delly →
1.1.8-1 →
armhf → 2023-10-15 06:33:55
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| delly 1.1.8-1 (armhf) Sun, 15 Oct 2023 06:30:57 +0000 |
+==============================================================================+
Package: delly
Version: 1.1.8-1
Source Version: 1.1.8-1
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-4fdc4b70-51c7-4b54-9578-3f06c676545e' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/delly-kFhBYs/resolver-hFuUR9' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.8 MB]
Fetched 29.0 MB in 5s (5496 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-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: 'delly' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/delly.git
Please use:
git clone https://salsa.debian.org/med-team/delly.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3751 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main delly 1.1.8-1 (dsc) [2110 B]
Get:2 http://172.17.4.1/private trixie-staging/main delly 1.1.8-1 (tar) [3744 kB]
Get:3 http://172.17.4.1/private trixie-staging/main delly 1.1.8-1 (diff) [5244 B]
Fetched 3751 kB in 0s (7672 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/delly-kFhBYs/delly-1.1.8' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/delly-kFhBYs' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libboost-date-time-dev, libboost-program-options-dev, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libhts-dev, libbz2-dev, zlib1g-dev, chrpath, debhelper, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libboost-date-time-dev, libboost-program-options-dev, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libhts-dev, libbz2-dev, zlib1g-dev, chrpath, debhelper, 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
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [797 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [829 B]
Fetched 2235 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils chrpath
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
libblkid1 libboost-date-time-dev libboost-date-time1.74-dev
libboost-date-time1.74.0 libboost-filesystem-dev libboost-filesystem1.74-dev
libboost-filesystem1.74.0 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-program-options-dev
libboost-program-options1.74-dev libboost-program-options1.74.0
libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization1.74-dev
libboost-serialization1.74.0 libboost-system-dev libboost-system1.74-dev
libboost-system1.74.0 libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu-dev
libicu72 liblzma-dev libmagic-mgc libmagic1 libmount1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsmartcols1 libssh2-1 libsub-override-perl
libtool libuchardet0 libuuid1 libxml2 m4 man-db mount po-debconf
sensible-utils util-linux zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-graph1.74-dev libboost-graph-parallel1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev
libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev
libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev
libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcurl4-doc
libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev pkg-config icu-doc liblzma-doc cryptsetup-bin libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
nfs-common libmail-box-perl dosfstools kbd util-linux-extra
util-linux-locales
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
publicsuffix libltdl-dev uuid-runtime libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils chrpath debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl
libboost-date-time-dev libboost-date-time1.74-dev libboost-date-time1.74.0
libboost-filesystem-dev libboost-filesystem1.74-dev
libboost-filesystem1.74.0 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-program-options-dev
libboost-program-options1.74-dev libboost-program-options1.74.0
libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization1.74-dev
libboost-serialization1.74.0 libboost-system-dev libboost-system1.74-dev
libboost-system1.74.0 libboost1.74-dev libbrotli1 libbz2-dev libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu-dev
libicu72 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libpsl5 librtmp1 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2
m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils
zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
7 upgraded, 69 newly installed, 0 to remove and 20 not upgraded.
Need to get 48.4 MB of archives.
After this operation, 308 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-2.2 [86.0 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-2.2 [1107 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-2.2 [133 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-2.2 [144 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-2.2 [166 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-2.2 [101 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-2.2 [27.9 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-2 [1033 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-2.2 [80.6 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
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Get:17 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
