lumpy-sv →
0.3.1+dfsg-6+b9 →
armhf → 2022-08-25 22:44:14
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| lumpy-sv 0.3.1+dfsg-6+b9 (armhf) Thu, 25 Aug 2022 22:34:34 +0000 |
+==============================================================================+
Package: lumpy-sv
Version: 0.3.1+dfsg-6+b9
Source Version: 0.3.1+dfsg-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-4a68e85c-d061-4882-89b2-3b1b23e853b4' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.2 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.1 MB]
Fetched 27.4 MB in 12s (2205 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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://172.17.4.1/private bookworm-staging/main lumpy-sv 0.3.1+dfsg-6 (dsc) [2269 B]
Get:2 http://172.17.4.1/private bookworm-staging/main lumpy-sv 0.3.1+dfsg-6 (tar) [112 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main lumpy-sv 0.3.1+dfsg-6 (diff) [39.2 MB]
Fetched 39.3 MB in 5s (7879 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/lumpy-sv-pZQSZP/lumpy-sv-0.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-pZQSZP' 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-HXoFET/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-HXoFET/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-HXoFET/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-HXoFET/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3724 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:
krb5-locales libpam-cap 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 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (46.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12802 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-HXoFET/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-HXoFET/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ Packages [642 B]
Fetched 2542 B in 1s (4622 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 libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dmsetup dwz file gettext
gettext-base groff-base intltool-debian libapparmor1 libarchive-zip-perl
libargon2-1 libbamtools-dev libbamtools2.5.1 libbrotli1 libcryptsetup12
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libdevmapper1.02.1 libelf1 libexpat1 libfastahack-dev
libfastahack0 libfdisk1 libfile-stripnondeterminism-perl libgzstream-dev
libgzstream0 libhts-dev libhts3 libhtscodecs2 libicu71 libip4tc2 libjson-c5
libkmod2 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librtmp1 libsqlite3-dev libssh2-1 libssl-dev
libsub-override-perl libsystemd-shared libtool libuchardet0 libxml2 m4
man-db media-types po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3-pysam python3.10 python3.10-minimal samtools systemd
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-tomli python3-installer 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
python3.10-venv python3.10-doc binfmt-support cwltool systemd-container
systemd-homed systemd-userdbd systemd-boot libfido2-1 libtss2-esys-3.0.2-0
libtss2-mu0 libtss2-rc0 policykit-1
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl default-dbus-system-bus | dbus-system-bus
systemd-timesyncd | time-daemon
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dmsetup dwz file gettext
gettext-base groff-base intltool-debian libapparmor1 libarchive-zip-perl
libargon2-1 libbamtools-dev libbamtools2.5.1 libbrotli1 libcryptsetup12
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libdevmapper1.02.1 libelf1 libexpat1 libfastahack-dev
libfastahack0 libfdisk1 libfile-stripnondeterminism-perl libgzstream-dev
libgzstream0 libhts-dev libhts3 libhtscodecs2 libicu71 libip4tc2 libjson-c5
libkmod2 liblzma-dev libmagic-mgc libmagic1 libmpdec3 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librtmp1 libsqlite3-dev libssh2-1 libssl-dev
libsub-override-perl libsystemd-shared libtool libuchardet0 libxml2 m4
man-db media-types po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3-pysam python3.10 python3.10-minimal samtools
sbuild-build-depends-lumpy-sv-dummy systemd zlib1g-dev
0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded.
Need to get 40.8 MB of archives.
After this operation, 149 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HXoFET/apt_archive ./ sbuild-build-depends-lumpy-sv-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libargon2-1 armhf 0~20171227-0.3 [19.6 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf dmsetup armhf 2:1.02.185-1 [91.8 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libdevmapper1.02.1 armhf 2:1.02.185-1 [134 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libjson-c5 armhf 0.16-1 [40.0 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libcryptsetup12 armhf 2:2.5.0-2 [225 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libfdisk1 armhf 2.38.1-1 [237 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libkmod2 armhf 30+20220630-3 [51.8 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libapparmor1 armhf 3.0.7-1 [98.9 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libip4tc2 armhf 1.8.8-1 [32.9 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libsystemd-shared armhf 251.3-1+rpi1 [1526 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf systemd armhf 251.3-1+rpi1 [2985 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.6-1 [813 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.6-1 [1520 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.6-1 [1596 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.6-1 [545 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-2 [34.2 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-2 [1364 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-8 [171 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-8 [510 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.9 [195 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-8 [1219 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.9 [1070 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.6-1 [79.9 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.6-1 [141 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220819+rpi1 [114 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-10+b1 [135 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-10+b1 [178 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.48.0-2 [72.1 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.84.0-2 [315 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.84.0-2 [392 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.12-1 [60.5 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.12-1 [51.8 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-10 [23.9 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-10 [26.3 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-1 [6504 B]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-1 [6940 B]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.2.2-1 [53.1 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2+b1 [339 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2+b1 [4045 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.39.2-1 [896 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.5-2 [2116 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf python3-pysam armhf 0.17.0+ds-2+b1 [1834 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.13-4 [525 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up systemd (251.3-1+rpi1) ...
