |     motif_count = NAN;
      |                   ^~~
ahmm.cpp:746:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  746 |     exact_motif_count = NAN;
      |                         ^~~
ahmm.cpp:747:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  747 |     motif_m = NAN;
      |               ^~~
ahmm.cpp:748:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  748 |     motif_xid = NAN;
      |                 ^~~
ahmm.cpp:750:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  750 |     rflank_start[MODEL] = NAN;
      |                           ^~~
ahmm.cpp:751:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  751 |     rflank_start[READ] = NAN;
      |                          ^~~
ahmm.cpp:752:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  752 |     rflank_end[MODEL] = NAN;
      |                         ^~~
ahmm.cpp:753:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  753 |     rflank_end[READ] = NAN;
      |                        ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_indels.o -c annotate_indels.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_indels2.o -c annotate_indels2.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_regions.o -c annotate_regions.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_variants.o -c annotate_variants.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_vntrs.o -c annotate_vntrs.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o augmented_bam_record.o -c augmented_bam_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_genotyping_buffered_reader.o -c bcf_genotyping_buffered_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_single_genotyping_buffered_reader.o -c bcf_single_genotyping_buffered_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bam_ordered_reader.o -c bam_ordered_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp
bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)':
bcf_ordered_writer.cpp:162:114: warning: format '%d' expects argument of type 'int', but argument 8 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  162 |                         fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n",
      |                                                                                                                 ~^
      |                                                                                                                  |
      |                                                                                                                  int
      |                                                                                                                 %lld
bcf_ordered_writer.cpp:162:123: warning: format '%d' expects argument of type 'int', but argument 10 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  162 |                         fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n",
      |                                                                                                                          ~^
      |                                                                                                                           |
      |                                                                                                                           int
      |                                                                                                                          %lld
bcf_ordered_writer.cpp:162:187: warning: format '%d' expects argument of type 'int', but argument 12 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  162 |                         fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n",
      |                                                                                                                                                                                          ~^
      |                                                                                                                                                                                           |
      |                                                                                                                                                                                           int
      |                                                                                                                                                                                          %lld
bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write_hdr()':
bcf_ordered_writer.cpp:129:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
  129 |     bcf_hdr_write(file, hdr);
      |     ~~~~~~~~~~~~~^~~~~~~~~~~
bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)':
bcf_ordered_writer.cpp:195:18: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)', declared with attribute warn_unused_result [-Wunused-result]
  195 |         bcf_write(file, hdr, v);
      |         ~~~~~~~~~^~~~~~~~~~~~~~
bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::flush(bool)':
bcf_ordered_writer.cpp:245:22: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)', declared with attribute warn_unused_result [-Wunused-result]
  245 |             bcf_write(file, hdr, buffer.back());
      |             ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
bcf_ordered_writer.cpp:261:30: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)', declared with attribute warn_unused_result [-Wunused-result]
  261 |                     bcf_write(file, hdr, buffer.back());
      |                     ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_synced_reader.o -c bcf_synced_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bed.o -c bed.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_motif_picker.o -c candidate_motif_picker.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_region_extractor.o -c candidate_region_extractor.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o cat.o -c cat.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o chmm.o -c chmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o complex_genotyping_record.o -c complex_genotyping_record.cpp
chmm.cpp: In member function 'void CHMM::clear_statistics()':
chmm.cpp:1106:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1106 |     lflank_start[MODEL] = NAN;
      |                           ^~~
