delly →
0.8.7-1 →
armhf → 2021-01-23 07:19:10
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| delly 0.8.7-1 (armhf) Sat, 23 Jan 2021 06:56:58 +0000 |
+==============================================================================+
Package: delly
Version: 0.8.7-1
Source Version: 0.8.7-1
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-af9fdd8e-b8f2-4475-b02c-2e4ce363b6aa' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.1 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.1 MB]
Fetched 25.2 MB in 26s (975 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: 'delly' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/delly.git
Please use:
git clone https://salsa.debian.org/med-team/delly.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 93.2 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main delly 0.8.7-1 (dsc) [2074 B]
Get:2 http://172.17.0.1/private bullseye-staging/main delly 0.8.7-1 (tar) [86.9 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main delly 0.8.7-1 (diff) [4204 B]
Fetched 93.2 kB in 0s (980 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/delly-rX3Mvq/delly-0.8.7' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/delly-rX3Mvq' 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-QrbMeS/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-QrbMeS/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-QrbMeS/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2836 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils krb5-locales libnss-nis libnss-nisplus 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 79 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-QrbMeS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12543 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libboost-date-time-dev, libboost-program-options-dev, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libhts-dev, libbz2-dev, zlib1g-dev, chrpath
Filtered Build-Depends: debhelper-compat (= 13), libboost-date-time-dev, libboost-program-options-dev, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libhts-dev, libbz2-dev, zlib1g-dev, chrpath
dpkg-deb: building package 'sbuild-build-depends-delly-dummy' in '/<<BUILDDIR>>/resolver-QrbMeS/apt_archive/sbuild-build-depends-delly-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-delly-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-QrbMeS/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Sources [557 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ Packages [635 B]
Fetched 2525 B in 1s (3155 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install delly 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:
krb5-locales libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev chrpath debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
icu-devtools intltool-debian libarchive-zip-perl libboost-date-time-dev
libboost-date-time1.74-dev libboost-date-time1.74.0 libboost-filesystem-dev
libboost-filesystem1.74-dev libboost-filesystem1.74.0 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
libboost-serialization1.74-dev libboost-serialization1.74.0
libboost-system-dev libboost-system1.74-dev libboost-system1.74.0
libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libgnutls30 libhts-dev libhts3 libicu-dev
libicu67 liblzma-dev liblzma5 libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db po-debconf 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-exception1.74-dev libboost-fiber1.74-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-stacktrace1.74-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 gnutls-bin 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 chrpath debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
icu-devtools intltool-debian libarchive-zip-perl libboost-date-time-dev
libboost-date-time1.74-dev libboost-date-time1.74.0 libboost-filesystem-dev
libboost-filesystem1.74-dev libboost-filesystem1.74.0 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
libboost-serialization1.74-dev libboost-serialization1.74.0
libboost-system-dev libboost-system1.74-dev libboost-system1.74.0
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-delly-dummy zlib1g-dev
The following packages will be upgraded:
libgnutls30 liblzma5
2 upgraded, 67 newly installed, 0 to remove and 77 not upgraded.
Need to get 48.7 MB of archives.
After this operation, 298 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QrbMeS/apt_archive ./ sbuild-build-depends-delly-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libgnutls30 armhf 3.7.0-5 [1275 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf liblzma5 armhf 5.2.5-1.0 [158 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.1 [188 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.10.0-1 [25.6 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.10.0-1 [15.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-3 [162 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20201015-2 [162 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.1 [1010 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-6 [172 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libboost1.74-dev armhf 1.74.0-3 [9532 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libboost-date-time1.74.0 armhf 1.74.0-3 [241 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0-3 [319 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0-3 [388 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libboost-date-time1.74-dev armhf 1.74.0-3 [250 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libboost-date-time-dev armhf 1.74.0.3 [4332 B]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem1.74.0 armhf 1.74.0-3 [274 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libboost-system1.74.0 armhf 1.74.0-3 [241 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libboost-system1.74-dev armhf 1.74.0-3 [242 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem1.74-dev armhf 1.74.0-3 [284 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem-dev armhf 1.74.0.3 [4368 B]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.74.0 armhf 1.74.0-3 [447 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-6 [9229 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.74-dev armhf 1.74.0-3 [553 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0-3 [259 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0-3 [269 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3 [4316 B]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0-3 [334 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.74-dev armhf 1.74.0-3 [374 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options-dev armhf 1.74.0.3 [4340 B]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libboost-system-dev armhf 1.74.0.3 [4468 B]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1 [301 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1 [375 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.7-1 [40.3 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libgnutls30:armhf (3.7.0-5) ...
