lumpy-sv →
0.3.1+dfsg-6+b3 →
armhf → 2022-08-23 00:15:08
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| lumpy-sv 0.3.1+dfsg-6+b3 (armhf) Tue, 23 Aug 2022 00:02:03 +0000 |
+==============================================================================+
Package: lumpy-sv
Version: 0.3.1+dfsg-6+b3
Source Version: 0.3.1+dfsg-6
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-b4650943-84a5-4b47-82db-b9b42fa1c07f' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-l4dcaH/resolver-QFmxTJ' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| 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 21s (1302 kB/s)
Reading package lists...
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 7s (5596 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/lumpy-sv-l4dcaH/lumpy-sv-0.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-l4dcaH' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| 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, build-essential, fakeroot
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, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [437 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [524 B]
Fetched 1918 B in 0s (22.1 kB/s)
Reading package lists...
Reading package lists...
Install main 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
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 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 libhtscodecs2 libicu71
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 libssl3
libsub-override-perl 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 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
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 bsdextrautils 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 libhtscodecs2 libicu71
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 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-main-dummy zlib1g-dev
The following packages will be upgraded:
libssl3
1 upgraded, 68 newly installed, 0 to remove and 10 not upgraded.
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Get:38 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-8 [1219 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
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Get:42 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.10.6-1 [79.9 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.10.6-1 [141 kB]
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Get:45 http://172.17.4.1/private bookworm-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-10+b1 [135 kB]
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Get:47 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.48.0-1 [72.1 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.84.0-2 [315 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.84.0-2 [392 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.12-1 [60.5 kB]
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Get:58 http://172.17.4.1/private bookworm-staging/main armhf libgzstream0 armhf 1.5+git20171107.9a20658-1 [6504 B]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libgzstream-dev armhf 1.5+git20171107.9a20658-1 [6940 B]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.2.2-1 [53.1 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2+b1 [339 kB]
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Get:65 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libsqlite3-dev armhf 3.39.2-1 [896 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.5-2 [2116 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf python3-pysam armhf 0.17.0+ds-2+b1 [1834 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf samtools armhf 1.13-4 [525 kB]
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.38.90.20220713-2+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_3.5.52 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 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.35-3 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 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 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 libctf-nobfd0_2.38.90.20220713-2+rpi1 libctf0_2.38.90.20220713-2+rpi1 libcurl3-gnutls_7.84.0-2 libcurl4-gnutls-dev_7.84.0-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.263 libdebhelper-perl_13.9 libdeflate-dev_1.12-1 libdeflate0_1.12-1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.29-1 libfastahack-dev_1.0.0+dfsg-10 libfastahack0_1.0.0+dfsg-10 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.1.0-7+rpi1 libgcc-s1_12.1.0-7+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.1.0-7+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libgzstream-dev_1.5+git20171107.9a20658-1 libgzstream0_1.5+git20171107.9a20658-1 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2+b1 libhts3_1.13+ds-2+b1 libhtscodecs2_1.2.2-1 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.12+dfsg-2 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2.1 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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-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sysvinit-utils_3.04-1 tar_1.34+dfsg-1 tzdata_2022a-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+b2 zlib1g-dev_1:1.2.11.dfsg-4+b2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: lumpy-sv
Binary: lumpy-sv, lumpy-sv-examples
Architecture: any all
Version: 0.3.1+dfsg-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Nilesh Patra <nilesh@debian.org>
Homepage: https://github.com/arq5x/lumpy-sv
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv
Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git
Testsuite: autopkgtest
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
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lumpy-sv deb science optional arch=any
lumpy-sv-examples deb science optional arch=all
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-----END PGP SIGNATURE-----
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig._72csFIO/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 /<<PKGBUILDDIR>>
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+b3
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=b1a4a50b076d45168d85858aa150e93f
JOURNAL_STREAM=8:26928
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-b4650943-84a5-4b47-82db-b9b42fa1c07f
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c57116
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package lumpy-sv
dpkg-buildpackage: info: source version 0.3.1+dfsg-6+b3
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 '/<<PKGBUILDDIR>>'
Cleaning up.
#rm -Rf /lib
#rm -f /src/api/*.o
#rm -f /src/api/internal/*.o
#rm -Rf /include
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
[ -d bin ] || mkdir -p bin
[ -d bin ] || mkdir -p bin
[ -d obj ] || mkdir -p obj
make --no-print-directory -C src/filter/
cp scripts/lumpyexpress bin/lumpyexpress
[ -d bin ] || mkdir -p bin
> bin/lumpyexpress.config
cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz
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 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) {
| ^
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 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) {
| ^
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) {
| ^
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) {
| ~~^~~~~~
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 ../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 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) {
| ^
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 )
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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) {
| ^
* 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
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) {
| ^
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 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_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 ../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_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) {
| ^
* 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 ../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_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_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) {
| ^
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) {
| ^
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) {
| ^
* 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) {
| ^
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 /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \
-lgzstream -lz -lm -ldl -lpthread
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
debian/rules override_dh_python3
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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+b3_armhf.deb'.
dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-6+b3_armhf.deb'.
