shapeit4 →
4.2.0+dfsg-1 →
armhf → 2021-02-09 07:31:42
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| shapeit4 4.2.0+dfsg-1 (armhf) Tue, 09 Feb 2021 07:22:41 +0000 |
+==============================================================================+
Package: shapeit4
Version: 4.2.0+dfsg-1
Source Version: 4.2.0+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-39cca5ea-d1bf-43ca-af01-764d815e28dd' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/shapeit4-GRCq7K/resolver-l7JCXJ' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
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Reading package lists...
+------------------------------------------------------------------------------+
| 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 59.0 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main shapeit4 4.2.0+dfsg-1 (dsc) [2147 B]
Get:2 http://172.17.0.1/private bullseye-staging/main shapeit4 4.2.0+dfsg-1 (tar) [59.0 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main shapeit4 4.2.0+dfsg-1 (diff) [5188 B]
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I: NOTICE: Log filtering will replace 'build/shapeit4-GRCq7K/shapeit4-4.2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/shapeit4-GRCq7K' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
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Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
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Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libicu-dev libicu67
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-date-time1.74-dev
libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-python1.74-dev libboost-random1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev pkg-config 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
publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0
libboost-program-options-dev libboost-program-options1.74-dev
libboost-program-options1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libicu-dev libicu67
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils
zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 2 not upgraded.
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libboost1.74-dev:armhf (1.74.0-8) ...
Setting up bsdextrautils (2.36.1-6) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libboost-iostreams1.74.0:armhf (1.74.0-8) ...
Setting up libboost-program-options1.74.0:armhf (1.74.0-8) ...
Setting up libdebhelper-perl (13.3.3) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.42.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libboost-program-options1.74-dev:armhf (1.74.0-8) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libboost-program-options-dev:armhf (1.74.0.3+b1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libboost-regex1.74.0:armhf (1.74.0-8) ...
Setting up autopoint (0.21-4) ...
Setting up icu-devtools (67.1-6) ...
Setting up liblzma-dev:armhf (5.2.5-1.0) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.14) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up libdeflate-dev:armhf (1.7-1) ...
Setting up libelf1:armhf (0.182+20210205-1) ...
Setting up libicu-dev:armhf (67.1-6) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libfile-stripnondeterminism-perl (1.11.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up dwz (0.13+20210126-1) ...
Setting up libboost-regex1.74-dev:armhf (1.74.0-8) ...
Setting up groff-base (1.22.4-6) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.11-4) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libboost-iostreams1.74-dev:armhf (1.74.0-8) ...
Setting up libboost-iostreams-dev:armhf (1.74.0.3+b1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.3.3) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-6 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210126-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-6+rpi1 gcc-9-base_9.3.0-20+rpi1 gettext_0.21-4 gettext-base_0.21-4 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_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-6 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblkid1_2.36.1-6 libboost-iostreams-dev_1.74.0.3+b1 libboost-iostreams1.74-dev_1.74.0-8 libboost-iostreams1.74.0_1.74.0-8 libboost-program-options-dev_1.74.0.3+b1 libboost-program-options1.74-dev_1.74.0-8 libboost-program-options1.74.0_1.74.0-8 libboost-regex1.74-dev_1.74.0-8 libboost-regex1.74.0_1.74.0-8 libboost1.74-dev_1.74.0-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libcurl3-gnutls_7.74.0-1 libcurl4-gnutls-dev_7.74.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.182+20210205-1 libext2fs2_1.45.7-1 libfakeroot_1.25.3-1.1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libicu-dev_67.1-6 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-1+rpi1 liblzma-dev_5.2.5-1.0 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.7-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1i-3 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: shapeit4