(Reading database ... 13069 files and directories currently installed.)
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-5+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.1-1+rpi1 gcc-10_10.2.1-1+rpi1 libc6-dev_2.31-5+rpi1 libstdc++-10-dev_10.2.1-1+rpi1 libstdc++6_10.2.1-1+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1
Package versions: adduser_3.118 apt_2.1.12 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-3 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-1 binutils_2.35.1-5+rpi1 binutils-arm-linux-gnueabihf_2.35.1-5+rpi1 binutils-common_2.35.1-5+rpi1 bsdextrautils_2.36.1-2 bsdutils_1:2.36.1-2 build-essential_12.8 bzip2_1.0.8-4 chrpath_0.16-2 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.1-1+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.10.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-2 file_1:5.39-3 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.1-1+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.1-1+rpi1 gcc-10-base_10.2.1-1+rpi1 gettext_0.21-3 gettext-base_0.21-3 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 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libboost-regex1.74.0_1.74.0-3 libboost-serialization1.74-dev_1.74.0-3 libboost-serialization1.74.0_1.74.0-3 libboost-system-dev_1.74.0.3 libboost-system1.74-dev_1.74.0-3 libboost-system1.74.0_1.74.0-3 libboost1.74-dev_1.74.0-3 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-5+rpi1 libc-dev-bin_2.31-5+rpi1 libc6_2.31-5+rpi1 libc6-dev_2.31-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.1-1+rpi1 libcom-err2_1.45.6-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-5+rpi1 libctf0_2.35.1-5+rpi1 libcurl3-gnutls_7.74.0-1 libcurl4-gnutls-dev_7.74.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255+b1 libdebhelper-perl_13.3.1 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-3 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.10.0-1 libgcc-10-dev_10.2.1-1+rpi1 libgcc-s1_10.2.1-1+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-1+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu-dev_67.1-6 libicu67_67.1-6 libidn2-0_2.3.0-4 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_1.5.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.2-2 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_2.36.1-2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-1 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_0.23.21-2 libpam-cap_1:2.44-1 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_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.1 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_2.5.0-3+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.12-3 libsmartcols1_2.36.1-2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.1-1+rpi1 libstdc++6_10.2.1-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-4+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-15 libubsan1_10.2.1-1+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-4+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-2 libxml2_2.9.10+dfsg-6.3 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1 login_1:4.8.1-1 logsave_1.45.6-1 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_2.36.1-2 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-6 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-core-dummy_0.invalid.0 sbuild-build-depends-delly-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020d-1 util-linux_2.36.1-2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.eI7pVjh2/trustedkeys.kbx': General error
gpgv: Signature made Sun Jan 17 14:35:43 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./delly_0.8.7-1.dsc
dpkg-source: info: extracting delly in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking delly_0.8.7.orig.tar.xz
dpkg-source: info: unpacking delly_0.8.7-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-af9fdd8e-b8f2-4475-b02c-2e4ce363b6aa
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package delly
dpkg-buildpackage: info: source version 0.8.7-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
if [ -r src/htslib/Makefile ]; then cd src/htslib && make clean; fi
rm -f .htslib src/delly .htslib.o src/delly.o .htslib
rm -f src/delly
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf src/dpe src/delly bin/delly
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
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- BUILT_PROGRAMS="src/delly src/dpe" PARALLEL=1
make -j4 "INSTALL=install --strip-program=true" "BUILT_PROGRAMS=src/delly src/dpe" PARALLEL=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