chmm.cpp:1107:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1107 |     lflank_start[READ] = NAN;
      |                          ^~~
chmm.cpp:1108:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1108 |     lflank_end[MODEL] = NAN;
      |                         ^~~
chmm.cpp:1109:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1109 |     lflank_end[READ] = NAN;
      |                        ^~~
chmm.cpp:1110:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1110 |     motif_start[MODEL] = NAN;
      |                          ^~~
chmm.cpp:1111:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1111 |     motif_start[READ] = NAN;
      |                         ^~~
chmm.cpp:1112:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1112 |     motif_end[MODEL] = NAN;
      |                        ^~~
chmm.cpp:1113:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1113 |     motif_end[READ] = NAN;
      |                       ^~~
chmm.cpp:1114:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1114 |     rflank_start[MODEL] = NAN;
      |                           ^~~
chmm.cpp:1115:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1115 |     rflank_start[READ] = NAN;
      |                          ^~~
chmm.cpp:1116:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1116 |     rflank_end[MODEL] = NAN;
      |                         ^~~
chmm.cpp:1117:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1117 |     rflank_end[READ] = NAN;
      |                        ^~~
chmm.cpp:1118:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1118 |     motif_count = NAN;
      |                   ^~~
chmm.cpp:1119:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1119 |     exact_motif_count = NAN;
      |                         ^~~
chmm.cpp:1120:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1120 |     motif_m = NAN;
      |               ^~~
chmm.cpp:1121:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
 1121 |     motif_xid = NAN;
      |                 ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_concordance.o -c compute_concordance.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features.o -c compute_features.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features2.o -c compute_features2.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_rl_dist.o -c compute_rl_dist.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o config.o -c config.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_multiallelics.o -c consolidate_multiallelics.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_vntrs.o -c consolidate_vntrs.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate.o -c consolidate.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o construct_probes.o -c construct_probes.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose.o -c decompose.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose2.o -c decompose2.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose_blocksub.o -c decompose_blocksub.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o discover.o -c discover.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o duplicate.o -c duplicate.cpp
In file included from bcf_ordered_reader.h:27,
                 from program.h:32,
                 from discover.h:27,
                 from discover.cpp:24:
discover.cpp: In member function 'bool {anonymous}::Igor::filter_read(bam1_t*)':
hts_utils.h:124:40: warning: narrowing conversion of '(s->bam1_t::core.bam1_core_t::pos + 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
  124 | #define bam_get_pos1(s) ((s)->core.pos + 1)
      |                         ~~~~~~~~~~~~~~~^~~~
discover.cpp:355:45: note: in expansion of macro 'bam_get_pos1'
  355 |                         kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
      |                                             ^~~~~~~~~~~~
discover.cpp:355:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
  355 |                         kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimate.o -c estimate.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimator.o -c estimator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o extract_vntrs.o -c extract_vntrs.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter.o -c filter.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter_overlap.o -c filter_overlap.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o flank_detector.o -c flank_detector.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_aligner.o -c fuzzy_aligner.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_partition.o -c fuzzy_partition.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o gencode.o -c gencode.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genome_interval.o -c genome_interval.cpp
fuzzy_partition.cpp: In member function 'void {anonymous}::Igor::initialize()':
fuzzy_partition.cpp:153:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
  153 |         bcf_hdr_sync(odr->hdr);
      |         ~~~~~~~~~~~~^~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotype.o -c genotype.cpp
In file included from bam_ordered_reader.h:27,
                 from genotype.h:27,
                 from genotype.cpp:24:
genotype.cpp: In member function 'bool {anonymous}::Igor::filter_read(bam1_t*)':
hts_utils.h:124:40: warning: narrowing conversion of '(s->bam1_t::core.bam1_core_t::pos + 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
  124 | #define bam_get_pos1(s) ((s)->core.pos + 1)
      |                         ~~~~~~~~~~~~~~~^~~~
genotype.cpp:304:45: note: in expansion of macro 'bam_get_pos1'
  304 |                         kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
      |                                             ^~~~~~~~~~~~
genotype.cpp:304:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
  304 |                         kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotyping_record.o -c genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ghmm.o -c ghmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hts_utils.o -c hts_utils.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hfilter.o -c hfilter.cpp
hts_utils.cpp: In function 'void bcf_hdr_print(bcf_hdr_t*)':
hts_utils.cpp:428:33: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
  428 |     if ( h->dirty ) bcf_hdr_sync(h);