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Get:33 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libboost1.74-dev armhf 1.74.0+ds1-23 [9511 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libboost-date-time1.74.0 armhf 1.74.0+ds1-23 [218 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization1.74.0 armhf 1.74.0+ds1-23 [296 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libboost-serialization1.74-dev armhf 1.74.0+ds1-23 [363 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libboost-date-time1.74-dev armhf 1.74.0+ds1-23 [227 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libboost-date-time-dev armhf 1.74.0.3+b4 [4604 B]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libboost-filesystem1.74.0 armhf 1.74.0+ds1-23 [250 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libboost-system1.74.0 armhf 1.74.0+ds1-23 [218 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libboost-system1.74-dev armhf 1.74.0+ds1-23 [219 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libboost-filesystem1.74-dev armhf 1.74.0+ds1-23 [261 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libboost-filesystem-dev armhf 1.74.0.3+b4 [4636 B]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-23 [421 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74-dev armhf 1.74.0+ds1-23 [526 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0+ds1-23 [236 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0+ds1-23 [245 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libboost-program-options1.74.0 armhf 1.74.0+ds1-23 [307 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libboost-program-options1.74-dev armhf 1.74.0+ds1-23 [345 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libboost-program-options-dev armhf 1.74.0.3+b4 [4616 B]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libboost-system-dev armhf 1.74.0.3+b4 [4744 B]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.56.0-1 [60.5 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.3.0-3 [351 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.3.0-3 [435 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.1-1 [61.6 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.17+ds-1 [374 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.4-0.1 [269 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.17+ds-1 [1507 kB]
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-2.2 bsdutils_1:2.39.2-2.2 build-essential_12.9 bzip2_1.0.8-5+b2 chrpath_0.16-2 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.6 debianutils_5.13 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+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_0.21-13 gettext-base_0.21-13 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-2 gzip_1.12-1 hostname_3.23+nmu1 icu-devtools_72.1-3 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.6-1 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.40-2+rpi2 libblkid1_2.39.2-2.2 libboost-date-time-dev_1.74.0.3+b4 libboost-date-time1.74-dev_1.74.0+ds1-23 libboost-date-time1.74.0_1.74.0+ds1-23 libboost-filesystem-dev_1.74.0.3+b4 libboost-filesystem1.74-dev_1.74.0+ds1-23 libboost-filesystem1.74.0_1.74.0+ds1-23 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0+ds1-23 libboost-iostreams1.74.0_1.74.0+ds1-23 libboost-program-options-dev_1.74.0.3+b4 libboost-program-options1.74-dev_1.74.0+ds1-23 libboost-program-options1.74.0_1.74.0+ds1-23 libboost-regex1.74-dev_1.74.0+ds1-23 libboost-regex1.74.0_1.74.0+ds1-23 libboost-serialization1.74-dev_1.74.0+ds1-23 libboost-serialization1.74.0_1.74.0+ds1-23 libboost-system-dev_1.74.0.3+b4 libboost-system1.74-dev_1.74.0+ds1-23 libboost-system1.74.0_1.74.0+ds1-23 libboost1.74-dev_1.74.0+ds1-23 libbrotli1_1.0.9-2+b3 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.36-9+rpi1+deb12u1 libc-dev-bin_2.36-9+rpi1+deb12u1 libc6_2.36-9+rpi1+deb12u1 libc6-dev_2.36-9+rpi1+deb12u1 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcc1-0_12.2.0-14+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.40-2+rpi2 libctf0_2.40-2+rpi2 libcurl3-gnutls_8.3.0-3 libcurl4-gnutls-dev_8.3.0-3 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270 libdebhelper-perl_13.11.6 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.21.22+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 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libpam0g_1.5.2-7 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsmartcols1_2.39.2-2.2 libsqlite3-0_3.43.1-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl3_3.0.11-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring5_1.1-2 libuuid1_2.39.2-2.2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-1 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20230808-1 mount_2.39.2-2.2 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-1 tar_1.34+dfsg-1.2 tzdata_2023c-10 usr-is-merged_37 util-linux_2.39.2-2.2 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: delly
Binary: delly
Architecture: any
Version: 1.1.8-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: https://github.com/dellytools/delly
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/delly
Vcs-Git: https://salsa.debian.org/med-team/delly.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libboost-date-time-dev, libboost-program-options-dev, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libhts-dev, libbz2-dev, zlib1g-dev, chrpath, debhelper
Package-List:
delly deb science optional arch=any
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Files:
d803b6a94d7f64c179b7feda0f25679c 3743720 delly_1.1.8.orig.tar.xz
d4a36fee1946cb9cca003d1109ccbf5c 5244 delly_1.1.8-1.debian.tar.xz
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gpgv: Signature made Thu Oct 12 14:54:17 2023 UTC
