libseqlib →
1.2.0+dfsg-11 →
armhf → 2023-12-20 10:49:19
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| libseqlib 1.2.0+dfsg-11 (armhf) Wed, 20 Dec 2023 10:36:37 +0000 |
+==============================================================================+
Package: libseqlib
Version: 1.2.0+dfsg-11
Source Version: 1.2.0+dfsg-11
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-1f8d88c1-0fb8-43e0-b626-b2f41b42ee55' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/libseqlib-EgBOhN/resolver-xeVc4Q' 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 [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 11s (2771 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: 'libseqlib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/libseqlib.git
Please use:
git clone https://salsa.debian.org/med-team/libseqlib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 167 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main libseqlib 1.2.0+dfsg-11 (dsc) [2401 B]
Get:2 http://172.17.4.1/private trixie-staging/main libseqlib 1.2.0+dfsg-11 (tar) [149 kB]
Get:3 http://172.17.4.1/private trixie-staging/main libseqlib 1.2.0+dfsg-11 (diff) [15.5 kB]
Fetched 167 kB in 0s (1124 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libseqlib-EgBOhN/libseqlib-1.2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libseqlib-EgBOhN' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev | libcurl4-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev, 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 [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [465 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [546 B]
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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 util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils d-shlibs
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblkid1
libbrotli1 libbwa-dev libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libfml-dev libfml0 libhts-dev libhts3
libhtscodecs2 libicu72 libjsoncpp-dev libjsoncpp25 liblzma-dev liblzma5
libmagic-mgc libmagic1 libmount1 libnghttp2-14 libpipeline1 libpkgconf3
libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
librtmp1 libsmartcols1 libssh2-1 libssw-dev libssw0 libsub-override-perl
libtool libuchardet0 libuuid1 libxml2 m4 man-db media-types mount netbase
pkg-config pkg-kde-tools pkgconf pkgconf-bin po-debconf python3
python3-minimal python3.11 python3.11-minimal util-linux util-linux-extra
xz-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff samtools libcurl4-doc libgnutls28-dev
libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc
cryptsetup-bin libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser nfs-common cdbs libmail-box-perl python3-doc
python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support
dosfstools kbd util-linux-locales
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
publicsuffix libltdl-dev uuid-runtime libwww-perl libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils d-shlibs debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbwa-dev
libbz2-dev libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libfml-dev libfml0 libhts-dev libhts3
libhtscodecs2 libicu72 libjsoncpp-dev libjsoncpp25 liblzma-dev libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib
libpython3.11-minimal libpython3.11-stdlib librtmp1 libssh2-1 libssw-dev
libssw0 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
media-types netbase pkg-config pkg-kde-tools pkgconf pkgconf-bin po-debconf
python3 python3-minimal python3.11 python3.11-minimal
sbuild-build-depends-main-dummy zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 liblzma5 libmount1 libsmartcols1 libuuid1 mount
util-linux util-linux-extra xz-utils
10 upgraded, 68 newly installed, 0 to remove and 60 not upgraded.
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Get:49 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-2 bsdutils_1:2.39.3-2 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 d-shlibs_0.105 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+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++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+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_0.21-14 gettext-base_0.21-14 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_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-2 libbrotli1_1.1.0-2 libbwa-dev_0.7.17-7 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.4.0-2+rpi1 libcurl4-gnutls-dev_8.4.0-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libfml-dev_0.1+git20190320.b499514-1+rpi1 libfml0_0.1+git20190320.b499514-1+rpi1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+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_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.5.2-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjsoncpp-dev_1.9.5-6 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 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libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-2 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-3 libssl1.1_1.1.1o-1 libssl3_3.0.11-1 libssw-dev_1.1-14 libssw0_1.1-14 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231016-1 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_13.2.0-5+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.3-2 nano_7.2-1 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.32_5.32.1-6 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 pkg-config_1.8.1-1 pkg-kde-tools_0.15.38 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-minimal_3.11.4-5 python3.11_3.11.7-2 python3.11-minimal_3.11.7-2 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_3.08-3 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_38 util-linux_2.39.3-2 util-linux-extra_2.39.3-2 xz-utils_5.4.5-0.1 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: libseqlib