      |                     ~~~~~~~~~~~~^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_annotator.o -c indel_annotator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_genotyping_record.o -c indel_genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o index.o -c index.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o info2tab.o -c info2tab.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval_tree.o -c interval_tree.cpp
info2tab.cpp: In member function 'void {anonymous}::Igor::info2tab()':
info2tab.cpp:278:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  278 |             fprintf(out, "%s\t%d", bcf_get_chrom(h, v), bcf_get_pos1(v));
      |                               ~^
      |                                |
      |                                int
      |                               %lld
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval.o -c interval.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lfhmm.o -c lfhmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm.o -c lhmm.cpp
lfhmm.cpp: In member function 'void LFHMM::collect_statistics(int32_t, int32_t, int32_t)':
lfhmm.cpp:761:33: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  761 |             rflank_end[MODEL] = NAN;
      |                                 ^~~
lfhmm.cpp: In member function 'void LFHMM::clear_statistics()':
lfhmm.cpp:868:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  868 |     lflank_start[MODEL] = NAN;
      |                           ^~~
lfhmm.cpp:869:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  869 |     lflank_start[READ] = NAN;
      |                          ^~~
lfhmm.cpp:870:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  870 |     lflank_end[MODEL] = NAN;
      |                         ^~~
lfhmm.cpp:871:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  871 |     lflank_end[READ] = NAN;
      |                        ^~~
lfhmm.cpp:872:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  872 |     motif_start[MODEL] = NAN;
      |                          ^~~
lfhmm.cpp:873:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  873 |     motif_start[READ] = NAN;
      |                         ^~~
lfhmm.cpp:874:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  874 |     motif_end[MODEL] = NAN;
      |                        ^~~
lfhmm.cpp:875:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  875 |     motif_end[READ] = NAN;
      |                       ^~~
lfhmm.cpp:876:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  876 |     motif_count = NAN;
      |                   ^~~
lfhmm.cpp:877:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  877 |     exact_motif_count = NAN;
      |                         ^~~
lfhmm.cpp:878:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  878 |     motif_m = NAN;
      |               ^~~
lfhmm.cpp:879:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  879 |     motif_xid = NAN;
      |                 ^~~
lfhmm.cpp:881:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  881 |     rflank_start[MODEL] = NAN;
      |                           ^~~
lfhmm.cpp:882:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  882 |     rflank_start[READ] = NAN;
      |                          ^~~
lfhmm.cpp:883:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  883 |     rflank_end[MODEL] = NAN;
      |                         ^~~
lfhmm.cpp:884:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  884 |     rflank_end[READ] = NAN;
      |                        ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm1.o -c lhmm1.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o liftover.o -c liftover.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o log_tool.o -c log_tool.cpp
In file included from /usr/include/c++/9/vector:72,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/bits/stl_vector.h: In static member function 'static double LogTool::pl2log10_varp(uint32_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In static member function 'static double LogTool::log10fact(uint32_t)':
/usr/include/c++/9/bits/vector.tcc:121:4: 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)...);
      |    ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: 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 /usr/include/c++/9/vector:67,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/bits/stl_vector.h: In static member function 'static double LogTool::pl2prob(uint32_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/bits/vector.tcc:121:4: 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 /usr/include/c++/9/vector:67,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/bits/stl_vector.h: In static member function 'static double LogTool::pl2pl_one_minus_p(uint32_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from ./utils.h:33,
                 from ./log_tool.h:30,
                 from log_tool.cpp:24:
/usr/include/c++/9/bits/vector.tcc:121:4: 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)...);
      |    ^~~~~~~~~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge.o -c merge.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_candidate_variants.o -c merge_candidate_variants.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_genotypes.o -c merge_genotypes.cpp
merge_genotypes.cpp: In member function 'void {anonymous}::Igor::initialize()':
merge_genotypes.cpp:215:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
  215 |         bcf_hdr_sync(odw->hdr);
      |         ~~~~~~~~~~~~^~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o milk_filter.o -c milk_filter.cpp
milk_filter.cpp: In member function 'void {anonymous}::Igor::milk_filter()':
milk_filter.cpp:456:53: warning: format '%d' expects argument of type 'int', but argument 5 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
  456 |       fprintf(stderr,"Processing %d variants at %s:%d\n", nread + 1, bcf_seqname(odw->hdr,nv), nv->pos);
      |                                                    ~^                                          ~~~~~~~
      |                                                     |                                              |
      |                                                     int                                            hts_pos_t {aka long long int}
      |                                                    %lld