if [ -r src/htslib/Makefile ]; then cd src/htslib && autoheader && autoconf && ./configure --disable-s3 --disable-gcs --disable-libcurl --disable-plugins && make && make lib-static && cd ../../ && touch .htslib; fi
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -isystem /<<PKGBUILDDIR>>/src/htslib/ -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive -fopenmp -DOPENMP -O3 -fno-tree-vectorize -DNDEBUG src/delly.cpp -o src/delly -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -L/<<PKGBUILDDIR>>/src/htslib/ -L/<<PKGBUILDDIR>>/src/htslib//lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lhts -lz -llzma -lbz2 -Wl,-rpath,/<<PKGBUILDDIR>>/src/htslib/
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -isystem /<<PKGBUILDDIR>>/src/htslib/ -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive -fopenmp -DOPENMP -O3 -fno-tree-vectorize -DNDEBUG src/dpe.cpp -o src/dpe -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -L/<<PKGBUILDDIR>>/src/htslib/ -L/<<PKGBUILDDIR>>/src/htslib//lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lhts -lz -llzma -lbz2 -Wl,-rpath,/<<PKGBUILDDIR>>/src/htslib/
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:602,
from /usr/include/boost/graph/adjacency_list.hpp:27,
from src/dpe.cpp:5:
/usr/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
from /usr/include/boost/property_map/vector_property_map.hpp:14,
from /usr/include/boost/property_map/property_map.hpp:602,
from /usr/include/boost/graph/adjacency_list.hpp:27,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/boost/progress.hpp:23:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp> instead.'
23 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp> or <boost/timer/progress_display.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/timer.hpp:21:1: note: '#pragma message: This header is deprecated. Use the facilities in <boost/timer/timer.hpp> instead.'
21 | BOOST_HEADER_DEPRECATED( "the facilities in <boost/timer/timer.hpp>" )
| ^~~~~~~~~~~~~~~~~~~~~~~
In file included from src/coral.h:18,
from src/delly.cpp:22:
src/scan.h: In instantiation of 'void torali::scan(const TConfig&, const torali::LibraryInfo&, std::vector<std::vector<torali::ScanWindow> >&) [with TConfig = torali::CountDNAConfig]':
src/coral.h:707:29: required from here
src/scan.h:99:23: warning: comparison of unsigned expression in '>= 0' is always true [-Wtype-limits]
99 | if ((it->lower() >= 0) && (it->upper() < hdr->target_len[refIndex])) {
| ~~~~~~~~~~~~~^~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/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 torali::CNV&}; _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<torali::CNV>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/stl_vector.h: In function 'void torali::parseVcfCNV(const TConfig&, bam_hdr_t*, std::vector<torali::CNV>&) [with TConfig = torali::CountDNAConfig]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/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 = {torali::BpCNV}; _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<torali::BpCNV>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {torali::CNV}; _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<torali::CNV>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void torali::mergeCNVs(const TConfig&, std::vector<torali::CNV>&, std::vector<torali::CNV>&) [with TConfig = torali::CountDNAConfig]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/move/algorithm.hpp:32,
from /usr/include/boost/move/move.hpp:32,
from /usr/include/boost/unordered/unordered_set.hpp:19,
from /usr/include/boost/unordered_set.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:20,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<torali::SortCNVs<torali::CNV> >]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' 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<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In function 'void torali::callCNVs(const TConfig&, const std::pair<unsigned int, unsigned int>&, const std::vector<short unsigned int>&, const std::vector<short unsigned int>&, const TGcBias&, const TCoverage&, const bam_hdr_t*, int32_t, std::vector<torali::CNV>&) [with TConfig = torali::CountDNAConfig; TGcBias = std::vector<torali::GcBias>; TCoverage = std::vector<short unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::BpCNV*, std::vector<torali::BpCNV> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::BpCNV*, std::vector<torali::BpCNV> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::BpCNV*, std::vector<torali::BpCNV> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/move/algorithm.hpp:32,
from /usr/include/boost/move/move.hpp:32,
from /usr/include/boost/unordered/unordered_set.hpp:19,