gpgv: using RSA key 2D65BC1EB9665A6E97F9730AB3F5945285219E1F
gpgv: issuer "rmb@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./delly_1.1.8-1.dsc: no acceptable signature found
dpkg-source: info: extracting delly in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking delly_1.1.8.orig.tar.xz
dpkg-source: info: unpacking delly_1.1.8-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying reproducible.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
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
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-4fdc4b70-51c7-4b54-9578-3f06c676545e
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package delly
dpkg-buildpackage: info: source version 1.1.8-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
if [ -r src/htslib/Makefile ]; then cd src/htslib && make clean; fi
rm -f src/delly src/delly.o
rm -f src/delly
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf src/dpe src/delly bin/delly
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- BUILT_PROGRAMS="src/delly" PARALLEL=1
make -j4 "INSTALL=install --strip-program=true" BUILT_PROGRAMS=src/delly PARALLEL=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -isystem /usr/include/htslib/ -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing -fpermissive -fopenmp -DOPENMP -O3 -fno-tree-vectorize -DNDEBUG src/delly.cpp src/edlib.cpp -o src/delly -Wl,-z,relro -Wl,-z,now -L/usr/include/htslib/ -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time -lhts -lz -llzma -lbz2 -Wl,-rpath,/usr/include/htslib/
In file included from src/util.h:15,
from src/delly.h:32,
from src/delly.cpp:18:
src/tags.h:76:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
76 | struct SortSVs : public std::binary_function<TSV, TSV, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from src/delly.cpp:3:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
src/util.h:61:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
61 | struct SortCNVs : public std::binary_function<TCNV, TCNV, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/delly.h:35:
src/coverage.h:51:31: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
51 | struct SortBp : public std::binary_function<TRecord, TRecord, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/shortpe.h:36,
from src/delly.h:38:
src/junction.h:37:40: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
37 | struct SortSRBamRecord : public std::binary_function<TSRBamRecord, TSRBamRecord, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
src/junction.h:80:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
80 | struct SortJunction : public std::binary_function<TJunction, TJunction, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/shortpe.h:37:
src/cluster.h:42:39: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
42 | struct SortBamRecords : public std::binary_function<TRecord, TRecord, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
src/cluster.h:71:40: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
71 | struct SortEdgeRecords : public std::binary_function<TRecord, TRecord, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/delly.cpp:21:
src/merge.h:68:34: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
68 | struct SortIScores : public std::binary_function<TRecord, TRecord, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/coral.h:17,
from src/delly.cpp:23:
src/scan.h:33:39: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
33 | struct SortScanWindow : public std::binary_function<TScanWindow, TScanWindow, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/coral.h:19:
src/cnv.h:42:41: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
42 | struct SortSVBreakpoint : public std::binary_function<TSVBp, TSVBp, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/pangenome.h:33,
from src/delly.cpp:26:
src/gfa.h:43:34: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
43 | struct SortLinks : public std::binary_function<TLink, TLink, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/pangenome.h:34:
src/gaf.h:41:40: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
41 | struct SortAlignRecord : public std::binary_function<TRecord, TRecord, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/delly.cpp:27:
src/markdup.h:62:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
62 | struct SortSVEvents : public std::binary_function<TSV, TSV, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/delly.cpp:28:
src/compvcf.h:65:41: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
65 | struct SortCompSVRecord : public std::binary_function<TSV, TSV, bool>
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from src/junction.h:16:
src/assemble.h: In instantiation of ‘void torali::consensusWfa(const TAlign&, std::string&) [with TAlign = boost::multi_array<char, 2>; std::string = std::__cxx11::basic_string<char>]’:
src/assemble.h:703:19: required from ‘int torali::msaWfa(const TConfig&, TSplitReadSet&, std::string&, const std::string&, const std::string&) [with TConfig = TeguaConfig; TSplitReadSet = std::vector<std::__cxx11::basic_string<char> >; std::string = std::__cxx11::basic_string<char>]’
src/assemble.h:866:12: required from ‘void torali::assemble(const TConfig&, const TValidRegion&, std::vector<StructuralVariantRecord>&, TSRStore&) [with TConfig = TeguaConfig; TValidRegion = std::vector<boost::icl::interval_set<unsigned int> >; TSRStore = std::vector<boost::unordered::unordered_map<std::pair<int, unsigned int>, std::vector<SeqSlice> > >]’