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Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target -> /lib/systemd/system/remote-fs.target.
Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service -> /lib/systemd/system/systemd-pstore.service.
Initializing machine ID from random generator.
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.38.90.20220713-2+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.1.0-7+rpi1 gcc-12_12.1.0-7+rpi1 libc6-dev_2.33-8+rpi1 libstdc++-12-dev_12.1.0-7+rpi1 libstdc++6_12.1.0-7+rpi1 linux-libc-dev_5.18.14-1+rpi1
Package versions: adduser_3.123 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-8 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.0 bash_5.1-6.1 binutils_2.38.90.20220713-2+rpi1 binutils-arm-linux-gnueabihf_2.38.90.20220713-2+rpi1 binutils-common_2.38.90.20220713-2+rpi1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_8.32-4.1 cpp_4:12.1.0-3+rpi1 cpp-12_12.1.0-7+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.9 debianutils_5.7-0.3 dh-autoreconf_20 dh-python_5.20220819+rpi1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.35-3 dmsetup_2:1.02.185-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.1.0-3+rpi1 g++-12_12.1.0-7+rpi1 gcc_4:12.1.0-3+rpi1 gcc-12_12.1.0-7+rpi1 gcc-12-base_12.1.0-7+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-8 gettext-base_0.21-8 gnupg_2.2.35-3 gnupg-l10n_2.2.35-3 gnupg-utils_2.2.35-3 gpg_2.2.35-3 gpg-agent_2.2.35-3 gpg-wks-client_2.2.35-3 gpg-wks-server_2.2.35-3 gpgconf_2.2.35-3 gpgsm_2.2.35-3 gpgv_2.2.35-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapparmor1_3.0.7-1 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.1.0-7+rpi1 libassuan0_2.5.5-4 libatomic1_12.1.0-7+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbamtools-dev_2.5.1+dfsg-10+b1 libbamtools2.5.1_2.5.1+dfsg-10+b1 libbinutils_2.38.90.20220713-2+rpi1 libblkid1_2.38.1-1 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.33-8+rpi1 libc-dev-bin_2.33-8+rpi1 libc6_2.33-8+rpi1 libc6-dev_2.33-8+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.1.0-7+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 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libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1 libsqlite3-0_3.39.2-1 libsqlite3-dev_3.39.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.5-2 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libstdc++-12-dev_12.1.0-7+rpi1 libstdc++6_12.1.0-7+rpi1 libsub-override-perl_0.09-3 libsystemd-shared_251.3-1+rpi1 libsystemd0_251.3-1+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.1.0-7+rpi1 libuchardet0_0.0.7-1 libudev1_251.3-1+rpi1 libunistring2_1.0-1 libuuid1_2.38.1-1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.14-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-2 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38.1-1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-distutils_3.10.6-1 python3-lib2to3_3.10.6-1 python3-minimal_3.10.6-1 python3-pysam_0.17.0+ds-2+b1 python3.10_3.10.6-1 python3.10-minimal_3.10.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 samtools_1.13-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-lumpy-sv-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 systemd_251.3-1+rpi1 sysvinit-utils_3.04-1 tar_1.34+dfsg-1 tzdata_2022c-1 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.WxwpB2Jw/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 15 05:26:01 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./lumpy-sv_0.3.1+dfsg-6.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-6.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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.3.1+dfsg-6+b9
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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-4a68e85c-d061-4882-89b2-3b1b23e853b4
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-6+b9
dpkg-buildpackage: info: source distribution bookworm-staging
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
make --no-print-directory -C src/filter/
cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
[ -d bin ] || mkdir -p bin
cp scripts/lumpyexpress bin/lumpyexpress
[ -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
In file included from bedFile.cpp:12:
bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
- Building in src/utils/version
* compiling version.cpp
- Building in src/utils/fileType
* compiling fileType.cpp
- Building in src/utils/bedFilePE
* compiling bedFilePE.cpp
In file included from bedFilePE.h:12,
from bedFilePE.cpp:15:
../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
- 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
In file included from BamAncillary.h:12,
from BamAncillary.cpp:12:
..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from BamAncillary.h:12,
from BamAncillary.cpp:12:
..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
- 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
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
In file included from SV_BreakPoint.h:19,
from SV_Evidence.h:22,
from SV_Evidence.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_BreakPoint.cpp:16:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from lumpy.cpp:20:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from SV_Pair.cpp:15:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
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) {
| ~~^~~~~~
In file included from SV_BreakPoint.h:19,
from SV_Evidence.h:22,
from lumpy.cpp:24:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_Pair.cpp:19:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
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;
| ^~~~~~~~~~~~~~
../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long long unsigned int]’:
../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string<char>; CHR_POS = long long unsigned int]’
SV_BreakPoint.cpp:1286:14: required from here
