shapeit4 →
4.1+dfsg-1 →
armhf → 2020-01-10 00:05:04
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| shapeit4 4.1+dfsg-1 (armhf) Thu, 09 Jan 2020 23:56:40 +0000 |
+==============================================================================+
Package: shapeit4
Version: 4.1+dfsg-1
Source Version: 4.1+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-de7cdbc8-9b41-4948-9449-eccdb1c34720' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 12s (2015 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: 'shapeit4' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/shapeit4.git
Please use:
git clone https://salsa.debian.org/med-team/shapeit4.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 52.3 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main shapeit4 4.1+dfsg-1 (dsc) [2133 B]
Get:2 http://172.17.0.1/private bullseye-staging/main shapeit4 4.1+dfsg-1 (tar) [52.3 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main shapeit4 4.1+dfsg-1 (diff) [5328 B]
Fetched 52.3 MB in 19s (2724 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/shapeit4-8PLr7u/shapeit4-4.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/shapeit4-8PLr7u' 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-ws4bgj/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-ws4bgj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ws4bgj/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-ws4bgj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9841 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:
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 0 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-ws4bgj/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12242 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 (= 12), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev
Filtered Build-Depends: debhelper-compat (= 12), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev
dpkg-deb: building package 'sbuild-build-depends-shapeit4-dummy' in '/<<BUILDDIR>>/resolver-ws4bgj/apt_archive/sbuild-build-depends-shapeit4-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-shapeit4-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-ws4bgj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Sources [531 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ Packages [606 B]
Fetched 2470 B in 0s (11.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install shapeit4 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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0
libboost-program-options-dev libboost-program-options1.67-dev
libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0
libboost1.67-dev libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls
libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu-dev libicu63
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev
libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-locale1.67-dev libboost-log1.67-dev
libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev
libboost-numpy1.67-dev libboost-python1.67-dev libboost-random1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
krb5-doc krb5-user icu-doc liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0
libboost-program-options-dev libboost-program-options1.67-dev
libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0
libboost1.67-dev libbrotli1 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls
libdebhelper-perl libdeflate0 libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libhts-dev libhts2 libicu-dev libicu63
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4
man-db po-debconf sbuild-build-depends-shapeit4-dummy sensible-utils
zlib1g-dev
0 upgraded, 65 newly installed, 0 to remove and 0 not upgraded.
Need to get 45.9 MB of archives.
After this operation, 271 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ws4bgj/apt_archive ./ sbuild-build-depends-shapeit4-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-1 [29.5 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 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 12.7.3 [174 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [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 1.6.3-1 [23.6 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 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 2.62.4-1 [1138 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [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 12.7.3 [1019 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-2 [163 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.67.0 armhf 1.67.0-13 [430 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-2 [8846 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.67-dev armhf 1.67.0-13 [527 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.67.0 armhf 1.67.0-13 [245 kB]
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Get:44 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.67.0.2+b9 [4232 B]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.67.0 armhf 1.67.0-13 [330 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.67-dev armhf 1.67.0-13 [374 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options-dev armhf 1.67.0.2+b9 [4264 B]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-1 [78.0 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-12 [275 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-12 [4141 kB]
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Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libboost-program-options1.67.0:armhf (1.67.0-13) ...
Setting up libpipeline1:armhf (1.5.2-1) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libboost-program-options1.67-dev:armhf (1.67.0-13) ...
Setting up libglib2.0-0:armhf (2.62.4-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up libdebhelper-perl (12.7.3) ...
Setting up libbrotli1:armhf (1.0.7-6) ...
Setting up libnghttp2-14:armhf (1.40.0-1) ...
Setting up libmagic1:armhf (1:5.37-6) ...
Setting up libdeflate0 (1.5-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.37-6) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libboost-program-options-dev:armhf (1.67.0.2+b9) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up icu-devtools (63.2-2) ...