Binary: libseqlib2, libseqlib-dev
Architecture: any
Version: 1.2.0+dfsg-11
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/walaj/SeqLib
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/libseqlib
Vcs-Git: https://salsa.debian.org/med-team/libseqlib.git
Build-Depends: debhelper-compat (= 13), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev | libcurl4-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev
Package-List:
libseqlib-dev deb libdevel optional arch=any
libseqlib2 deb libs optional arch=any
Checksums-Sha1:
584cb70cc2d11d595f26ec50763d11ca570395c5 148996 libseqlib_1.2.0+dfsg.orig.tar.xz
89ee20e44e0e76c6efce309a56e33556a76149bd 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz
Checksums-Sha256:
408ee92e5041ff45d9d259d1507ef783e74c565d02e0c623ef0a67a7c387b953 148996 libseqlib_1.2.0+dfsg.orig.tar.xz
9e85fd66de1a1e1fcb576e045cfd1fefbeed75b222450032dfdc0b39a39ba2ea 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz
Files:
8d8f26bf4fd751789bbc53bd7319355a 148996 libseqlib_1.2.0+dfsg.orig.tar.xz
6f36289dd0bbde1824dc445037845166 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz
Dgit: 279a189ccc52e73b124a50bcfe14717ee68c64d8 debian archive/debian/1.2.0+dfsg-11 https://git.dgit.debian.org/libseqlib
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gpgv: Signature made Thu Dec 14 22:09:04 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libseqlib_1.2.0+dfsg-11.dsc: no acceptable signature found
dpkg-source: info: extracting libseqlib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libseqlib_1.2.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking libseqlib_1.2.0+dfsg-11.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 adapt_to_debian_fermi-lite.patch
dpkg-source: info: applying fix_fermi-lite_usage.patch
dpkg-source: info: applying fix_htslib_usage.patch
dpkg-source: info: applying fml_include_path.patch
dpkg-source: info: applying dynamic_lib.patch
dpkg-source: info: applying use_debian_packaged_jsoncpp.patch
dpkg-source: info: applying use_debian_packaged_ssw.patch
dpkg-source: info: applying pkg-config.patch
Check disk space
----------------
Sufficient free space for build
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=7507367173ad4858a061fdd2cf60741a
JOURNAL_STREAM=8:39174
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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-1f8d88c1-0fb8-43e0-b626-b2f41b42ee55
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c12583
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 libseqlib
dpkg-buildpackage: info: source version 1.2.0+dfsg-11
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with pkgkde_symbolshelper
dh_clean
debian/rules binary-arch
dh binary-arch --with pkgkde_symbolshelper
dh_update_autotools_config -a
dh_autoreconf -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT'
configure.ac:6: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:6: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:6: the top level
configure.ac:19: warning: The macro `AC_PROG_LIBTOOL' is obsolete.
configure.ac:19: You should run autoupdate.
aclocal.m4:122: AC_PROG_LIBTOOL is expanded from...
configure.ac:19: the top level
configure.ac:17: installing './compile'
configure.ac:19: installing './config.guess'
configure.ac:19: installing './config.sub'
configure.ac:4: installing './install-sh'
configure.ac:4: installing './missing'
src/Makefile.am: installing './depcomp'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ranlib... ranlib
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for file... file
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... (cached) ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing lzma_code... -llzma
checking for library containing BZ2_bzBuffToBuffDecompress... -lbz2
checking for library containing clock_gettime... none required
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for htslib... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/seqtools/Makefile
config.status: creating libseqlib.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FastqReader.lo `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BFC.lo `test -f 'BFC.cpp' || echo './'`BFC.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-ReadFilter.lo `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-SeqPlot.lo `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-FastqReader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BFC.cpp -fPIC -DPIC -o .libs/libseqlib_la-BFC.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -fPIC -DPIC -o .libs/libseqlib_la-SeqPlot.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -fPIC -DPIC -o .libs/libseqlib_la-ReadFilter.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FastqReader.cpp -o libseqlib_la-FastqReader.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BFC.cpp -o libseqlib_la-BFC.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-GenomicRegion.lo `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -fPIC -DPIC -o .libs/libseqlib_la-GenomicRegion.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-RefGenome.lo `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -fPIC -DPIC -o .libs/libseqlib_la-RefGenome.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c SeqPlot.cpp -o libseqlib_la-SeqPlot.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c RefGenome.cpp -o libseqlib_la-RefGenome.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamWriter.lo `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamReader.lo `test -f 'BamReader.cpp' || echo './'`BamReader.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamWriter.cpp -o libseqlib_la-BamWriter.o >/dev/null 2>&1
