lumpy-sv →
0.3.1+dfsg-5 →
armhf → 2021-01-15 13:01:33
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| lumpy-sv 0.3.1+dfsg-5 (armhf) Fri, 15 Jan 2021 12:54:52 +0000 |
+==============================================================================+
Package: lumpy-sv
Version: 0.3.1+dfsg-5
Source Version: 0.3.1+dfsg-5
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-f7ce16c9-254a-4570-81ae-80b1d9377c20' 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 11s (2323 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-5 (dsc) [2271 B]
Get:2 http://172.17.0.1/private bullseye-staging/main lumpy-sv 0.3.1+dfsg-5 (tar) [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main lumpy-sv 0.3.1+dfsg-5 (diff) [39.2 MB]
Fetched 39.3 MB in 7s (5704 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/lumpy-sv-dgLo8R/lumpy-sv-0.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-dgLo8R' 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-QBaO9u/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-QBaO9u/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-QBaO9u/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3750 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 66 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-QBaO9u/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 (56.3 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 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-QBaO9u/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-QBaO9u/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QBaO9u/apt_archive ./ Packages [644 B]
Fetched 2544 B in 1s (4050 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 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 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 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libfastahack-dev libfastahack0
libfile-stripnondeterminism-perl libgnutls30 libgzstream-dev libgzstream0
libhts-dev libhts3 libicu67 liblzma-dev liblzma5 libmagic-mgc libmagic1
libncurses6 libncursesw6 libnghttp2-14 libpipeline1 libpsl5
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libsqlite3-dev libssh2-1 libssl-dev libssl1.1
libsub-override-perl libtinfo6 libtool libuchardet0 libxml2 m4 mailcap
man-db media-types mime-support po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3-pysam python3.9 python3.9-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 gnutls-bin 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
python3.9-venv python3.9-doc binfmt-support cwltool
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl 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 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1 libfastahack-dev libfastahack0
libfile-stripnondeterminism-perl libgzstream-dev libgzstream0 libhts-dev
libhts3 libicu67 liblzma-dev libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librtmp1 libsigsegv2 libsqlite3-dev libssh2-1 libssl-dev
libsub-override-perl libtool libuchardet0 libxml2 m4 mailcap man-db
media-types mime-support po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3-pysam python3.9 python3.9-minimal
samtools sbuild-build-depends-lumpy-sv-dummy zlib1g-dev
The following packages will be upgraded:
libgnutls30 liblzma5 libncursesw6 libssl1.1 libtinfo6
5 upgraded, 68 newly installed, 0 to remove and 61 not upgraded.
Need to get 36.8 MB of archives.
After this operation, 112 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QBaO9u/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 1.1.1i-1 [1272 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1-1+rpi1 [789 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 python3.9-minimal armhf 3.9.1-1+rpi1 [1625 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.1-1 [37.8 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf media-types all 1.1.0 [19.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf mailcap all 3.68 [31.6 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf liblzma5 armhf 5.2.5-1.0 [158 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20201114-2 [328 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20201114-2 [105 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.1-1+rpi1 [1654 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.1-1+rpi1 [461 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.1-1 [21.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.1-1 [64.1 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libgnutls30 armhf 3.7.0-5 [1275 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-3 [170 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-3 [32.4 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-3 [509 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.1 [188 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-3 [162 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20201015-2 [162 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-5 [8288 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-3 [1214 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.1 [1010 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.9.1-2 [77.2 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.9.1-2 [143 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20201102 [99.3 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7+b1 [135 kB]
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Get:52 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1 [301 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1 [375 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
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Get:61 http://172.17.0.1/private bullseye-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-7 [23.9 kB]
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Get:63 http://172.17.0.1/private bullseye-staging/main armhf libgzstream0 armhf 1.5+dfsg-5 [6268 B]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libgzstream-dev armhf 1.5+dfsg-5 [6728 B]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libsqlite3-dev armhf 3.34.0-1 [852 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1i-1 [1575 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf python3-pysam armhf 0.15.4+ds-3+b1 [1344 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.11-1 [502 kB]
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
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 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-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+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 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.18.3-4 libacl1_2.2.53-8 libapt-pkg6.0_2.1.12 libarchive-zip-perl_1.68-1 libasan6_10.2.1-1+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1+b1 libbamtools-dev_2.5.1+dfsg-7+b1 libbamtools2.5.1_2.5.1+dfsg-7+b1 libbinutils_2.35.1-5+rpi1 libblkid1_2.36.1-2 libbrotli1_1.0.9-2+b1 libbz2-1.0_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 libexpat1_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfastahack-dev_1.0.0+dfsg-7 libfastahack0_1.0.0+dfsg-7 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 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 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_67.1-5 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 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 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 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-1+rpi1 libpython3.9-stdlib_3.9.1-1+rpi1 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 libsqlite3-dev_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-2 libssl-dev_1.1.1i-1 libssl1.1_1.1.1i-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+20201114-2 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 mailcap_3.68 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_1.1.0 mime-support_3.66 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 python3_3.9.1-1 python3-distutils_3.9.1-2 python3-lib2to3_3.9.1-2 python3-minimal_3.9.1-1 python3-pysam_0.15.4+ds-3+b1 python3.9_3.9.1-1+rpi1 python3.9-minimal_3.9.1-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 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_1.32+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.oXpoqlV1/trustedkeys.kbx': General error
gpgv: Signature made Wed Jan 13 09:54:42 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 ./lumpy-sv_0.3.1+dfsg-5.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-5.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 disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-f7ce16c9-254a-4570-81ae-80b1d9377c20
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package lumpy-sv
dpkg-buildpackage: info: source version 0.3.1+dfsg-5
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
make --no-print-directory -C src/filter/
cp scripts/lumpyexpress bin/lumpyexpress
cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
[ -d obj ] || mkdir -p obj
> bin/lumpyexpress.config
[ -d bin ] || mkdir -p bin
Building lumpy:
=========================================================
#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
* compiling SV_Pair.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
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
* 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_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
* 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
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_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_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 3873708 new size 3885059
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-5_armhf.deb'.
dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../lumpy-sv_0.3.1+dfsg-5_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)
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Build finished at 2021-01-15T13:01:27Z
Finished
--------
I: Built successfully
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| Changes |
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lumpy-sv_0.3.1+dfsg-5_armhf.changes:
------------------------------------
Format: 1.8
Date: Wed, 13 Jan 2021 10:34:36 +0100
Source: lumpy-sv
Binary: lumpy-sv lumpy-sv-dbgsym
Architecture: armhf
Version: 0.3.1+dfsg-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
lumpy-sv - general probabilistic framework for structural variant discovery
Closes: 980005
Changes:
lumpy-sv (0.3.1+dfsg-5) unstable; urgency=medium
.
* Fix configure patch according to a hint of Ken Yamaguchi
Closes: #980005
* Standards-Version: 4.5.1 (routine-update)
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
lumpy-sv-dbgsym_0.3.1+dfsg-5_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 1968076 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-5
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-5)
Section: debug
Priority: optional
Description: debug symbols for lumpy-sv
Build-Ids: 06a23e46a117762a69fc442ef823883bb3432932 d2dd38f0f1935675a80c8bd892195953f5fa48b9
drwxr-xr-x root/root 0 2021-01-13 09:34 ./
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 2050548 2021-01-13 09:34 ./usr/lib/debug/.build-id/06/a23e46a117762a69fc442ef823883bb3432932.debug
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/debug/.build-id/d2/
-rw-r--r-- root/root 11484 2021-01-13 09:34 ./usr/lib/debug/.build-id/d2/dd38f0f1935675a80c8bd892195953f5fa48b9.debug
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1580 2021-01-13 09:34 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/lumpy-sv.debug
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-01-13 09:34 ./usr/share/doc/lumpy-sv-dbgsym -> lumpy-sv
lumpy-sv_0.3.1+dfsg-5_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 157988 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-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 541
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 2021-01-13 09:34 ./
drwxr-xr-x root/root 0 2021-01-13 09:34 ./etc/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./etc/lumpy-sv/
-rw-r--r-- root/root 380 2021-01-13 09:34 ./etc/lumpy-sv/lumpyexpress.config
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/bin/
-rwxr-xr-x root/root 382484 2021-01-13 09:34 ./usr/bin/lumpy
-rwxr-xr-x root/root 9900 2021-01-13 09:34 ./usr/bin/lumpy_filter
-rwxr-xr-x root/root 17556 2021-01-13 09:34 ./usr/bin/lumpyexpress
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./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 691 2021-01-13 09:34 ./usr/share/doc/lumpy-sv/changelog.Debian.gz
-rw-r--r-- root/root 2725 2021-01-13 09:34 ./usr/share/doc/lumpy-sv/copyright
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/lumpy-sv/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/
-rwxr-xr-x root/root 931 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/bedpe_sort.py
-rwxr-xr-x root/root 1764 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/check_sorting.py
-rwxr-xr-x root/root 2612 2021-01-13 09:34 ./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 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
-rwxr-xr-x root/root 1819 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/get_coverages.py
-rwxr-xr-x root/root 766 2021-01-13 09:34 ./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 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/l_merge.py
-rwxr-xr-x root/root 1984 2021-01-13 09:34 ./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 17556 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/lumpyexpress
lrwxrwxrwx root/root 0 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/lumpyexpress.config -> /etc/lumpy-sv/lumpyexpress.config
-rwxr-xr-x root/root 3510 2021-01-13 09:34 ./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 2021-01-13 09:34 ./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 2021-01-13 09:34 ./usr/share/lumpy-sv/scripts/vcfToBedpe
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/man/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/man/man1/
-rw-r--r-- root/root 882 2021-01-13 09:34 ./usr/share/man/man1/lumpy.1.gz
-rw-r--r-- root/root 328 2021-01-13 09:34 ./usr/share/man/man1/lumpy_filter.1.gz
-rw-r--r-- root/root 728 2021-01-13 09:34 ./usr/share/man/man1/lumpyexpress.1.gz
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/python3/
drwxr-xr-x root/root 0 2021-01-13 09:34 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root 137 2021-01-13 09:34 ./usr/share/python3/runtime.d/lumpy-sv.rtupdate
+------------------------------------------------------------------------------+
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| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 377132
Build-Time: 125
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 230
Job: lumpy-sv_0.3.1+dfsg-5
Machine Architecture: armhf
Package: lumpy-sv
Package-Time: 395
Source-Version: 0.3.1+dfsg-5
Space: 377132
Status: successful
Version: 0.3.1+dfsg-5
--------------------------------------------------------------------------------
Finished at 2021-01-15T13:01:27Z
Build needed 00:06:35, 377132k disk space