lumpy-sv →
0.3.1+dfsg-4 →
armhf → 2020-11-09 11:25:02
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| lumpy-sv 0.3.1+dfsg-4 (armhf) Mon, 09 Nov 2020 11:12:03 +0000 |
+==============================================================================+
Package: lumpy-sv
Version: 0.3.1+dfsg-4
Source Version: 0.3.1+dfsg-4
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-56db5228-70c4-4de4-9417-8f50b71fcbc1' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.7 MB in 24s (1016 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: 'lumpy-sv' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/lumpy-sv.git
Please use:
git clone https://salsa.debian.org/med-team/lumpy-sv.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 39.3 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main lumpy-sv 0.3.1+dfsg-4 (dsc) [2275 B]
Get:2 http://172.17.0.1/private bullseye-staging/main lumpy-sv 0.3.1+dfsg-4 (tar) [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main lumpy-sv 0.3.1+dfsg-4 (diff) [39.2 MB]
Fetched 39.3 MB in 4s (9991 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/lumpy-sv-zDZRMM/lumpy-sv-0.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-zDZRMM' 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-bzXTNQ/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-bzXTNQ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-bzXTNQ/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-bzXTNQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2744 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 netbase sensible-utils
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 24 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-bzXTNQ/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 (23.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12726 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, python3-pysam
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, python3-pysam
dpkg-deb: building package 'sbuild-build-depends-lumpy-sv-dummy' in '/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive/sbuild-build-depends-lumpy-sv-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-lumpy-sv-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-bzXTNQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ Packages [644 B]
Fetched 2544 B in 1s (3119 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install lumpy-sv 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 netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf dh-python
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.1
libbrotli1 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libfastahack-dev libfastahack0
libfile-stripnondeterminism-perl libglib2.0-0 libgzstream-dev libgzstream0
libhts-dev libhts3 libicu67 liblzma-dev libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib librtmp1 libsigsegv2 libsqlite3-dev libssh2-1 libssl-dev
libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
mime-support po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3-pysam python3.8 python3.8-minimal samtools
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libbamtools-doc libcurl4-doc
libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev pkg-config liblzma-doc sqlite3-doc libssl-doc libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv
python3.8-doc binfmt-support cwltool
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf dh-python
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.1
libbrotli1 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libfastahack-dev libfastahack0
libfile-stripnondeterminism-perl libglib2.0-0 libgzstream-dev libgzstream0
libhts-dev libhts3 libicu67 liblzma-dev libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal
libpython3.8-stdlib librtmp1 libsigsegv2 libsqlite3-dev libssh2-1 libssl-dev
libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3-pysam python3.8 python3.8-minimal samtools
sbuild-build-depends-lumpy-sv-dummy zlib1g-dev
The following packages will be upgraded:
libssl1.1
1 upgraded, 68 newly installed, 0 to remove and 23 not upgraded.
Need to get 36.1 MB of archives.
After this operation, 116 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-bzXTNQ/apt_archive ./ sbuild-build-depends-lumpy-sv-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [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 libssl1.1 armhf 1.1.1h-1 [1271 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.6-1 [752 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.6-1 [1552 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.6-1 [37.7 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.6-1 [1654 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.6-1 [422 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.6-1 [20.9 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.6-1 [64.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
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Get:30 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.2-1 [1176 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.1 [578 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.6-1 [78.4 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.6-1 [145 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20201102 [99.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7 [133 kB]
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Get:48 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-3 [63.0 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.72.0-1 [371 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-6 [20.3 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-6 [23.7 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libgzstream0 armhf 1.5+dfsg-5 [6268 B]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libgzstream-dev armhf 1.5+dfsg-5 [6728 B]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20200918-1 [79.5 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libsqlite3-dev armhf 3.33.0-1 [847 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1h-1 [1573 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf python3-pysam armhf 0.15.4+ds-3 [1589 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.11-1 [502 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up autotools-dev (20180224.1) ...
Setting up libsqlite3-dev:armhf (3.33.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20200918-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-7) ...
Setting up libssl-dev:armhf (1.1.1h-1) ...
Setting up autopoint (0.19.8.1-10) ...
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Setting up libpython3-stdlib:armhf (3.8.6-1) ...
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Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
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Setting up python3 (3.8.6-1) ...
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Setting up libbamtools-dev:armhf (2.5.1+dfsg-7) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
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Setting up groff-base (1.22.4-5) ...