dpkg-genbuildinfo --build=any -O../lumpy-sv_0.3.1+dfsg-6+b3_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../lumpy-sv_0.3.1+dfsg-6+b3_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 2022-08-23T00:14:55Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
lumpy-sv_0.3.1+dfsg-6+b3_armhf.changes:
---------------------------------------
Format: 1.8
Date: Tue, 23 Aug 2022 00:10:36 +0000
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+b3
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
lumpy-sv - general probabilistic framework for structural variant discovery
Changes:
lumpy-sv (0.3.1+dfsg-6+b3) 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:
c6f1498ec0268ab92936c20dbe31d6ff 2087864 debug optional lumpy-sv-dbgsym_0.3.1+dfsg-6+b3_armhf.deb
f16adca46f5d11ddfb9e695b3ec88c23 6972 science optional lumpy-sv_0.3.1+dfsg-6+b3_armhf.buildinfo
d01c1f5ec0680603ab0b62f1b57b2f67 159284 science optional lumpy-sv_0.3.1+dfsg-6+b3_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: lumpy-sv (0.3.1+dfsg-6)
Binary: lumpy-sv lumpy-sv-dbgsym
Architecture: armhf
Version: 0.3.1+dfsg-6+b3
Binary-Only-Changes:
lumpy-sv (0.3.1+dfsg-6+b3) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi4 based autobuilder <root@raspbian.org> Tue, 23 Aug 2022 00:10:36 +0000
Checksums-Md5:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 23 Aug 2022 00:14:53 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
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 (= 3.5.52),
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),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14-1),
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),
gettext (= 0.21-8),
gettext-base (= 0.21-8),
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),
libacl1 (= 2.3.1-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.1.0-7+rpi1),
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),
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),
libctf-nobfd0 (= 2.38.90.20220713-2+rpi1),
libctf0 (= 2.38.90.20220713-2+rpi1),
libcurl3-gnutls (= 7.84.0-2),
libcurl4-gnutls-dev (= 7.84.0-2),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.263),
libdebhelper-perl (= 13.9),
libdeflate-dev (= 1.12-1),
libdeflate0 (= 1.12-1),
libdpkg-perl (= 1.21.9+rpi1),
libelf1 (= 0.187-1),
libexpat1 (= 2.4.8-1),
libfastahack-dev (= 1.0.0+dfsg-10),
libfastahack0 (= 1.0.0+dfsg-10),
libffi8 (= 3.4.2-4),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libgcc-12-dev (= 12.1.0-7+rpi1),
libgcc-s1 (= 12.1.0-7+rpi1),
libgcrypt20 (= 1.10.1-2+b2),
libgdbm-compat4 (= 1.23-1),
libgdbm6 (= 1.23-1),
libgmp10 (= 2:6.2.1+dfsg1-1),
libgnutls30 (= 3.7.7-2),
libgomp1 (= 12.1.0-7+rpi1),
libgpg-error0 (= 1.45-2),
libgssapi-krb5-2 (= 1.20-1),
libgzstream-dev (= 1.5+git20171107.9a20658-1),
libgzstream0 (= 1.5+git20171107.9a20658-1),
libhogweed6 (= 3.7.3-1),
libhts-dev (= 1.13+ds-2+b1),
libhts3 (= 1.13+ds-2+b1),
libhtscodecs2 (= 1.2.2-1),
libicu71 (= 71.1-3),
libidn2-0 (= 2.3.3-1),
libisl23 (= 0.25-1),
libk5crypto3 (= 1.20-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20-1),
libkrb5support0 (= 1.20-1),
libldap-2.5-0 (= 2.5.12+dfsg-2),
liblz4-1 (= 1.9.3-2),
liblzma-dev (= 5.2.5-2.1),
liblzma5 (= 5.2.5-2.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmount1 (= 2.38.1-1),
libmpc3 (= 1.2.1-2),
libmpdec3 (= 2.5.1-2+rpi1),
libmpfr6 (= 4.1.0-3),
libncurses6 (= 6.3+20220423-2),
libncursesw6 (= 6.3+20220423-2),
libnettle8 (= 3.7.3-1),
libnghttp2-14 (= 1.48.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.24.1-1),
libpam-modules (= 1.4.0-13),
libpam-modules-bin (= 1.4.0-13),
libpam-runtime (= 1.4.0-13),
libpam0g (= 1.4.0-13),
libpcre2-8-0 (= 10.40-1+b2),
libpcre3 (= 2:8.39-14),
libperl5.34 (= 5.34.0-5),
libpipeline1 (= 1.5.6-2),
libpsl5 (= 0.21.0-1.2),
libpython3-stdlib (= 3.10.5-3),
libpython3.10-minimal (= 3.10.6-1),
libpython3.10-stdlib (= 3.10.6-1),
libreadline8 (= 8.1.2-1.2),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg-6+b1),
libsasl2-modules-db (= 2.1.28+dfsg-6+b1),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsmartcols1 (= 2.38.1-1),
libsqlite3-0 (= 3.39.2-1),
libsqlite3-dev (= 3.39.2-1),
libssh2-1 (= 1.10.0-3+b1),
libssl-dev (= 3.0.5-2),
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),
libsystemd0 (= 251.3-1+rpi1),
libtasn1-6 (= 4.18.0-4),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.2-2.1),
libtirpc-dev (= 1.3.2-2.1),
libtirpc3 (= 1.3.2-2.1),
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),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 5.18.14-1+rpi1),
login (= 1:4.11.1+dfsg1-2),
lsb-base (= 11.2+rpi1),
m4 (= 1.4.19-1),
make (= 4.3-4.1),
man-db (= 2.10.2-1),
mawk (= 1.3.4.20200120-3.1),