Setting up libboost-iostreams1.67.0:armhf (1.67.0-13) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (63.2-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libbz2-dev:armhf (1.0.8-2) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libboost-regex1.67.0:armhf (1.67.0-13) ...
Setting up libtool (2.4.6-11) ...
Setting up libboost-regex1.67-dev:armhf (1.67.0-13) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libboost-iostreams1.67-dev:armhf (1.67.0-13) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.67.0-2) ...
Setting up libboost-iostreams-dev:armhf (1.67.0.2+b9) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts2:armhf (1.9-12) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-12) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.3) ...
Setting up sbuild-build-depends-shapeit4-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-22+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblkid1_2.34-0.1 libboost-iostreams-dev_1.67.0.2+b9 libboost-iostreams1.67-dev_1.67.0-13 libboost-iostreams1.67.0_1.67.0-13 libboost-program-options-dev_1.67.0.2+b9 libboost-program-options1.67-dev_1.67.0-13 libboost-program-options1.67.0_1.67.0-13 libboost-regex1.67-dev_1.67.0-13 libboost-regex1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-22+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdeflate0_1.5-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-12 libhts2_1.9-12 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-1 libpsl5_0.20.2-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-shapeit4-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 18 21:43:06 2019 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./shapeit4_4.1+dfsg-1.dsc
dpkg-source: info: extracting shapeit4 in /<<BUILDDIR>>/shapeit4-4.1+dfsg
dpkg-source: info: unpacking shapeit4_4.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking shapeit4_4.1+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_shared_libs.patch
dpkg-source: info: applying cherry-pick-ebf584e700.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-de7cdbc8-9b41-4948-9449-eccdb1c34720
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package shapeit4
dpkg-buildpackage: info: source version 4.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/shapeit4-4.1+dfsg'
rm -f obj/*.o bin/shapeit4
make[1]: Leaving directory '/<<BUILDDIR>>/shapeit4-4.1+dfsg'
dh_clean
debian/rules build-arch
dh build-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>>/shapeit4-4.1+dfsg'
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/genotype_set.cpp -o obj/genotype_set.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/haplotype_set.cpp -o obj/haplotype_set.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/variant_map.cpp -o obj/variant_map.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader1.cpp -o obj/genotype_reader1.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from src/containers/haplotype_set.h:27,
from src/io/genotype_reader.h:28,
from src/io/genotype_reader1.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
In file included from src/containers/haplotype_set.h:27,
from src/containers/haplotype_set.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader2.cpp -o obj/genotype_reader2.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/gmap_reader.cpp -o obj/gmap_reader.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/haplotype_writer.cpp -o obj/haplotype_writer.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/9/vector:72,
from src/utils/otools.h:26,
from src/containers/haplotype_set.h:25,
from src/containers/haplotype_set.cpp:22:
/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 src/utils/otools.h:26,
from src/containers/haplotype_set.h:25,
from src/containers/haplotype_set.cpp:22:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void haplotype_set::initializePBWTmapping(variant_map&)':
/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 src/containers/haplotype_set.h:27,
from src/io/genotype_reader.h:28,
from src/io/genotype_reader2.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void haplotype_set::searchIBD2matching(variant_map&, double, double, double, double, int)':
/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 src/containers/haplotype_set.h:27,
from src/io/haplotype_writer.h:28,
from src/io/haplotype_writer.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
In file included from /usr/include/c++/9/vector:72,
from src/utils/otools.h:26,
from src/io/gmap_reader.h:25,
from src/io/gmap_reader.cpp:23:
/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>::
| ^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/main.cpp -o obj/main.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment.cpp -o obj/haplotype_segment.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/9/vector:67,
from src/utils/otools.h:26,
from src/io/gmap_reader.h:25,