Setting up python3-lib2to3 (3.8.6-1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up samtools (1.11-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
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Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-lumpy-sv-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc1-2 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-python_4.20201102 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-13+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 krb5-locales_1.17-10 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbamtools-dev_2.5.1+dfsg-7 libbamtools2.5.1_2.5.1+dfsg-7 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbrotli1_1.0.9-2 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-13+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4-gnutls-dev_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfastahack-dev_1.0.0+dfsg-6 libfastahack0_1.0.0+dfsg-6 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libgzstream-dev_1.5+dfsg-5 libgzstream0_1.5+dfsg-5 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.53+dfsg-1+rpi1 libldap-common_2.4.53+dfsg-1+rpi1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 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-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.1 libpython3-stdlib_3.8.6-1 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libsqlite3-dev_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1h-1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.4-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.4-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 python3_3.8.6-1 python3-distutils_3.8.6-1 python3-lib2to3_3.8.6-1 python3-minimal_3.8.6-1 python3-pysam_0.15.4+ds-3 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-lumpy-sv-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 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.1NLPxUY7/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 6 06:20:33 2020 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./lumpy-sv_0.3.1+dfsg-4.dsc
dpkg-source: info: extracting lumpy-sv in /<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg
dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying lumpyexpress.config.patch
dpkg-source: info: applying fix_shebang.patch
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-56db5228-70c4-4de4-9417-8f50b71fcbc1
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package lumpy-sv
dpkg-buildpackage: info: source version 0.3.1+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
Cleaning up.
#rm -Rf /lib
#rm -f /src/api/*.o
#rm -f /src/api/internal/*.o
#rm -Rf /include
make[1]: Leaving directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch --with python3
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
[ -d bin ] || mkdir -p bin
[ -d bin ] || mkdir -p bin
[ -d obj ] || mkdir -p obj
make --no-print-directory -C src/filter/
cp scripts/lumpyexpress bin/lumpyexpress
[ -d bin ] || mkdir -p bin
> bin/lumpyexpress.config
Building lumpy:
cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
=========================================================
#make --no-print-directory --directory= api
for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \
echo "- Building in $dir"; \
make --no-print-directory -C $dir; \
echo ""; \
done
- Building in src/utils/bedFile
* compiling bedFile.cpp
cp src/filter/lumpy_filter bin
- Building in src/utils/version
* compiling version.cpp
- Building in src/utils/fileType
* compiling fileType.cpp
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
- Building in src/utils/genomeFile
* compiling genomeFile.cpp
genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
61 | long c2;
| ^~
- Building in src/utils/BamTools-Ancillary
* compiling BamAncillary.cpp
* compiling BamAncillary.cpp
- Building in src/utils/sequenceUtilities
* compiling sequenceUtils.cpp
- Building in src/lumpy
* compiling lumpy.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o
* compiling SV_Pair.cpp
* compiling SV_Evidence.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o
* compiling SV_BreakPoint.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o
SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’:
SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable]
266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr;
| ^~~~~~~~~~~~~~
SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable]
266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr;
| ^~~~~~~~~~~~~~
SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’:
SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
81 | for (j = 0; j < size; ++j) {
| ~~^~~~~~
* compiling SV_Bedpe.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o
SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’:
SV_BreakPoint.cpp:708:17: warning: ‘max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
708 | *trim_end = r;
| ^
SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector<SV_BreakPoint*>&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’:
SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1662 | CHR_POS abs_max_r = m_start_r + r_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized in this function [-Wmaybe-uninitialized]
1650 | CHR_POS abs_max_l = m_start_l + l_max_i;
| ^~~~~~~
* compiling SV_SplitRead.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o
* compiling SV_SplitReadReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o
SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’:
SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
538 | if ( min_mapping_quality < reader->min_mapping_threshold )
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* compiling SV_PairReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o