Binary: shapeit4, shapeit4-example
Architecture: any all
Version: 4.2.0+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Dylan Aïssi <daissi@debian.org>
Homepage: https://odelaneau.github.io/shapeit4/
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/shapeit4
Vcs-Git: https://salsa.debian.org/med-team/shapeit4.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev
Package-List:
shapeit4 deb science optional arch=any
shapeit4-example deb doc optional arch=all
Checksums-Sha1:
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3465efda50590f9dc0b9f5825949df21d07c9dd1 5188 shapeit4_4.2.0+dfsg-1.debian.tar.xz
Checksums-Sha256:
f9a9276b1bcc218a2e7cb79bc8e1ff34e97ec0d87892713fc83d50a002ae5d25 58963660 shapeit4_4.2.0+dfsg.orig.tar.xz
f337cbdfa05ca06945d8825f165bba1d35225af2984c87d7e34f31292bb5ec3d 5188 shapeit4_4.2.0+dfsg-1.debian.tar.xz
Files:
efa9b0cf6f97568a5bb66466c06f78c7 58963660 shapeit4_4.2.0+dfsg.orig.tar.xz
360ca7fda9da2f870d645fb1ee6d835f 5188 shapeit4_4.2.0+dfsg-1.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.Dtbvu_Kc/trustedkeys.kbx': General error
gpgv: Signature made Thu Feb 4 10:25:33 2021 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_4.2.0+dfsg-1.dsc
dpkg-source: info: extracting shapeit4 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking shapeit4_4.2.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking shapeit4_4.2.0+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_shared_libs.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/buildd
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-39cca5ea-d1bf-43ca-af01-764d815e28dd
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c100878
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package shapeit4
dpkg-buildpackage: info: source version 4.2.0+dfsg-1
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 '/<<PKGBUILDDIR>>'
rm -f obj/*.o bin/shapeit4.2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/bitmatrix.cpp -o obj/bitmatrix.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/genotype_set.cpp -o obj/genotype_set.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/haplotype_set.cpp -o obj/haplotype_set.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/variant_map.cpp -o obj/variant_map.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
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:28:109: 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/bitmatrix.cpp:22:
src/containers/bitmatrix.h: In function ‘unsigned int abracadabra(const unsigned int&, const unsigned int&)’:
src/containers/bitmatrix.h:28:109: 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.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader1.cpp -o obj/genotype_reader1.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader2.cpp -o obj/genotype_reader2.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/10/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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/gmap_reader.cpp -o obj/gmap_reader.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/10/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++/10/bits/stl_vector.h: In member function ‘void haplotype_set::initializePBWTmapping(variant_map&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/graph_writer.cpp -o obj/graph_writer.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/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:28:109: 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/io/genotype_reader.h:28,
from src/io/genotype_reader1.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
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:28:109: 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/io/genotype_reader.h:28,
from src/io/genotype_reader2.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/haplotype_writer.cpp -o obj/haplotype_writer.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/10/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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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:28:109: 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/io/haplotype_writer.h:28,
from src/io/haplotype_writer.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
In file included from /usr/include/c++/10/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++/10/bits/stl_vector.h: In member function ‘void gmap_reader::readGeneticMapFile(std::string)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
src/io/haplotype_writer.cpp: In member function ‘void haplotype_writer::writeHaplotypes(std::string)’:
src/io/haplotype_writer.cpp:59:15: warning: ignoring return value of ‘int bcf_hdr_write(htsFile*, bcf_hdr_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
59 | bcf_hdr_write(fp, hdr);