from src/io/gmap_reader.cpp:23:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void gmap_reader::readGeneticMapFile(std::string)':
/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);
| ^~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/builder.cpp -o obj/builder.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/phaser/phaser_header.h:29,
from src/main.cpp:23:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/models/haplotype_segment.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/pbwt_solver.cpp -o obj/pbwt_solver.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/compute_job.cpp -o obj/compute_job.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_build.cpp -o obj/genotype_build.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_managment.cpp -o obj/genotype_managment.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from src/containers/haplotype_set.h:27,
from src/modules/pbwt_solver.h:26,
from src/modules/pbwt_solver.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
src/modules/pbwt_solver.cpp: In member function 'void pbwt_solver::sweep(genotype_set&)':
src/modules/pbwt_solver.cpp:93:57: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
93 | if (s > thresh) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; }
| ^~~~
src/modules/pbwt_solver.cpp:94:45: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
94 | else if (s < -thresh) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; }
| ^~~~
src/modules/pbwt_solver.cpp:103:49: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; }
| ^~~~
src/modules/pbwt_solver.cpp:103:68: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; }
| ^~~~
src/modules/pbwt_solver.cpp:104:53: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
104 | else if (s0 == -2 && s1 == 2) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; }
| ^~~~
src/modules/pbwt_solver.cpp:105:71: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
105 | else if (s0 == 2 && s1 == -2) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; }
| ^~~~
src/modules/pbwt_solver.cpp:134:26: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
134 | else Guess[h+0] = -1.0;
| ^~~~
src/modules/pbwt_solver.cpp:136:26: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits<std::allocator<char>, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow]
136 | else Guess[h+1] = -1.0;
| ^~~~
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/objects/compute_job.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_mask.cpp -o obj/genotype_mask.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_prune.cpp -o obj/genotype_prune.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_sweep.cpp -o obj/genotype_sweep.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/hmm_parameters.cpp -o obj/hmm_parameters.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/variant.cpp -o obj/variant.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/otools.h:35,
from src/objects/genotype/genotype_header.h:25,
from src/objects/genotype/genotype_prune.cpp:22:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
In file included from /usr/include/c++/9/queue:62,
from src/utils/otools.h:28,
from src/objects/genotype/genotype_header.h:25,
from src/objects/genotype/genotype_prune.cpp:22:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >; _Distance = int; _Tp = Transition; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/otools.h:35,
from src/objects/genotype/genotype_header.h:25,
from src/objects/genotype/genotype_prune.cpp:22:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void genotype::performMerges(std::vector<double>&, std::vector<bool>&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/queue:62,
from src/utils/otools.h:28,
from src/objects/genotype/genotype_header.h:25,
from src/objects/genotype/genotype_prune.cpp:22:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >; _Distance = int; _Tp = TransStatistics; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from src/utils/otools.h:35,
from src/objects/genotype/genotype_header.h:25,
from src/objects/genotype/genotype_prune.cpp:22:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_finalise.cpp -o obj/phaser_finalise.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_initialise.cpp -o obj/phaser_initialise.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
/usr/include/c++/9/bits/stl_algo.h: In member function 'void genotype::mapMerges(std::vector<double>&, double, std::vector<bool>&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_management.cpp -o obj/phaser_management.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_initialise.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_finalise.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_parameters.cpp -o obj/phaser_parameters.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_management.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/shapeit4-4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_algorithm.cpp -o obj/phaser_algorithm.o -Isrc -I/sbuild-nonexistent/Tools/htslib-1.9 -I/usr/include