* compiling SV_BedpeReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o
* compiling SV_BamReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o
* compiling SV_InterChromBamReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o
SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins<SV_BreakPoint*>&)’:
SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long long unsigned int’} [-Wsign-compare]
208 | ( bam.Position < pos ) ) {
| ~~~~~~~~~~~~~^~~~~
* compiling SV_EvidenceReader.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o
* compiling SV_Tools.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o
* compiling SV_VcfVariant.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o
* compiling log_space.cpp
g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o
SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’:
SV_Tools.cpp:156:7: warning: ‘last’ may be used uninitialized in this function [-Wmaybe-uninitialized]
156 | *end = last;
| ~~~~~^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/bamtools/api/BamAlignment.h:17,
from /usr/include/bamtools/api/BamReader.h:14,
from /usr/include/bamtools/api/BamMultiReader.h:17,
from SV_Tools.cpp:16:
/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 UCSCElement<int>&}; _Tp = UCSCElement<int>; _Alloc = std::allocator<UCSCElement<int> >]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<UCSCElement<int>, std::allocator<UCSCElement<int> > >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/bamtools/api/BamAlignment.h:17,
from /usr/include/bamtools/api/BamReader.h:14,
from /usr/include/bamtools/api/BamMultiReader.h:17,
from SV_Tools.cpp:16:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int]’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<UCSCElement<int>*, std::vector<UCSCElement<int>, std::allocator<UCSCElement<int> > > >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
* linking lumpy
g++ -Wl,-z,relro -Wl,-z,now -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \
-L../utils//BamTools/lib/ -lbamtools \
-lz -L /<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \
-lgzstream -lz -lm -ldl -lpthread
make[1]: Leaving directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam
cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam
dh_install
rm -f debian/lumpy-sv*/usr/share/lumpy-sv/scripts/lumpyexpress.config
make[1]: Leaving directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
debian/rules override_dh_python3
make[1]: Entering directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
dh_python3 --shebang=/usr/bin/python3
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/bedpe_sort.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/check_sorting.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/cnvanator_to_bedpes.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_coverages.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/get_exclude_regions.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_merge.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/l_sort.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/pairend_distro.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/prob_bedpe_to_bedgraph.py
I: dh_python3 tools:114: replacing shebang in debian/lumpy-sv/usr/share/lumpy-sv/scripts/vcfToBedpe
make[1]: Leaving directory '/<<BUILDDIR>>/lumpy-sv-0.3.1+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 3873699 new size 3884954
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: debian/lumpy-sv/usr/bin/lumpy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-4_armhf.deb'.
dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../lumpy-sv_0.3.1+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-11-09T11:24:54Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
lumpy-sv_0.3.1+dfsg-4_armhf.changes:
------------------------------------
Format: 1.8
Date: Fri, 06 Nov 2020 11:30:49 +0530
Source: lumpy-sv
Binary: lumpy-sv lumpy-sv-dbgsym
Architecture: armhf
Version: 0.3.1+dfsg-4
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
lumpy-sv - general probabilistic framework for structural variant discovery
Closes: 973622
Changes:
lumpy-sv (0.3.1+dfsg-4) unstable; urgency=medium
.
* Link only in lumpy-sv binary (Closes: #973622)
Checksums-Sha1:
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e62301f744aa3ac5ec9cd8a698ea375fa5c52377cada6def6218f65b7b9f7e9a 6427 lumpy-sv_0.3.1+dfsg-4_armhf.buildinfo
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Files:
e37355f65c47586569b9405e307bc920 1967912 debug optional lumpy-sv-dbgsym_0.3.1+dfsg-4_armhf.deb
17c10793bced4d47ad720386c721a751 6427 science optional lumpy-sv_0.3.1+dfsg-4_armhf.buildinfo
f3d900051ff70f7c5919c4cf8fb46839 157776 science optional lumpy-sv_0.3.1+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
lumpy-sv-dbgsym_0.3.1+dfsg-4_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 1967912 bytes: control archive=652 bytes.
426 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: lumpy-sv-dbgsym
Source: lumpy-sv
Version: 0.3.1+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2030
Depends: lumpy-sv (= 0.3.1+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for lumpy-sv
Build-Ids: 7d6c05ef2720605f1e2abfed7c7a600fffde66b3 c67f654b330271cb5822585914cc58e41ceaa9b7
drwxr-xr-x root/root 0 2020-11-06 06:00 ./
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/lib/debug/
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drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1584 2020-11-06 06:00 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/lumpy-sv.debug
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-06 06:00 ./usr/share/doc/lumpy-sv-dbgsym -> lumpy-sv
lumpy-sv_0.3.1+dfsg-4_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 157776 bytes: control archive=1996 bytes.