| ~~~~~~~~~~~~~^~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/main.cpp -o obj/main.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_double.cpp -o obj/haplotype_segment_double.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_single.cpp -o obj/haplotype_segment_single.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/builder.cpp -o obj/builder.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/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_single.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:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/phaser/phaser_header.h:29,
from src/main.cpp:23:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment_double.h:26,
from src/models/haplotype_segment_double.cpp:22:
src/containers/bitmatrix.h: In function ‘unsigned int abracadabra(const unsigned int&, const unsigned int&)’:
src/containers/bitmatrix.h:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_double.h:26,
from src/models/haplotype_segment_double.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/models/haplotype_segment_single.cpp:22:
src/containers/bitmatrix.h: In function ‘unsigned int abracadabra(const unsigned int&, const unsigned int&)’:
src/containers/bitmatrix.h:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/models/haplotype_segment_single.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/pbwt_solver.cpp -o obj/pbwt_solver.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/compute_job.cpp -o obj/compute_job.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_build.cpp -o obj/genotype_build.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_managment.cpp -o obj/genotype_managment.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/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:28:109: 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/modules/pbwt_solver.h:26,
from src/modules/pbwt_solver.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
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:28:109: 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/objects/compute_job.h:27,
from src/objects/compute_job.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_mask.cpp -o obj/genotype_mask.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_prune.cpp -o obj/genotype_prune.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_sweep.cpp -o obj/genotype_sweep.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/hmm_parameters.cpp -o obj/hmm_parameters.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/variant.cpp -o obj/variant.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
In file included from /usr/include/c++/10/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++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >; _Distance = int; _Tp = Transition; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
In file included from /usr/include/c++/10/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++/10/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++/10/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++/10/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
/usr/include/c++/10/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
/usr/include/c++/10/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++/10/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++/10/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++/10/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++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function ‘void genotype::mapMerges(std::vector<double>&, double, std::vector<bool>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<TransStatistics*, std::vector<TransStatistics> >’ changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function ‘void genotype::performMerges(std::vector<double>&, std::vector<bool>&)’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Transition*, std::vector<Transition> >’ changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_algorithm.cpp -o obj/phaser_algorithm.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_finalise.cpp -o obj/phaser_finalise.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_initialise.cpp -o obj/phaser_initialise.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_management.cpp -o obj/phaser_management.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/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_single.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:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_algorithm.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment_single.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:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_finalise.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment_single.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:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_initialise.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_parameters.cpp -o obj/phaser_parameters.o -Isrc -I/<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/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_single.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:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_management.cpp:22:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