src/tegua.h:113:14: required from ‘int32_t torali::runTegua(TConfig&) [with TConfig = TeguaConfig; int32_t = int]’
src/tegua.h:383:19: required from here
src/assemble.h:273:17: warning: comparison of integer expressions of different signedness: ‘TAIndex’ {aka ‘int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type’ {aka ‘unsigned int’} [-Wsign-compare]
273 | if (j < readStart[i]) readStart[i] = j;
| ~~^~~~~~~~~~~~
src/assemble.h:274:17: warning: comparison of integer expressions of different signedness: ‘TAIndex’ {aka ‘int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type’ {aka ‘unsigned int’} [-Wsign-compare]
274 | if (j > readEnd[i]) readEnd[i] = j;
| ~~^~~~~~~~~~
src/assemble.h:284:16: warning: comparison of integer expressions of different signedness: ‘TAIndex’ {aka ‘int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type’ {aka ‘unsigned int’} [-Wsign-compare]
284 | if ((j >= readStart[i]) && (j <= readEnd[i])) {
| ~~~^~~~~~~~~~~~~~~~
src/assemble.h:284:39: warning: comparison of integer expressions of different signedness: ‘TAIndex’ {aka ‘int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<unsigned int>, unsigned int>::value_type’ {aka ‘unsigned int’} [-Wsign-compare]
284 | if ((j >= readStart[i]) && (j <= readEnd[i])) {
| ~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/string:50:
/usr/include/c++/12/bits/predefined_ops.h: In function ‘bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >; _Iterator2 = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >; _Compare = torali::SortCompSVRecord<torali::CompSVRecord>]’:
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
In file included from /usr/include/arm-linux-gnueabihf/c++/12/bits/c++allocator.h:33,
from /usr/include/c++/12/bits/allocator.h:46,
from /usr/include/c++/12/string:41:
In member function ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = char; _Args = {}; _Tp = char]’,
inlined from ‘typename std::enable_if<boost::detail::alloc_has_construct<void, A, T, Args ...>::value>::type boost::allocator_construct(A&, T*, Args&& ...) [with A = std::allocator<char>; T = char; Args = {}]’ at /usr/include/boost/core/allocator_access.hpp:432:16,
inlined from ‘void boost::alloc_construct_n(A&, T*, std::size_t) [with A = std::allocator<char>; T = char]’ at /usr/include/boost/core/alloc_construct.hpp:122:35,
inlined from ‘void boost::multi_array<T, NumDims, Allocator>::allocate_space() [with T = char; unsigned int NumDims = 2; Allocator = std::allocator<char>]’ at /usr/include/boost/multi_array.hpp:548:29,
inlined from ‘boost::multi_array<T, NumDims, Allocator>::multi_array(const Allocator&) [with T = char; unsigned int NumDims = 2; Allocator = std::allocator<char>]’ at /usr/include/boost/multi_array.hpp:156:19:
/usr/include/c++/12/bits/new_allocator.h:175:11: warning: ‘void* __builtin_memset(void*, int, unsigned int)’ offset 0 is out of the bounds [0, 0] [-Warray-bounds]
175 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from /usr/include/boost/move/algorithm.hpp:32,
from /usr/include/boost/move/move.hpp:32,
from /usr/include/boost/unordered/unordered_set.hpp:19,
from /usr/include/boost/unordered_set.hpp:17,
from /usr/include/boost/graph/adjacency_list.hpp:20,
from src/delly.h:8:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/boost/graph/adjacency_list.hpp:16:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const torali::CompSVRecord&}; _Tp = torali::CompSVRecord; _Alloc = std::allocator<torali::CompSVRecord>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<torali::CompSVRecord>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const torali::CNV&}; _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<torali::CNV>::iterator’ changed in GCC 7.1
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 = torali::CNV; _Alloc = std::allocator<torali::CNV>]’,
inlined from ‘void torali::parseVcfCNV(const TConfig&, bam_hdr_t*, std::vector<CNV>&) [with TConfig = CountDNAConfig]’ at src/cnv.h:549:16:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {torali::BpCNV}; _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<torali::BpCNV>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {torali::CNV}; _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<torali::CNV>::iterator’ changed in GCC 7.1
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {torali::CNV}; _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void torali::mergeCNVs(const TConfig&, std::vector<CNV>&, std::vector<CNV>&) [with TConfig = CountDNAConfig]’ at src/cnv.h:86:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’,
inlined from ‘void torali::mergeCNVs(const TConfig&, std::vector<CNV>&, std::vector<CNV>&) [with TConfig = CountDNAConfig]’ at src/cnv.h:88:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’,
inlined from ‘void torali::mergeCNVs(const TConfig&, std::vector<CNV>&, std::vector<CNV>&) [with TConfig = CountDNAConfig]’ at src/cnv.h:100:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<torali::SortCNVs<torali::CNV> >]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
In file included from /usr/include/c++/12/bits/stl_algo.h:60:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Distance = int; _Tp = torali::CompSVRecord; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’,
inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’ at /usr/include/c++/12/bits/stl_algo.h:1887:34,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38:
/usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