In file included from /usr/include/c++/13/vector:72,
from ../SeqLib/ReadFilter.h:7,
from ReadFilter.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const SeqLib::Filter::AbstractRule&}; _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator<SeqLib::Filter::AbstractRule>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<SeqLib::Filter::AbstractRule>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator<SeqLib::Filter::AbstractRule>]’,
inlined from ‘void SeqLib::Filter::ReadFilter::AddRule(const SeqLib::Filter::AbstractRule&)’ at ReadFilter.cpp:139:31:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator<SeqLib::Filter::AbstractRule>]’,
inlined from ‘void SeqLib::Filter::ReadFilterCollection::CheckHasIncluder()’ at ReadFilter.cpp:282:31:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BWAWrapper.lo `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator<SeqLib::Filter::AbstractRule>]’,
inlined from ‘SeqLib::Filter::ReadFilterCollection::ReadFilterCollection(const std::string&, const SeqLib::BamHeader&)’ at ReadFilter.cpp:252:33:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator<SeqLib::Filter::AbstractRule>]’,
inlined from ‘SeqLib::Filter::ReadFilterCollection::ReadFilterCollection(const std::string&, const SeqLib::BamHeader&)’ at ReadFilter.cpp:259:31:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72,
from ../SeqLib/BWAWrapper.h:5,
from BWAWrapper.cpp:9:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const mem_aln_t&}; _Tp = mem_aln_t; _Alloc = std::allocator<mem_aln_t>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<mem_aln_t>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/algorithm:61,
from ../SeqLib/BWAWrapper.h:7:
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1792 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1812 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
In file included from /usr/include/c++/13/bits/stl_algo.h:61:
/usr/include/c++/13/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Distance = int; _Tp = mem_aln_t; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’:
/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c ReadFilter.cpp -o libseqlib_la-ReadFilter.o >/dev/null 2>&1
/usr/include/c++/13/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’:
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1918 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = mem_aln_t; _Alloc = std::allocator<mem_aln_t>]’,
inlined from ‘void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const’ at BWAWrapper.cpp:297:18:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = bool (*)(const mem_aln_t&, const mem_aln_t&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const’ at BWAWrapper.cpp:301:14:
/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1947 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1948 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1949 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’ at /usr/include/c++/13/bits/stl_algo.h:1950:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<mem_aln_t*, vector<mem_aln_t> >; _Compare = bool (*)(const mem_aln_t&, const mem_aln_t&)]’ at /usr/include/c++/13/bits/stl_algo.h:4894:18,
inlined from ‘void SeqLib::BWAWrapper::AlignSequence(const std::string&, const std::string&, SeqLib::BamRecordVector&, bool, double, int) const’ at BWAWrapper.cpp:301:14:
/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1864 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamReader.cpp -o libseqlib_la-BamReader.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BWAWrapper.cpp -o libseqlib_la-BWAWrapper.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c GenomicRegion.cpp -o libseqlib_la-GenomicRegion.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamRecord.lo `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamRecord.o
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-FermiAssembler.lo `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FermiAssembler.cpp -fPIC -DPIC -o .libs/libseqlib_la-FermiAssembler.o
In file included from /usr/include/c++/13/vector:72,
from ../SeqLib/BamRecord.h:6,
from BamRecord.cpp:1:
/usr/include/c++/13/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++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> SeqLib::BamRecord::GetSmartDoubleTag(const std::string&) const’ at BamRecord.cpp:578:15:
/usr/include/c++/13/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++/13/bits/stl_vector.h:1296:21,
inlined from ‘std::vector<double> SeqLib::BamRecord::GetSmartDoubleTag(const std::string&) const’ at BamRecord.cpp:580:20:
/usr/include/c++/13/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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamRecord.cpp -o libseqlib_la-BamRecord.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c FermiAssembler.cpp -o libseqlib_la-FermiAssembler.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c -o libseqlib_la-BamHeader.lo `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamHeader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamHeader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -c BamHeader.cpp -o libseqlib_la-BamHeader.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link g++ -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -version-info 2:0 -lfml `/usr/bin/pkg-config --libs htslib` `/usr/bin/pkg-config --libs jsoncpp` -lssw -Wl,-z,relro -Wl,-z,now -o libseqlib.la -rpath /usr/lib/arm-linux-gnueabihf libseqlib_la-FastqReader.lo libseqlib_la-BFC.lo libseqlib_la-ReadFilter.lo libseqlib_la-SeqPlot.lo libseqlib_la-GenomicRegion.lo libseqlib_la-RefGenome.lo libseqlib_la-BamWriter.lo libseqlib_la-BamReader.lo libseqlib_la-BWAWrapper.lo libseqlib_la-BamRecord.lo libseqlib_la-FermiAssembler.lo libseqlib_la-BamHeader.lo -lbz2 -llzma -lz -pthread