In file included from src/containers/haplotype_set.h:27,
from src/objects/compute_job.h:27,
from src/models/haplotype_segment_single.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:28:109: 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/objects/compute_job.h:27,
from src/models/haplotype_segment_single.h:26,
from src/phaser/phaser_header.h:29,
from src/phaser/phaser_parameters.cpp:23:
src/containers/haplotype_set.h: In member function ‘bool IBD2track::merge(const IBD2track&)’:
src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type]
53 | }
| ^
g++ -std=c++11 -Wl,-z,relro -Wl,-z,now -O3 obj/bitmatrix.o 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/graph_writer.o obj/haplotype_writer.o obj/main.o obj/haplotype_segment_double.o obj/haplotype_segment_single.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_algorithm.o obj/phaser_finalise.o obj/phaser_initialise.o obj/phaser_management.o obj/phaser_parameters.o -lhts -lboost_iostreams -lboost_program_options -o bin/shapeit4.2 -lz -lbz2 -lm -lpthread -llzma
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
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 -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: debian/shapeit4/usr/bin/shapeit4.2 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/shapeit4.2 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' in '../shapeit4_4.2.0+dfsg-1_armhf.deb'.
dpkg-deb: building package 'shapeit4-dbgsym' in '../shapeit4-dbgsym_4.2.0+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../shapeit4_4.2.0+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 2021-02-09T07:31:33Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
shapeit4_4.2.0+dfsg-1_armhf.changes:
------------------------------------
Format: 1.8
Date: Thu, 04 Feb 2021 11:20:55 +0100
Source: shapeit4
Binary: shapeit4 shapeit4-dbgsym
Architecture: armhf
Version: 4.2.0+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
shapeit4 - fast and accurate method for estimation of haplotypes (phasing)
Changes:
shapeit4 (4.2.0+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
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Files:
980f0356ac5b70527084761dfc390274 3509844 debug optional shapeit4-dbgsym_4.2.0+dfsg-1_armhf.deb
0a71807b5ba610f34b29aa43aed4a7c3 5979 science optional shapeit4_4.2.0+dfsg-1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: shapeit4
Binary: shapeit4 shapeit4-dbgsym
Architecture: armhf
Version: 4.2.0+dfsg-1
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 09 Feb 2021 07:31:32 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-14),
automake (= 1:1.16.3-2),
autopoint (= 0.21-4),
autotools-dev (= 20180224.1+nmu1),
base-files (= 11+rpi1),
base-passwd (= 3.5.48),
bash (= 5.1-2),
binutils (= 2.35.1-7+rpi1),
binutils-arm-linux-gnueabihf (= 2.35.1-7+rpi1),
binutils-common (= 2.35.1-7+rpi1),
bsdextrautils (= 2.36.1-6),
bsdutils (= 1:2.36.1-6),
build-essential (= 12.9),
bzip2 (= 1.0.8-4),
coreutils (= 8.32-4),
cpp (= 4:10.2.1-1+rpi1),
cpp-10 (= 10.2.1-6+rpi1),
dash (= 0.5.11+git20200708+dd9ef66-5),
debconf (= 1.5.74),
debhelper (= 13.3.3),
debianutils (= 4.11.2),
dh-autoreconf (= 19),
dh-strip-nondeterminism (= 1.11.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.20.7.1+rpi1),
dpkg-dev (= 1.20.7.1+rpi1),
dwz (= 0.13+20210126-1),
file (= 1:5.39-3),
findutils (= 4.8.0-1),
g++ (= 4:10.2.1-1+rpi1),
g++-10 (= 10.2.1-6+rpi1),
gcc (= 4:10.2.1-1+rpi1),
gcc-10 (= 10.2.1-6+rpi1),
gcc-10-base (= 10.2.1-6+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
grep (= 3.6-1),
groff-base (= 1.22.4-6),
gzip (= 1.10-2),
hostname (= 3.23),
icu-devtools (= 67.1-6),
init-system-helpers (= 1.60),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-10),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 10.2.1-6+rpi1),
libatomic1 (= 10.2.1-6+rpi1),
libattr1 (= 1:2.4.48-6),
libaudit-common (= 1:3.0-2),
libaudit1 (= 1:3.0-2),
libbinutils (= 2.35.1-7+rpi1),
libblkid1 (= 2.36.1-6),
libboost-iostreams-dev (= 1.74.0.3+b1),
libboost-iostreams1.74-dev (= 1.74.0-8),
libboost-iostreams1.74.0 (= 1.74.0-8),
libboost-program-options-dev (= 1.74.0.3+b1),
libboost-program-options1.74-dev (= 1.74.0-8),
libboost-program-options1.74.0 (= 1.74.0-8),
libboost-regex1.74-dev (= 1.74.0-8),
libboost-regex1.74.0 (= 1.74.0-8),
libboost1.74-dev (= 1.74.0-8),
libbrotli1 (= 1.0.9-2+b1),
libbz2-1.0 (= 1.0.8-4),
libbz2-dev (= 1.0.8-4),
libc-bin (= 2.31-9+rpi1),
libc-dev-bin (= 2.31-9+rpi1),
libc6 (= 2.31-9+rpi1),
libc6-dev (= 2.31-9+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcc1-0 (= 10.2.1-6+rpi1),
libcom-err2 (= 1.45.7-1),
libcrypt-dev (= 1:4.4.17-1),
libcrypt1 (= 1:4.4.17-1),
libctf-nobfd0 (= 2.35.1-7+rpi1),
libctf0 (= 2.35.1-7+rpi1),
libcurl3-gnutls (= 7.74.0-1),
libcurl4-gnutls-dev (= 7.74.0-1),
libdb5.3 (= 5.3.28+dfsg1-0.6),
libdebconfclient0 (= 0.256),
libdebhelper-perl (= 13.3.3),
libdeflate-dev (= 1.7-1),
libdeflate0 (= 1.7-1),