from /usr/include/boost/unordered_set.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:20,
from src/delly.h:8,
from src/delly.cpp:17:
/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<torali::CNV*, std::vector<torali::CNV> >; _Distance = int; _Tp = torali::CNV; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/move/algorithm.hpp:32,
from /usr/include/boost/move/move.hpp:32,
from /usr/include/boost/unordered/unordered_set.hpp:19,
from /usr/include/boost/unordered_set.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:20,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' 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<torali::CNV*, std::vector<torali::CNV> >' 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<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/boost/graph/adjacency_list.hpp:16,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/vector.tcc: In function 'void torali::vcfOutput(const TConfig&, const std::vector<Property>&, const TJunctionCountMap&, const TReadCountMap&, const TCountMap&) [with TConfig = torali::Config; TStructuralVariantRecord = torali::StructuralVariantRecord; TJunctionCountMap = std::vector<std::vector<torali::JunctionCount> >; TReadCountMap = std::vector<std::vector<torali::ReadCount> >; TCountMap = std::vector<std::vector<torali::SpanningCount> >]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void torali::vcfOutput(const TConfig&, const std::vector<Property>&, const TJunctionCountMap&, const TReadCountMap&, const TCountMap&) [with TConfig = torali::TeguaConfig; TStructuralVariantRecord = torali::StructuralVariantRecord; TJunctionCountMap = std::vector<std::vector<torali::JunctionCount> >; TReadCountMap = std::vector<std::vector<torali::ReadCount> >; TCountMap = std::vector<std::vector<torali::SpanningCount> >]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/move/algorithm.hpp:32,
from /usr/include/boost/move/move.hpp:32,
from /usr/include/boost/unordered/unordered_set.hpp:19,
from /usr/include/boost/unordered_set.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:20,
from src/delly.h:8,
from src/delly.cpp:17:
/usr/include/c++/10/bits/stl_algo.h: In function 'int32_t torali::bamCount(const TConfig&, const torali::LibraryInfo&, const std::vector<torali::GcBias>&, const std::pair<unsigned int, unsigned int>&) [with TConfig = torali::CountDNAConfig]':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >' 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<torali::CNV*, std::vector<torali::CNV> >' 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<torali::CNV*, std::vector<torali::CNV> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
chrpath -d src/dpe src/delly
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# avoiding redundant compile of delly
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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/delly/usr/bin/delly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/delly/usr/bin/dpe 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/delly/usr/bin/delly debian/delly/usr/bin/dpe were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'delly' in '../delly_0.8.7-1_armhf.deb'.
dpkg-deb: building package 'delly-dbgsym' in '../delly-dbgsym_0.8.7-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../delly_0.8.7-1_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 2021-01-23T07:18:51Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
delly_0.8.7-1_armhf.changes:
----------------------------
Format: 1.8
Date: Sun, 17 Jan 2021 15:27:47 +0100
Source: delly
Binary: delly delly-dbgsym
Architecture: armhf
Version: 0.8.7-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
delly - Structural variant discovery by read analysis
Changes:
delly (0.8.7-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.5.1 (routine-update)
Checksums-Sha1:
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2d173c8a58dcccdfd8ad009c74d07cdf0467a771 6394 delly_0.8.7-1_armhf.buildinfo
dfe2bf14e04fc912e384cb21d36cd8a8addb9897 245384 delly_0.8.7-1_armhf.deb
Checksums-Sha256:
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2e54c2c652cce1a3fe3f85cd6369997b962ef161f77b761888e04bc3f7816bf4 245384 delly_0.8.7-1_armhf.deb
Files:
233572aeb9cbbc823c954671d2489ce8 4798408 debug optional delly-dbgsym_0.8.7-1_armhf.deb
f7c611a94facb68aa4c87a2c8c17cf1d 6394 science optional delly_0.8.7-1_armhf.buildinfo
eab3e46854757be5429375c9db8dc9d5 245384 science optional delly_0.8.7-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
delly-dbgsym_0.8.7-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 4798408 bytes: control archive=640 bytes.