94 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
87 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
89 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
96 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {torali::BpCNV}; _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void torali::callCNVs(const TConfig&, const std::pair<unsigned int, unsigned int>&, const std::vector<short unsigned int>&, const std::vector<short unsigned int>&, const TGcBias&, const TCoverage&, const bam_hdr_t*, int32_t, std::vector<CNV>&) [with TConfig = CountDNAConfig; TGcBias = std::vector<GcBias>; TCoverage = std::vector<short unsigned int>]’ at src/cnv.h:366:38:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::BpCNV*, std::vector<torali::BpCNV> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {torali::BpCNV}; _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void torali::callCNVs(const TConfig&, const std::pair<unsigned int, unsigned int>&, const std::vector<short unsigned int>&, const std::vector<short unsigned int>&, const TGcBias&, const TCoverage&, const bam_hdr_t*, int32_t, std::vector<CNV>&) [with TConfig = CountDNAConfig; TGcBias = std::vector<GcBias>; TCoverage = std::vector<short unsigned int>]’ at src/cnv.h:396:35:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::BpCNV*, std::vector<torali::BpCNV> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {torali::BpCNV}; _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = torali::BpCNV; _Alloc = std::allocator<torali::BpCNV>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void torali::callCNVs(const TConfig&, const std::pair<unsigned int, unsigned int>&, const std::vector<short unsigned int>&, const std::vector<short unsigned int>&, const TGcBias&, const TCoverage&, const bam_hdr_t*, int32_t, std::vector<CNV>&) [with TConfig = CountDNAConfig; TGcBias = std::vector<GcBias>; TCoverage = std::vector<short unsigned int>]’ at src/cnv.h:417:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::BpCNV*, std::vector<torali::BpCNV> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {torali::CNV}; _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = torali::CNV; _Alloc = std::allocator<torali::CNV>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void torali::callCNVs(const TConfig&, const std::pair<unsigned int, unsigned int>&, const std::vector<short unsigned int>&, const std::vector<short unsigned int>&, const TGcBias&, const TCoverage&, const bam_hdr_t*, int32_t, std::vector<CNV>&) [with TConfig = CountDNAConfig; TGcBias = std::vector<GcBias>; TCoverage = std::vector<short unsigned int>]’ at src/cnv.h:474:16:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Distance = int; _Tp = torali::CNV; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘torali::BoLog<TPrecision>::BoLog() [with TPrecision = double]’ at src/bolog.h:18:89,
inlined from ‘void torali::vcfOutput(const TConfig&, const std::vector<Property>&, const TJunctionCountMap&, const TReadCountMap&, const TCountMap&) [with TConfig = Config; TStructuralVariantRecord = StructuralVariantRecord; TJunctionCountMap = std::vector<std::vector<JunctionCount> >; TReadCountMap = std::vector<std::vector<ReadCount> >; TCountMap = std::vector<std::vector<SpanningCount> >]’ at src/modvcf.h:325:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘torali::BoLog<TPrecision>::BoLog() [with TPrecision = double]’ at src/bolog.h:18:89,
inlined from ‘void torali::vcfOutput(const TConfig&, const std::vector<Property>&, const TJunctionCountMap&, const TReadCountMap&, const TCountMap&) [with TConfig = TeguaConfig; TStructuralVariantRecord = StructuralVariantRecord; TJunctionCountMap = std::vector<std::vector<JunctionCount> >; TReadCountMap = std::vector<std::vector<ReadCount> >; TCountMap = std::vector<std::vector<SpanningCount> >]’ at src/modvcf.h:325:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘torali::BoLog<TPrecision>::BoLog() [with TPrecision = double]’ at src/bolog.h:18:89,
inlined from ‘void torali::vcfOutput(const TConfig&, const std::vector<Property>&, const TJunctionCountMap&, const TReadCountMap&, const TCountMap&) [with TConfig = AsmConfig; TStructuralVariantRecord = StructuralVariantRecord; TJunctionCountMap = std::vector<std::vector<JunctionCount> >; TReadCountMap = std::vector<std::vector<ReadCount> >; TCountMap = std::vector<std::vector<SpanningCount> >]’ at src/modvcf.h:325:17:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’,
inlined from ‘int32_t torali::runAsm(TConfig&) [with TConfig = AsmConfig]’ at src/asmode.h:399:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: warning: ‘<anonymous>’ may be used uninitialized [-Wmaybe-uninitialized]
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘int32_t torali::runAsm(TConfig&) [with TConfig = AsmConfig]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: by argument 4 of type ‘const std::vector<torali::ReadCount>::value_type&’ {aka ‘const torali::ReadCount&’} to ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’ declared here
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from src/delly.cpp:24:
src/asmode.h:399:39: note: ‘<anonymous>’ declared here
399 | rcMap[file_c].resize(svs.size(), ReadCount());
| ^~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = torali::CompSVRecord; _Alloc = std::allocator<torali::CompSVRecord>]’,