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
* 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
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from SV_Bedpe.cpp:14:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_BedpeReader.h:21,
from SV_Bedpe.cpp:17:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
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 [-Wmaybe-uninitialized]
1662 | CHR_POS abs_max_r = m_start_r + r_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here
1643 | unsigned int i, l_max_i, r_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized]
1650 | CHR_POS abs_max_l = m_start_l + l_max_i;
| ^~~~~~~
SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here
1643 | unsigned int i, l_max_i, r_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
In file included from SV_BreakPoint.h:19,
from SV_SplitReadReader.h:22,
from SV_SplitReadReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
from SV_SplitRead.cpp:15:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_SplitReadReader.h:22,
from SV_SplitRead.cpp:19:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_SplitRead.h:27,
from SV_SplitReadReader.cpp:16:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
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
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_PairReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
* 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
In file included from SV_BreakPoint.h:19,
from SV_Evidence.h:22,
from SV_Bedpe.h:18,
from SV_BedpeReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map<std::__cxx11::basic_string<char>, BamTools::BamAlignment>&, UCSCBins<SV_BreakPoint*>&, int, int, SV_SplitReadReader*)’:
SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
653 | free(new_split_read);
| ~~~~^~~~~~~~~~~~~~~~
SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’
641 | _reader);
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_BedpeReader.h:23,
from SV_Bedpe.h:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_BamReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_SplitRead.h:27,
from SV_BamReader.cpp:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
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_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
* 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
In file included from SV_EvidenceReader.h:20,
from SV_EvidenceReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_PairReader.h:22,
from SV_InterChromBamReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
from SV_SplitRead.h:27,
from SV_InterChromBamReader.cpp:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from SV_Tools.h:19,
from SV_Tools.cpp:24:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
* 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
In file included from SV_Tools.cpp:27:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
321 | for (register short i = 0; i < _binLevels; ++i) {
| ^
* 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
../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long long unsigned int]’:
../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string<char>; CHR_POS = long long unsigned int]’
SV_Tools.cpp:541:32: required from here
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
In file included from SV_BreakPoint.h:19,
from SV_VcfVariant.h:18,
from SV_VcfVariant.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
253 | for (register short i = 0; i < kBinLevels; ++i) {
| ^
SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’:
SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
156 | *end = last;
| ~~~~~^~~~~~
SV_Tools.cpp:143:13: note: ‘last’ was declared here
143 | int last;
| ^~~~
In file included from /usr/include/c++/12/vector:70,
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++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const UCSCElement<int>&}; _Tp = UCSCElement<int>; _Alloc = std::allocator<UCSCElement<int> >]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<UCSCElement<int>, std::allocator<UCSCElement<int> > >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = UCSCElement<int>; _Alloc = std::allocator<UCSCElement<int> >]’,
inlined from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int]’ at ../utils//UCSCBins/ucsc_bins.hpp:239:32:
/usr/include/c++/12/bits/stl_vector.h:1287:28: 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
1287 | _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
dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 4154642 new size 4166606
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -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-6+b9_armhf.deb'.
dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-6+b9_armhf.deb'.
dpkg-genbuildinfo --build=any -O../lumpy-sv_0.3.1+dfsg-6+b9_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../lumpy-sv_0.3.1+dfsg-6+b9_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 2022-08-25T22:44:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
lumpy-sv_0.3.1+dfsg-6+b9_armhf.changes:
---------------------------------------
Format: 1.8
Date: Fri, 15 Oct 2021 07:09:25 +0200
Source: lumpy-sv (0.3.1+dfsg-6)
Binary: lumpy-sv lumpy-sv-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 0.3.1+dfsg-6+b9
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
lumpy-sv - general probabilistic framework for structural variant discovery
Changes:
lumpy-sv (0.3.1+dfsg-6+b9) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Files:
612ead82efc17f491eee128871b6cb8f 2088088 debug optional lumpy-sv-dbgsym_0.3.1+dfsg-6+b9_armhf.deb
3eda1eb4eb6132799fc3c1635ecd6c40 7420 science optional lumpy-sv_0.3.1+dfsg-6+b9_armhf.buildinfo
4dff551ce763fead3a41a2263843baf0 159212 science optional lumpy-sv_0.3.1+dfsg-6+b9_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
lumpy-sv-dbgsym_0.3.1+dfsg-6+b9_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 2088088 bytes: control archive=656 bytes.