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_parameters.cpp:23:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_algorithm.cpp:22:
src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)':
src/containers/bitmatrix.h:28:112: warning: right shift count >= width of type [-Wshift-count-overflow]
28 | return static_cast<unsigned int>((static_cast<unsigned long int>(i1) * static_cast<unsigned long int>(i2)) >> 32);
| ^~
g++ -std=c++11 -Wl,-z,relro -Wl,-z,now -O3 obj/genotype_set.o obj/haplotype_set.o obj/variant_map.o obj/genotype_reader1.o obj/genotype_reader2.o obj/gmap_reader.o obj/haplotype_writer.o obj/main.o obj/haplotype_segment.o obj/builder.o obj/pbwt_solver.o obj/compute_job.o obj/genotype_build.o obj/genotype_managment.o obj/genotype_mask.o obj/genotype_prune.o obj/genotype_sweep.o obj/hmm_parameters.o obj/variant.o obj/phaser_finalise.o obj/phaser_initialise.o obj/phaser_management.o obj/phaser_parameters.o obj/phaser_algorithm.o -lhts -lboost_iostreams -lboost_program_options -o bin/shapeit4 -lz -lbz2 -lm -lpthread -llzma
make[1]: Leaving directory '/<<BUILDDIR>>/shapeit4-4.1+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/shapeit4/usr/bin/shapeit4 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/shapeit4/usr/bin/shapeit4 was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'shapeit4-dbgsym' in '../shapeit4-dbgsym_4.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'shapeit4' in '../shapeit4_4.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../shapeit4_4.1+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-01-10T00:05:00Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
shapeit4_4.1+dfsg-1_armhf.changes:
----------------------------------
Format: 1.8
Date: Wed, 18 Dec 2019 22:37:57 +0100
Source: shapeit4
Binary: shapeit4 shapeit4-dbgsym
Architecture: armhf
Version: 4.1+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
shapeit4 - fast and accurate method for estimation of haplotypes (phasing)
Changes:
shapeit4 (4.1+dfsg-1) unstable; urgency=medium
.
* New upstream release.
* Standards-Version: 4.4.1
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Files:
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e6f3bd53318d6ddeedac3a0cf13623f0 5886 science optional shapeit4_4.1+dfsg-1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
shapeit4-dbgsym_4.1+dfsg-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 3266960 bytes: control archive=540 bytes.
381 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: shapeit4-dbgsym
Source: shapeit4
Version: 4.1+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3378
Depends: shapeit4 (= 4.1+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for shapeit4
Build-Ids: 5856fe38d7fa4c4d949f7a3a0790ed2be1261437
drwxr-xr-x root/root 0 2019-12-18 21:37 ./
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/lib/
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/lib/debug/.build-id/58/
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drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/share/
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-12-18 21:37 ./usr/share/doc/shapeit4-dbgsym -> shapeit4
shapeit4_4.1+dfsg-1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 142592 bytes: control archive=800 bytes.
687 bytes, 14 lines control
262 bytes, 4 lines md5sums
Package: shapeit4
Version: 4.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 457
Depends: libboost-iostreams1.67.0, libboost-program-options1.67.0, libc6 (>= 2.29), libgcc1 (>= 1:3.5), libhts2 (>= 1.0), libstdc++6 (>= 5.2)
Suggests: shapeit4-example
Section: science
Priority: optional
Homepage: https://odelaneau.github.io/shapeit4/
Description: fast and accurate method for estimation of haplotypes (phasing)
Segmented HAPlotype Estimation and Imputation Tools version 4 (SHAPEIT4).
SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka
phasing) for SNP array and sequencing data.
drwxr-xr-x root/root 0 2019-12-18 21:37 ./
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/
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-rw-r--r-- root/root 2990 2019-12-18 21:37 ./usr/share/doc/shapeit4/copyright
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/share/man/
drwxr-xr-x root/root 0 2019-12-18 21:37 ./usr/share/man/man1/
-rw-r--r-- root/root 1160 2019-12-18 21:37 ./usr/share/man/man1/shapeit4.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 102732
Build-Time: 117
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 342
Job: shapeit4_4.1+dfsg-1
Machine Architecture: armhf
Package: shapeit4
Package-Time: 500
Source-Version: 4.1+dfsg-1
Space: 102732
Status: successful
Version: 4.1+dfsg-1
--------------------------------------------------------------------------------
Finished at 2020-01-10T00:05:00Z
Build needed 00:08:20, 102732k disk space