inlined from ‘bool torali::_loadCompSVs(CompvcfConfig&, const std::string&, std::vector<CompSVRecord>&)’ at src/compvcf.h:325:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = torali::SortCompSVRecord<torali::CompSVRecord>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘int torali::compvcfRun(CompvcfConfig&)’ at src/compvcf.h:358:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = torali::SortCompSVRecord<torali::CompSVRecord>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘int torali::compvcfRun(CompvcfConfig&)’ at src/compvcf.h:358:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = torali::SortCompSVRecord<torali::CompSVRecord>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘int torali::compvcfRun(CompvcfConfig&)’ at src/compvcf.h:359:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCompSVRecord<torali::CompSVRecord> >]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<torali::CompSVRecord*, vector<torali::CompSVRecord> >; _Compare = torali::SortCompSVRecord<torali::CompSVRecord>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘int torali::compvcfRun(CompvcfConfig&)’ at src/compvcf.h:359:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CompSVRecord*, std::vector<torali::CompSVRecord> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’,
inlined from ‘void torali::annotateCoverage(TConfig&, TSampleLibrary&, TSVs&, TCoverageCount&, TCountMap&, TSpanMap&) [with TConfig = Config; TSampleLibrary = std::vector<LibraryInfo>; TSVs = std::vector<StructuralVariantRecord>; TCoverageCount = std::vector<std::vector<ReadCount> >; TCountMap = std::vector<std::vector<JunctionCount> >; TSpanMap = std::vector<std::vector<SpanningCount> >]’ at src/coverage.h:265:30:
/usr/include/c++/12/bits/stl_vector.h:1032:25: warning: ‘<anonymous>’ may be used uninitialized [-Wmaybe-uninitialized]
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘void torali::annotateCoverage(TConfig&, TSampleLibrary&, TSVs&, TCoverageCount&, TCountMap&, TSpanMap&) [with TConfig = Config; TSampleLibrary = std::vector<LibraryInfo>; TSVs = std::vector<StructuralVariantRecord>; TCoverageCount = std::vector<std::vector<ReadCount> >; TCountMap = std::vector<std::vector<JunctionCount> >; TSpanMap = std::vector<std::vector<SpanningCount> >]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: by argument 4 of type ‘const std::vector<torali::ReadCount>::value_type&’ {aka ‘const torali::ReadCount&’} to ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’ declared here
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
src/coverage.h:265:43: note: ‘<anonymous>’ declared here
265 | covCount[file_c].resize(svs.size(), TCovPair());
| ^~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’,
inlined from ‘int32_t torali::runTegua(TConfig&) [with TConfig = TeguaConfig]’ at src/tegua.h:166:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: warning: ‘<anonymous>’ may be used uninitialized [-Wmaybe-uninitialized]
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘int32_t torali::runTegua(TConfig&) [with TConfig = TeguaConfig]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: by argument 4 of type ‘const std::vector<torali::ReadCount>::value_type&’ {aka ‘const torali::ReadCount&’} to ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’ declared here
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from src/delly.cpp:22:
src/tegua.h:166:39: note: ‘<anonymous>’ declared here
166 | rcMap[file_c].resize(svs.size(), ReadCount());
| ^~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’,
inlined from ‘int32_t torali::runGraph(TConfig&) [with TConfig = GraphConfig]’ at src/pangenome.h:772:26:
/usr/include/c++/12/bits/stl_vector.h:1032:25: warning: ‘<anonymous>’ may be used uninitialized [-Wmaybe-uninitialized]
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘int32_t torali::runGraph(TConfig&) [with TConfig = GraphConfig]’:
/usr/include/c++/12/bits/vector.tcc:523:5: note: by argument 4 of type ‘const std::vector<torali::ReadCount>::value_type&’ {aka ‘const torali::ReadCount&’} to ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = torali::ReadCount; _Alloc = std::allocator<torali::ReadCount>]’ declared here
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
src/pangenome.h:772:39: note: ‘<anonymous>’ declared here
772 | rcMap[file_c].resize(svs.size(), ReadCount());
| ^~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = torali::SortCNVs<torali::CNV>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘int32_t torali::bamCount(const TConfig&, const LibraryInfo&, const std::vector<GcBias>&, const std::pair<unsigned int, unsigned int>&) [with TConfig = CountDNAConfig]’ at src/coral.h:433:9:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<torali::SortCNVs<torali::CNV> >]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<torali::CNV*, vector<torali::CNV> >; _Compare = torali::SortCNVs<torali::CNV>]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘int32_t torali::bamCount(const TConfig&, const LibraryInfo&, const std::vector<GcBias>&, const std::pair<unsigned int, unsigned int>&) [with TConfig = CountDNAConfig]’ at src/coral.h:433:9:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<torali::CNV*, std::vector<torali::CNV> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
chrpath -d src/delly
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# avoiding redundant compile of delly
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/delly/usr/bin/delly contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/delly/usr/bin/delly was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'delly-dbgsym' in '../delly-dbgsym_1.1.8-1_armhf.deb'.