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o motif_tree.o -c motif_tree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o motif_map.o -c motif_map.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multi_partition.o -c multi_partition.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o needle.o -c needle.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o normalize.o -c normalize.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o nuclear_pedigree.o -c nuclear_pedigree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp
ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector<GenomeInterval>&)':
ordered_bcf_overlap_matcher.cpp:34:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   34 |     bcf_hdr_sync(odr->hdr);
      |     ~~~~~~~~~~~~^~~~~~~~~~
ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector<GenomeInterval>&, std::string)':
ordered_bcf_overlap_matcher.cpp:52:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
   52 |     bcf_hdr_sync(odr->hdr);
      |     ~~~~~~~~~~~~^~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o partition.o -c partition.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste.o -c paste.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_genotypes.o -c paste_genotypes.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pedigree.o -c pedigree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o peek.o -c peek.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pileup.o -c pileup.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pregex.o -c pregex.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_afs.o -c profile_afs.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_chm1.o -c profile_chm1.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_chrom.o -c profile_chrom.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_fic_hwe.o -c profile_fic_hwe.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_hwe.o -c profile_hwe.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_indels.o -c profile_indels.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_len.o -c profile_len.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_mendelian.o -c profile_mendelian.cpp
profile_mendelian.cpp: In member function 'void {anonymous}::Igor::initialize()':
profile_mendelian.cpp:191:25: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
  191 |             bcf_hdr_sync(odw->hdr);
      |             ~~~~~~~~~~~~^~~~~~~~~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_na12878.o -c profile_na12878.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_snps.o -c profile_snps.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_vntrs.o -c profile_vntrs.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o program.o -c program.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o read_filter.o -c read_filter.cpp
In file included from read_filter.h:30,
                 from read_filter.cpp:24:
read_filter.cpp: In member function 'bool ReadFilter::filter_read(bam_hdr_t*, bam1_t*)':
hts_utils.h:124:40: warning: narrowing conversion of '(s->bam1_t::core.bam1_core_t::pos + 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
  124 | #define bam_get_pos1(s) ((s)->core.pos + 1)
      |                         ~~~~~~~~~~~~~~~^~~~
read_filter.cpp:95:41: note: in expansion of macro 'bam_get_pos1'
   95 |                     kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
      |                                         ^~~~~~~~~~~~
read_filter.cpp:95:91: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long long int'} to 'int32_t' {aka 'int'} [-Wnarrowing]
   95 |                     kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1};
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o reference_sequence.o -c reference_sequence.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm.o -c rfhmm.cpp
rfhmm.cpp: In member function 'void RFHMM::clear_statistics()':
rfhmm.cpp:833:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  833 |     lflank_start[MODEL] = NAN;
      |                           ^~~
rfhmm.cpp:834:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  834 |     lflank_start[READ] = NAN;
      |                          ^~~
rfhmm.cpp:835:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  835 |     lflank_end[MODEL] = NAN;
      |                         ^~~
rfhmm.cpp:836:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  836 |     lflank_end[READ] = NAN;
      |                        ^~~
rfhmm.cpp:837:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  837 |     motif_start[MODEL] = NAN;
      |                          ^~~
rfhmm.cpp:838:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  838 |     motif_start[READ] = NAN;
      |                         ^~~
rfhmm.cpp:839:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  839 |     motif_end[MODEL] = NAN;
      |                        ^~~
rfhmm.cpp:840:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  840 |     motif_end[READ] = NAN;
      |                       ^~~
rfhmm.cpp:841:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  841 |     rflank_start[MODEL] = NAN;
      |                           ^~~
rfhmm.cpp:842:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  842 |     rflank_start[READ] = NAN;
      |                          ^~~
rfhmm.cpp:843:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  843 |     rflank_end[MODEL] = NAN;
      |                         ^~~
rfhmm.cpp:844:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  844 |     rflank_end[READ] = NAN;
      |                        ^~~
rfhmm.cpp:845:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  845 |     motif_count = NAN;
      |                   ^~~
rfhmm.cpp:846:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  846 |     exact_motif_count = NAN;
      |                         ^~~
rfhmm.cpp:847:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  847 |     motif_m = NAN;
      |               ^~~
rfhmm.cpp:848:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  848 |     motif_xid = NAN;
      |                 ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm_x.o -c rfhmm_x.cpp
rfhmm_x.cpp: In member function 'void RFHMM_X::clear_statistics()':
rfhmm_x.cpp:928:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  928 |     lflank_start[MODEL] = NAN;
      |                           ^~~