447 bytes, 12 lines control
300 bytes, 3 lines md5sums
Package: lumpy-sv-dbgsym
Source: lumpy-sv (0.3.1+dfsg-6)
Version: 0.3.1+dfsg-6+b9
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2132
Depends: lumpy-sv (= 0.3.1+dfsg-6+b9)
Section: debug
Priority: optional
Description: debug symbols for lumpy-sv
Build-Ids: 5e30e24742865952436fac0f3b8e3a3284364636 a8adf02db598f2d1594f2a171a707b13de73c3c0
drwxr-xr-x root/root 0 2021-10-15 05:09 ./
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/lib/debug/.build-id/5e/
-rw-r--r-- root/root 2155520 2021-10-15 05:09 ./usr/lib/debug/.build-id/5e/30e24742865952436fac0f3b8e3a3284364636.debug
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drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1640 2021-10-15 05:09 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/lumpy-sv.debug
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-15 05:09 ./usr/share/doc/lumpy-sv-dbgsym -> lumpy-sv
lumpy-sv_0.3.1+dfsg-6+b9_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 159212 bytes: control archive=2012 bytes.
34 bytes, 1 lines conffiles
881 bytes, 16 lines control
2140 bytes, 29 lines md5sums
301 bytes, 12 lines * postinst #!/bin/sh
376 bytes, 12 lines * prerm #!/bin/sh
Package: lumpy-sv
Source: lumpy-sv (0.3.1+dfsg-6)
Version: 0.3.1+dfsg-6+b9
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 611
Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.33), libgcc-s1 (>= 3.5), libgzstream0 (>= 1.5+dfsg), libhts3 (>= 1.10), libstdc++6 (>= 11), 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 2021-10-15 05:09 ./
drwxr-xr-x root/root 0 2021-10-15 05:09 ./etc/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./etc/lumpy-sv/
-rw-r--r-- root/root 380 2021-10-15 05:09 ./etc/lumpy-sv/lumpyexpress.config
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/bin/
-rwxr-xr-x root/root 394772 2021-10-15 05:09 ./usr/bin/lumpy
-rwxr-xr-x root/root 67244 2021-10-15 05:09 ./usr/bin/lumpy_filter
-rwxr-xr-x root/root 17556 2021-10-15 05:09 ./usr/bin/lumpyexpress
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./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 227 2021-10-15 05:09 ./usr/share/doc/lumpy-sv/changelog.Debian.armhf.gz
-rw-r--r-- root/root 786 2021-10-15 05:09 ./usr/share/doc/lumpy-sv/changelog.Debian.gz
-rw-r--r-- root/root 2725 2021-10-15 05:09 ./usr/share/doc/lumpy-sv/copyright
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/lumpy-sv/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/
drwxr-xr-x root/root 0 2019-04-16 17:13 ./usr/share/lumpy-sv/scripts/bamkit/
-rwxr-xr-x root/root 931 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/bedpe_sort.py
-rwxr-xr-x root/root 1764 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/check_sorting.py
-rwxr-xr-x root/root 2612 2021-10-15 05:09 ./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 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
-rwxr-xr-x root/root 1819 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/get_coverages.py
-rwxr-xr-x root/root 766 2021-10-15 05:09 ./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 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/l_merge.py
-rwxr-xr-x root/root 1984 2021-10-15 05:09 ./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 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/lumpyexpress
lrwxrwxrwx root/root 0 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/lumpyexpress.config -> /etc/lumpy-sv/lumpyexpress.config
-rwxr-xr-x root/root 3510 2021-10-15 05:09 ./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 2021-10-15 05:09 ./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 2021-10-15 05:09 ./usr/share/lumpy-sv/scripts/vcfToBedpe
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/man/man1/
-rw-r--r-- root/root 882 2021-10-15 05:09 ./usr/share/man/man1/lumpy.1.gz
-rw-r--r-- root/root 328 2021-10-15 05:09 ./usr/share/man/man1/lumpy_filter.1.gz
-rw-r--r-- root/root 728 2021-10-15 05:09 ./usr/share/man/man1/lumpyexpress.1.gz
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/python3/
drwxr-xr-x root/root 0 2021-10-15 05:09 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root 137 2021-10-15 05:09 ./usr/share/python3/runtime.d/lumpy-sv.rtupdate
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 375004
Build-Time: 136
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 396
Job: lumpy-sv_0.3.1+dfsg-6
Machine Architecture: armhf
Package: lumpy-sv
Package-Time: 574
Source-Version: 0.3.1+dfsg-6
Space: 375004
Status: successful
Version: 0.3.1+dfsg-6+b9
--------------------------------------------------------------------------------
Finished at 2022-08-25T22:44:08Z
Build needed 00:09:34, 375004k disk space