dpkg-deb: building package 'delly' in '../delly_1.1.8-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../delly_1.1.8-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../delly_1.1.8-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-10-15T06:33:53Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
delly_1.1.8-1_armhf.changes:
----------------------------
Format: 1.8
Date: Thu, 12 Oct 2023 14:40:44 +0000
Source: delly
Binary: delly delly-dbgsym
Architecture: armhf
Version: 1.1.8-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Mohammed Bilal <rmb@debian.org>
Description:
delly - Structural variant discovery by read analysis
Changes:
delly (1.1.8-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.6.2 (routine-update)
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Files:
4c2fbf65d6dad886fd85ce417dcb36f7 6076116 debug optional delly-dbgsym_1.1.8-1_armhf.deb
464b79feca972089c3c6aa18393373e8 6645 science optional delly_1.1.8-1_armhf.buildinfo
bd58ed424785aaf2f149fdaadb4ca61a 304896 science optional delly_1.1.8-1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: delly
Binary: delly delly-dbgsym
Architecture: armhf
Version: 1.1.8-1
Checksums-Md5:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sun, 15 Oct 2023 06:33:53 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-13),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2.15-2),
binutils (= 2.40-2+rpi2),
binutils-arm-linux-gnueabihf (= 2.40-2+rpi2),
binutils-common (= 2.40-2+rpi2),
bsdextrautils (= 2.39.2-2.2),
bsdutils (= 1:2.39.2-2.2),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
chrpath (= 0.16-2),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-3+rpi1),
cpp-12 (= 12.2.0-14+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.6),
debianutils (= 5.13),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.8-4),
dpkg (= 1.21.22+rpi1),
dpkg-dev (= 1.21.22+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:12.2.0-3+rpi1),
g++-12 (= 12.2.0-14+rpi1),
gcc (= 4:12.2.0-3+rpi1),
gcc-12 (= 12.2.0-14+rpi1),
gcc-12-base (= 12.2.0-14+rpi1),
gettext (= 0.21-13),
gettext-base (= 0.21-13),
grep (= 3.11-3),
groff-base (= 1.23.0-2),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
icu-devtools (= 72.1-3),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-14+rpi1),
libatomic1 (= 12.2.0-14+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbinutils (= 2.40-2+rpi2),
libblkid1 (= 2.39.2-2.2),
libboost-date-time-dev (= 1.74.0.3+b4),
libboost-date-time1.74-dev (= 1.74.0+ds1-23),
libboost-date-time1.74.0 (= 1.74.0+ds1-23),
libboost-filesystem-dev (= 1.74.0.3+b4),
libboost-filesystem1.74-dev (= 1.74.0+ds1-23),
libboost-filesystem1.74.0 (= 1.74.0+ds1-23),
libboost-iostreams-dev (= 1.74.0.3+b4),
libboost-iostreams1.74-dev (= 1.74.0+ds1-23),
libboost-iostreams1.74.0 (= 1.74.0+ds1-23),
libboost-program-options-dev (= 1.74.0.3+b4),
libboost-program-options1.74-dev (= 1.74.0+ds1-23),
libboost-program-options1.74.0 (= 1.74.0+ds1-23),
libboost-regex1.74-dev (= 1.74.0+ds1-23),
libboost-regex1.74.0 (= 1.74.0+ds1-23),
libboost-serialization1.74-dev (= 1.74.0+ds1-23),
libboost-serialization1.74.0 (= 1.74.0+ds1-23),
libboost-system-dev (= 1.74.0.3+b4),
libboost-system1.74-dev (= 1.74.0+ds1-23),
libboost-system1.74.0 (= 1.74.0+ds1-23),
libboost1.74-dev (= 1.74.0+ds1-23),
libbrotli1 (= 1.0.9-2+b3),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.36-9+rpi1+deb12u1),
libc-dev-bin (= 2.36-9+rpi1+deb12u1),
libc6 (= 2.36-9+rpi1+deb12u1),
libc6-dev (= 2.36-9+rpi1+deb12u1),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 12.2.0-14+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.40-2+rpi2),
libctf0 (= 2.40-2+rpi2),
libcurl3-gnutls (= 8.3.0-3),
libcurl4-gnutls-dev (= 8.3.0-3),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.270),
libdebhelper-perl (= 13.11.6),
libdeflate-dev (= 1.18-1),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.21.22+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.2.0-14+rpi1),
libgcc-s1 (= 12.2.0-14+rpi1),
libgcrypt20 (= 1.10.2-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.1-4),
libgomp1 (= 12.2.0-14+rpi1),
libgpg-error0 (= 1.47-2),
libgssapi-krb5-2 (= 1.20.1-4),
libhogweed6 (= 3.9.1-2),
libhts-dev (= 1.17+ds-1),
libhts3 (= 1.17+ds-1),
libhtscodecs2 (= 1.5.1-1),
libicu-dev (= 72.1-3),
libicu72 (= 72.1-3),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-4),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-4),
libkrb5support0 (= 1.20.1-4),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.4-0.1),