404 bytes, 12 lines control
297 bytes, 3 lines md5sums
Package: delly-dbgsym
Source: delly
Version: 0.8.7-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4956
Depends: delly (= 0.8.7-1)
Section: debug
Priority: optional
Description: debug symbols for delly
Build-Ids: 37abd979f7ae731d3a951bd41c018e5093700bf6 cc5f72a2c43833df6a8d0f566a7c641a21128b80
drwxr-xr-x root/root 0 2021-01-17 14:27 ./
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/debug/.build-id/37/
-rw-r--r-- root/root 636300 2021-01-17 14:27 ./usr/lib/debug/.build-id/37/abd979f7ae731d3a951bd41c018e5093700bf6.debug
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/debug/.build-id/cc/
-rw-r--r-- root/root 4295468 2021-01-17 14:27 ./usr/lib/debug/.build-id/cc/5f72a2c43833df6a8d0f566a7c641a21128b80.debug
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 128608 2021-01-17 14:27 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/delly.debug
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-01-17 14:27 ./usr/share/doc/delly-dbgsym -> delly
delly_0.8.7-1_armhf.deb
-----------------------
new Debian package, version 2.0.
size 245384 bytes: control archive=972 bytes.
938 bytes, 16 lines control
358 bytes, 6 lines md5sums
Package: delly
Version: 0.8.7-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 796
Depends: libboost-filesystem1.74.0 (>= 1.74.0), libboost-iostreams1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libhts3 (>= 1.10), libstdc++6 (>= 9)
Section: science
Priority: optional
Homepage: https://github.com/dellytools/delly
Description: Structural variant discovery by read analysis
Delly performs Structural variant discovery by integrated paired-end and
split-read analysis. It discovers, genotypes and visualizes deletions,
tandem duplications, inversions and translocations at single-nucleotide
resolution in short-read massively parallel sequencing data. It uses
paired-ends, split-reads and read-depth to sensitively and accurately
delineate genomic rearrangements throughout the genome.
drwxr-xr-x root/root 0 2021-01-17 14:27 ./
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/bin/
-rwxr-xr-x root/root 685716 2021-01-17 14:27 ./usr/bin/delly
-rwxr-xr-x root/root 112268 2021-01-17 14:27 ./usr/bin/dpe
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/doc/delly/
-rw-r--r-- root/root 1047 2021-01-17 14:27 ./usr/share/doc/delly/changelog.Debian.gz
-rw-r--r-- root/root 2704 2021-01-17 14:27 ./usr/share/doc/delly/copyright
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/man/
drwxr-xr-x root/root 0 2021-01-17 14:27 ./usr/share/man/man1/
-rw-r--r-- root/root 291 2021-01-17 14:27 ./usr/share/man/man1/delly.1.gz
-rw-r--r-- root/root 336 2021-01-17 14:27 ./usr/share/man/man1/dpe.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 30892
Build-Time: 756
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 505
Job: delly_0.8.7-1
Machine Architecture: armhf
Package: delly
Package-Time: 1313
Source-Version: 0.8.7-1
Space: 30892
Status: successful
Version: 0.8.7-1
--------------------------------------------------------------------------------
Finished at 2021-01-23T07:18:51Z
Build needed 00:21:53, 30892k disc space