rfhmm_x.cpp:929:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  929 |     lflank_start[READ] = NAN;
      |                          ^~~
rfhmm_x.cpp:930:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  930 |     lflank_end[MODEL] = NAN;
      |                         ^~~
rfhmm_x.cpp:931:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  931 |     lflank_end[READ] = NAN;
      |                        ^~~
rfhmm_x.cpp:932:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  932 |     motif_start[MODEL] = NAN;
      |                          ^~~
rfhmm_x.cpp:933:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  933 |     motif_start[READ] = NAN;
      |                         ^~~
rfhmm_x.cpp:934:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  934 |     motif_end[MODEL] = NAN;
      |                        ^~~
rfhmm_x.cpp:935:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  935 |     motif_end[READ] = NAN;
      |                       ^~~
rfhmm_x.cpp:936:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  936 |     rflank_start[MODEL] = NAN;
      |                           ^~~
rfhmm_x.cpp:937:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  937 |     rflank_start[READ] = NAN;
      |                          ^~~
rfhmm_x.cpp:938:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  938 |     rflank_end[MODEL] = NAN;
      |                         ^~~
rfhmm_x.cpp:939:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  939 |     rflank_end[READ] = NAN;
      |                        ^~~
rfhmm_x.cpp:940:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  940 |     motif_count = NAN;
      |                   ^~~
rfhmm_x.cpp:941:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  941 |     exact_motif_count = NAN;
      |                         ^~~
rfhmm_x.cpp:942:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  942 |     motif_m = NAN;
      |               ^~~
rfhmm_x.cpp:943:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow]
  943 |     motif_xid = NAN;
      |                 ^~~
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rminfo.o -c rminfo.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o seq.o -c seq.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o set_ref.o -c set_ref.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o snp_genotyping_record.o -c snp_genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sort.o -c sort.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o subset.o -c subset.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sv_tree.o -c sv_tree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o svm_train.o -c svm_train.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o svm_predict.o -c svm_predict.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o tbx_ordered_reader.o -c tbx_ordered_reader.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o test.o -c test.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o trio.o -c trio.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o union_variants.o -c union_variants.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o uniq.o -c uniq.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o utils.o -c utils.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o validate.o -c validate.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o variant.o -c variant.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o variant_manip.o -c variant_manip.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o variant_filter.o -c variant_filter.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o view.o -c view.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr.o -c vntr.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_annotator.o -c vntr_annotator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_consolidator.o -c vntr_consolidator.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_extractor.o -c vntr_extractor.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_genotyping_record.o -c vntr_genotyping_record.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_tree.o -c vntr_tree.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntrize.o -c vntrize.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o wdp_ahmm.o -c wdp_ahmm.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o main.o -c main.cpp
g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/vt-0.57721+ds=. -fstack-protector-strong -Wformat -Werror=format-security -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o     -lz -lpthread -lbz2 -llzma -lcurl -lcrypto -lhts -lpcre2-8 -lsvm -lRmath -lR
make[1]: Leaving directory '/<<BUILDDIR>>/vt-0.57721+ds'
   dh_auto_test -a
	make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/vt-0.57721+ds'
test/test.sh
++++++++++++++++++++++
Tests for vt normalize
++++++++++++++++++++++
testing normalize
             output VCF file : NOT OK!!!
             output logs     : NOT OK!!!
+++++++++++++++++++++++++++++++
Tests for vt decompose_blocksub
+++++++++++++++++++++++++++++++
testing decompose_blocksub of even-length blocks
             output VCF file : ok
             output logs     : ok
testing decompose_blocksub with alignment
             output VCF file : ok
             output logs     : ok
testing decompose_blocksub of phased even-length blocks
             output VCF file : ok
             output logs     : ok
++++++++++++++++++++++
Tests for vt decompose
++++++++++++++++++++++
testing decompose for a triallelic variant
             output VCF file : ok
             output logs     : ok

Passed tests : 4 / 5
make[1]: *** [Makefile:164: test] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/vt-0.57721+ds'
dh_auto_test: error: make -j4 test returned exit code 2
make: *** [debian/rules:8: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-07-15T13:30:45Z

Finished
--------


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

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

Build Architecture: armhf
Build-Space: 0
Build-Time: 1494
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 731
Job: vt_0.57721+ds-2
Machine Architecture: armhf
Package: vt
Package-Time: 2277
Source-Version: 0.57721+ds-2
Space: 0
Status: failed
Version: 0.57721+ds-2
--------------------------------------------------------------------------------
Finished at 2020-07-15T13:30:45Z
Build needed 00:00:00, 0k disc space