34 bytes, 1 lines conffiles
847 bytes, 15 lines control
2057 bytes, 28 lines md5sums
279 bytes, 12 lines * postinst #!/bin/sh
390 bytes, 12 lines * prerm #!/bin/sh
Package: lumpy-sv
Version: 0.3.1+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 537
Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgzstream0 (>= 1.5+dfsg), libhts3 (>= 1.10), libstdc++6 (>= 5.2), python3:any, samblaster, samtools, python3, python3-pysam, python3-numpy, bamkit
Recommends: sambamba
Section: science
Priority: optional
Homepage: https://github.com/arq5x/lumpy-sv
Description: general probabilistic framework for structural variant discovery
LUMPY, a novel SV discovery framework that naturally integrates multiple
SV signals jointly across multiple samples. LUMPY yields improved
sensitivity, especially when SV signal is reduced owing to either low
coverage data or low intra-sample variant allele frequency.
drwxr-xr-x root/root 0 2020-11-06 06:00 ./
drwxr-xr-x root/root 0 2020-11-06 06:00 ./etc/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./etc/lumpy-sv/
-rw-r--r-- root/root 380 2020-11-05 19:45 ./etc/lumpy-sv/lumpyexpress.config
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/bin/
-rwxr-xr-x root/root 378388 2020-11-06 06:00 ./usr/bin/lumpy
-rwxr-xr-x root/root 9900 2020-11-06 06:00 ./usr/bin/lumpy_filter
-rwxr-xr-x root/root 17464 2020-11-06 06:00 ./usr/bin/lumpyexpress
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/doc/lumpy-sv/
-rw-r--r-- root/root 4503 2019-04-16 17:13 ./usr/share/doc/lumpy-sv/README.md.gz
-rw-r--r-- root/root 606 2020-11-06 06:00 ./usr/share/doc/lumpy-sv/changelog.Debian.gz
-rw-r--r-- root/root 2725 2020-11-06 05:58 ./usr/share/doc/lumpy-sv/copyright
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/lumpy-sv/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/
-rwxr-xr-x root/root 931 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/bedpe_sort.py
-rwxr-xr-x root/root 1764 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/check_sorting.py
-rwxr-xr-x root/root 2612 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/cnvanator_to_bedpes.py
-rw-r--r-- root/root 739 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/extract-sites.py
-rwxr-xr-x root/root 6216 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
-rwxr-xr-x root/root 1819 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/get_coverages.py
-rwxr-xr-x root/root 766 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/get_exclude_regions.py
-rw-r--r-- root/root 10926 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/l_bp.py
-rwxr-xr-x root/root 22140 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/l_merge.py
-rwxr-xr-x root/root 1984 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/l_sort.py
-rwxr-xr-x root/root 7592 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/lumpy_smooth
-rwxr-xr-x root/root 17464 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/lumpyexpress
lrwxrwxrwx root/root 0 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/lumpyexpress.config -> /etc/lumpy-sv/lumpyexpress.config
-rwxr-xr-x root/root 3510 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/pairend_distro.py
-rw-r--r-- root/root 2116 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/par-svtyper.sh
-rwxr-xr-x root/root 1313 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/prob_bedpe_to_bedgraph.py
-rwxr-xr-x root/root 745 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/run_histo.sh
-rwxr-xr-x root/root 1521 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/split_unmapped_to_fasta.pl
-rwxr-xr-x root/root 16316 2020-11-06 06:00 ./usr/share/lumpy-sv/scripts/vcfToBedpe
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/man/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/man/man1/
-rw-r--r-- root/root 882 2020-11-06 06:00 ./usr/share/man/man1/lumpy.1.gz
-rw-r--r-- root/root 328 2020-11-06 06:00 ./usr/share/man/man1/lumpy_filter.1.gz
-rw-r--r-- root/root 728 2020-11-06 06:00 ./usr/share/man/man1/lumpyexpress.1.gz
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/python3/
drwxr-xr-x root/root 0 2020-11-06 06:00 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root 137 2020-11-06 06:00 ./usr/share/python3/runtime.d/lumpy-sv.rtupdate
+------------------------------------------------------------------------------+
| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 377128
Build-Time: 356
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 329
Job: lumpy-sv_0.3.1+dfsg-4
Machine Architecture: armhf
Package: lumpy-sv
Package-Time: 771
Source-Version: 0.3.1+dfsg-4
Space: 377128
Status: successful
Version: 0.3.1+dfsg-4
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Finished at 2020-11-09T11:24:54Z
Build needed 00:12:51, 377128k disc space