media-types (= 8.0.0),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
patch (= 2.7.6-7),
perl (= 5.34.0-5),
perl-base (= 5.34.0-5),
perl-modules-5.34 (= 5.34.0-5),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.10.5-3),
python3-distutils (= 3.10.6-1),
python3-lib2to3 (= 3.10.6-1),
python3-minimal (= 3.10.5-3),
python3-pysam (= 0.17.0+ds-2+b1),
python3.10 (= 3.10.6-1),
python3.10-minimal (= 3.10.6-1),
readline-common (= 8.1.2-1.2),
rpcsvc-proto (= 1.4.2-4),
samtools (= 1.13-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.30),
sysvinit-utils (= 3.04-1),
tar (= 1.34+dfsg-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+b2),
zlib1g-dev (= 1:1.2.11.dfsg-4+b2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1661213436"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
lumpy-sv-dbgsym_0.3.1+dfsg-6+b3_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 2087864 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+b3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2133
Depends: lumpy-sv (= 0.3.1+dfsg-6+b3)
Section: debug
Priority: optional
Description: debug symbols for lumpy-sv
Build-Ids: 6927499feddae6ba96465ff7915db4209101e519 e53f657146cfbf8b5e99c90ffdb64c447648e15c
drwxr-xr-x root/root 0 2022-08-23 00:10 ./
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/debug/.build-id/69/
-rw-r--r-- root/root 2155532 2022-08-23 00:10 ./usr/lib/debug/.build-id/69/27499feddae6ba96465ff7915db4209101e519.debug
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/debug/.build-id/e5/
-rw-r--r-- root/root 11976 2022-08-23 00:10 ./usr/lib/debug/.build-id/e5/3f657146cfbf8b5e99c90ffdb64c447648e15c.debug
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 1636 2022-08-23 00:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/lumpy-sv.debug
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-08-23 00:10 ./usr/share/doc/lumpy-sv-dbgsym -> lumpy-sv
lumpy-sv_0.3.1+dfsg-6+b3_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 159284 bytes: control archive=2020 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+b3
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 2022-08-23 00:10 ./
drwxr-xr-x root/root 0 2022-08-23 00:10 ./etc/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/bin/
-rwxr-xr-x root/root 394772 2022-08-23 00:10 ./usr/bin/lumpy
-rwxr-xr-x root/root 67244 2022-08-23 00:10 ./usr/bin/lumpy_filter
-rwxr-xr-x root/root 17556 2022-08-23 00:10 ./usr/bin/lumpyexpress
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./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 223 2022-08-23 00:10 ./usr/share/doc/lumpy-sv/changelog.Debian.armhf.gz
-rw-r--r-- root/root 786 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/share/lumpy-sv/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/bedpe_sort.py
-rwxr-xr-x root/root 1764 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/check_sorting.py
-rwxr-xr-x root/root 2612 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/extractSplitReads_BwaMem
-rwxr-xr-x root/root 1819 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/get_coverages.py
-rwxr-xr-x root/root 766 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/l_merge.py
-rwxr-xr-x root/root 1984 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/lumpyexpress
lrwxrwxrwx root/root 0 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/lumpyexpress.config -> /etc/lumpy-sv/lumpyexpress.config
-rwxr-xr-x root/root 3510 2022-08-23 00:10 ./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 2022-08-23 00:10 ./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 2022-08-23 00:10 ./usr/share/lumpy-sv/scripts/vcfToBedpe
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/man/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/man/man1/
-rw-r--r-- root/root 882 2022-08-23 00:10 ./usr/share/man/man1/lumpy.1.gz
-rw-r--r-- root/root 328 2022-08-23 00:10 ./usr/share/man/man1/lumpy_filter.1.gz
-rw-r--r-- root/root 728 2022-08-23 00:10 ./usr/share/man/man1/lumpyexpress.1.gz
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/python3/
drwxr-xr-x root/root 0 2022-08-23 00:10 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root 137 2022-08-23 00:10 ./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 Type: any
Build-Space: 375004
Build-Time: 258
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 435
Job: lumpy-sv_0.3.1+dfsg-6
Machine Architecture: armhf
Package: lumpy-sv
Package-Time: 772
Source-Version: 0.3.1+dfsg-6
Space: 375004
Status: successful
Version: 0.3.1+dfsg-6+b3
--------------------------------------------------------------------------------
Finished at 2022-08-23T00:14:55Z
Build needed 00:12:52, 375004k disk space