libdpkg-perl (= 1.20.7.1+rpi1),
libelf1 (= 0.182+20210205-1),
libffi7 (= 3.3-5),
libfile-stripnondeterminism-perl (= 1.11.0-1),
libgcc-10-dev (= 10.2.1-6+rpi1),
libgcc-s1 (= 10.2.1-6+rpi1),
libgcrypt20 (= 1.8.7-2),
libgdbm-compat4 (= 1.19-2),
libgdbm6 (= 1.19-2),
libgmp10 (= 2:6.2.1+dfsg-1),
libgnutls30 (= 3.7.0-5),
libgomp1 (= 10.2.1-6+rpi1),
libgpg-error0 (= 1.38-2),
libgssapi-krb5-2 (= 1.18.3-4),
libhogweed6 (= 3.6-2),
libhts-dev (= 1.11-4),
libhts3 (= 1.11-4),
libicu-dev (= 67.1-6),
libicu67 (= 67.1-6),
libidn2-0 (= 2.3.0-5),
libisl23 (= 0.23-1),
libk5crypto3 (= 1.18.3-4),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-4),
libkrb5support0 (= 1.18.3-4),
libldap-2.4-2 (= 2.4.57+dfsg-1),
liblz4-1 (= 1.9.3-1+rpi1),
liblzma-dev (= 5.2.5-1.0),
liblzma5 (= 5.2.5-1.0),
libmagic-mgc (= 1:5.39-3),
libmagic1 (= 1:5.39-3),
libmount1 (= 2.36.1-6),
libmpc3 (= 1.2.0-1),
libmpfr6 (= 4.1.0-3),
libnettle8 (= 3.6-2),
libnghttp2-14 (= 1.42.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.23.22-1),
libpam-modules (= 1.4.0-2),
libpam-modules-bin (= 1.4.0-2),
libpam-runtime (= 1.4.0-2),
libpam0g (= 1.4.0-2),
libpcre2-8-0 (= 10.36-2),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.1-2),
libpipeline1 (= 1.5.3-1),
libpsl5 (= 0.21.0-1.2),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.27+dfsg-2),
libsasl2-modules-db (= 2.1.27+dfsg-2),
libseccomp2 (= 2.5.1-1+rpi1),
libselinux1 (= 3.1-2+b1),
libsigsegv2 (= 2.13-1),
libsmartcols1 (= 2.36.1-6),
libssh2-1 (= 1.9.0-2),
libssl1.1 (= 1.1.1i-3),
libstdc++-10-dev (= 10.2.1-6+rpi1),
libstdc++6 (= 10.2.1-6+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 247.2-5+rpi1),
libtasn1-6 (= 4.16.0-2),
libtinfo6 (= 6.2+20201114-2),
libtirpc-common (= 1.3.1-1),
libtirpc-dev (= 1.3.1-1),
libtirpc3 (= 1.3.1-1),
libtool (= 2.4.6-15),
libubsan1 (= 10.2.1-6+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 247.2-5+rpi1),
libunistring2 (= 0.9.10-4),
libuuid1 (= 2.36.1-6),
libxml2 (= 2.9.10+dfsg-6.3),
libzstd1 (= 1.4.8+dfsg-1),
linux-libc-dev (= 5.10.9-1+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4),
man-db (= 2.9.3-2),
mawk (= 1.3.4.20200120-2),
ncurses-base (= 6.2+20201114-2),
ncurses-bin (= 6.2+20201114-2),
patch (= 2.7.6-7),
perl (= 5.32.1-2),
perl-base (= 5.32.1-2),
perl-modules-5.32 (= 5.32.1-2),
po-debconf (= 1.0.21+nmu1),
sed (= 4.7-1),
sensible-utils (= 0.0.14),
sysvinit-utils (= 2.96-5),
tar (= 1.32+dfsg-1+rpi1),
util-linux (= 2.36.1-6),
xz-utils (= 5.2.5-1.0),
zlib1g (= 1:1.2.11.dfsg-2),
zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1612434055"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
shapeit4-dbgsym_4.2.0+dfsg-1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 3509844 bytes: control archive=536 bytes.
385 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: shapeit4-dbgsym
Source: shapeit4
Version: 4.2.0+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3617
Depends: shapeit4 (= 4.2.0+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for shapeit4
Build-Ids: 6c2921df1bb709e5e133ce0de1bef980131d73ab
drwxr-xr-x root/root 0 2021-02-04 10:20 ./
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/lib/debug/.build-id/6c/
-rw-r--r-- root/root 3693252 2021-02-04 10:20 ./usr/lib/debug/.build-id/6c/2921df1bb709e5e133ce0de1bef980131d73ab.debug
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-02-04 10:20 ./usr/share/doc/shapeit4-dbgsym -> shapeit4
shapeit4_4.2.0+dfsg-1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 150620 bytes: control archive=804 bytes.
714 bytes, 14 lines control
264 bytes, 4 lines md5sums
Package: shapeit4
Version: 4.2.0+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 484
Depends: libboost-iostreams1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libhts3 (>= 1.10), 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 2021-02-04 10:20 ./
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/bin/
lrwxrwxrwx root/root 0 2021-02-04 10:20 ./usr/bin/shapeit4 -> shapeit4.2
-rwxr-xr-x root/root 476680 2021-02-04 10:20 ./usr/bin/shapeit4.2
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/doc/shapeit4/
-rw-r--r-- root/root 517 2021-02-04 10:20 ./usr/share/doc/shapeit4/changelog.Debian.gz
-rw-r--r-- root/root 3076 2021-02-04 10:20 ./usr/share/doc/shapeit4/copyright
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/man/
drwxr-xr-x root/root 0 2021-02-04 10:20 ./usr/share/man/man1/
-rw-r--r-- root/root 1160 2021-02-04 10:20 ./usr/share/man/man1/shapeit4.1.gz
lrwxrwxrwx root/root 0 2021-02-04 10:20 ./usr/share/man/man1/shapeit4.2.1.gz -> shapeit4.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 125016
Build-Time: 198
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 294
Job: shapeit4_4.2.0+dfsg-1
Machine Architecture: armhf
Package: shapeit4
Package-Time: 532
Source-Version: 4.2.0+dfsg-1
Space: 125016
Status: successful
Version: 4.2.0+dfsg-1
--------------------------------------------------------------------------------
Finished at 2021-02-09T07:31:33Z
Build needed 00:08:52, 125016k disk space