liblzma5 (= 5.4.4-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.2-2.2),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.0-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.56.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.25.0-4),
libpam-modules (= 1.5.2-7),
libpam-modules-bin (= 1.5.2-7),
libpam-runtime (= 1.5.2-7),
libpam0g (= 1.5.2-7),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpsl5 (= 0.21.2-1+b1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-3),
libsasl2-modules-db (= 2.1.28+dfsg1-3),
libseccomp2 (= 2.5.4-1+rpi1+b1),
libselinux1 (= 3.5-1),
libsmartcols1 (= 2.39.2-2.2),
libssh2-1 (= 1.11.0-2),
libssl3 (= 3.0.11-1),
libstdc++-12-dev (= 12.2.0-14+rpi1),
libstdc++6 (= 12.2.0-14+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 252.12-1~deb12u1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtinfo6 (= 6.4+20230625-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 12.2.0-14+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 252.12-1~deb12u1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.2-2.2),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-1),
linux-libc-dev (= 6.1.38-1+rpi1),
login (= 1:4.13+dfsg1-1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.11.2-3),
mawk (= 1.3.4.20230808-1),
ncurses-base (= 6.4+20230625-2),
ncurses-bin (= 6.4+20230625-2),
patch (= 2.7.6-7),
perl (= 5.36.0-9),
perl-base (= 5.36.0-9),
perl-modules-5.36 (= 5.36.0-9),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-1),
tar (= 1.34+dfsg-1.2),
usr-is-merged (= 37),
util-linux (= 2.39.2-2.2),
xz-utils (= 5.4.4-0.1),
zlib1g (= 1:1.2.13.dfsg-3),
zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1697121644"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
delly-dbgsym_1.1.8-1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 6076116 bytes: control archive=528 bytes.
363 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: delly-dbgsym
Source: delly
Version: 1.1.8-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6180
Depends: delly (= 1.1.8-1)
Section: debug
Priority: optional
Description: debug symbols for delly
Build-Ids: 1f0af6f711426dea462fa664607e9487afc06e3b
drwxr-xr-x root/root 0 2023-10-12 14:40 ./
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/lib/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/lib/debug/.build-id/1f/
-rw-r--r-- root/root 6317484 2023-10-12 14:40 ./usr/lib/debug/.build-id/1f/0af6f711426dea462fa664607e9487afc06e3b.debug
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-10-12 14:40 ./usr/share/doc/delly-dbgsym -> delly
delly_1.1.8-1_armhf.deb
-----------------------
new Debian package, version 2.0.
size 304896 bytes: control archive=948 bytes.
951 bytes, 16 lines control
312 bytes, 5 lines md5sums
Package: delly
Version: 1.1.8-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 934
Depends: libboost-filesystem1.74.0 (>= 1.74.0+ds1), libboost-iostreams1.74.0 (>= 1.74.0+ds1), libboost-program-options1.74.0 (>= 1.74.0+ds1), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 4.9), libhts3 (>= 1.17), libstdc++6 (>= 11)
Section: science
Priority: optional
Homepage: https://github.com/dellytools/delly
Description: Structural variant discovery by read analysis
Delly performs Structural variant discovery by integrated paired-end and
split-read analysis. It discovers, genotypes and visualizes deletions,
tandem duplications, inversions and translocations at single-nucleotide
resolution in short-read massively parallel sequencing data. It uses
paired-ends, split-reads and read-depth to sensitively and accurately
delineate genomic rearrangements throughout the genome.
drwxr-xr-x root/root 0 2023-10-12 14:40 ./
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/bin/
-rwxr-xr-x root/root 939536 2023-10-12 14:40 ./usr/bin/delly
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/doc/delly/
-rw-r--r-- root/root 1120 2023-10-12 14:40 ./usr/share/doc/delly/changelog.Debian.gz
-rw-r--r-- root/root 2645 2023-10-12 14:39 ./usr/share/doc/delly/copyright
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/man/
drwxr-xr-x root/root 0 2023-10-12 14:40 ./usr/share/man/man1/
-rw-r--r-- root/root 291 2023-10-12 14:40 ./usr/share/man/man1/delly.1.gz
-rw-r--r-- root/root 336 2023-10-12 14:40 ./usr/share/man/man1/dpe.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 37348
Build-Time: 109
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 59
Job: delly_1.1.8-1
Machine Architecture: arm64
Package: delly
Package-Time: 176
Source-Version: 1.1.8-1
Space: 37348
Status: successful
Version: 1.1.8-1
--------------------------------------------------------------------------------
Finished at 2023-10-15T06:33:53Z
Build needed 00:02:56, 37348k disk space