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbeginS.o .libs/libseqlib_la-FastqReader.o .libs/libseqlib_la-BFC.o .libs/libseqlib_la-ReadFilter.o .libs/libseqlib_la-SeqPlot.o .libs/libseqlib_la-GenomicRegion.o .libs/libseqlib_la-RefGenome.o .libs/libseqlib_la-BamWriter.o .libs/libseqlib_la-BamReader.o .libs/libseqlib_la-BWAWrapper.o .libs/libseqlib_la-BamRecord.o .libs/libseqlib_la-FermiAssembler.o .libs/libseqlib_la-BamHeader.o -lfml -lhts -ljsoncpp -lssw -lbz2 -llzma -lz -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/13/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o -g -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libseqlib.so.2 -o .libs/libseqlib.so.2.0.0
libtool: link: (cd ".libs" && rm -f "libseqlib.so.2" && ln -s "libseqlib.so.2.0.0" "libseqlib.so.2")
libtool: link: (cd ".libs" && rm -f "libseqlib.so" && ln -s "libseqlib.so.2.0.0" "libseqlib.so")
libtool: link: ar cr .libs/libseqlib.a libseqlib_la-FastqReader.o libseqlib_la-BFC.o libseqlib_la-ReadFilter.o libseqlib_la-SeqPlot.o libseqlib_la-GenomicRegion.o libseqlib_la-RefGenome.o libseqlib_la-BamWriter.o libseqlib_la-BamReader.o libseqlib_la-BWAWrapper.o libseqlib_la-BamRecord.o libseqlib_la-FermiAssembler.o libseqlib_la-BamHeader.o
libtool: link: ranlib .libs/libseqlib.a
libtool: link: ( cd ".libs" && rm -f "libseqlib.la" && ln -s "../libseqlib.la" "libseqlib.la" )
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/libseqlib-1.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib"
mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
# Trick to get also headers moved by d-shlibmove
cp -a SeqLib debian # note: also GenomicRegionCollection.cpp is really needed by freebayes
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev debian/SeqLib usr/include \
--override s/libfml0-dev/libfml-dev/ \
--override s/libssw0-dev/libssw-dev/ \
src/.libs/libseqlib.so
Library package automatic movement utility
--> libfml-dev package exists.
--> libhts-dev package exists.
--> libjsoncpp-dev package exists.
--> libssw-dev package exists.
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libseqlib2/usr/lib/arm-linux-gnueabihf
mv src/.libs/libseqlib.a debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf
mv src/.libs/libseqlib.so debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/src/.libs/libseqlib.so.2 debian/libseqlib2/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/src/.libs/libseqlib.so.2.0.0 debian/libseqlib2/usr/lib/arm-linux-gnueabihf
PKGDEV=libseqlib-dev
PKGSHL=libseqlib2
install -d -m 755 debian/libseqlib-dev/usr/include
mv debian/SeqLib debian/libseqlib-dev/usr/include
mkdir -p /<<PKGBUILDDIR>>/debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
mv libseqlib.pc /<<PKGBUILDDIR>>/debian/libseqlib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -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: symbol err_fflush used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol bns_destroy used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol bns_dump used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol nst_nt4_table used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol mem_reg2aln used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol err_fwrite used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol kseq_read used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol bwt_bwtupdate_core used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: symbol bwa_verbose used by debian/libseqlib2/usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0 found in none of the libraries
dpkg-shlibdeps: warning: 12 other similar warnings have been skipped (use -v to see them all)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libseqlib2-dbgsym' in '../libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb'.
dpkg-deb: building package 'libseqlib2' in '../libseqlib2_1.2.0+dfsg-11_armhf.deb'.
dpkg-deb: building package 'libseqlib-dev' in '../libseqlib-dev_1.2.0+dfsg-11_armhf.deb'.
dpkg-genbuildinfo --build=any -O../libseqlib_1.2.0+dfsg-11_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../libseqlib_1.2.0+dfsg-11_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 2023-12-20T10:49:11Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libseqlib_1.2.0+dfsg-11_armhf.changes:
--------------------------------------
Format: 1.8
Date: Thu, 14 Dec 2023 23:01:06 +0100
Source: libseqlib
Binary: libseqlib-dev libseqlib2 libseqlib2-dbgsym
Architecture: armhf
Version: 1.2.0+dfsg-11
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
libseqlib-dev - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat
libseqlib2 - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat
Closes: 1047821
Changes:
libseqlib (1.2.0+dfsg-11) unstable; urgency=medium
.
* d/clean: new: cleanup leftovers. (Closes: #1047821)
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Files:
83ead2b24eb2902ec7486f4b5390c4b5 196576 libdevel optional libseqlib-dev_1.2.0+dfsg-11_armhf.deb
e6329cc1a503480f42b77f4f8b69a48f 2169204 debug optional libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb
18b8249ac1aa4ae1fea468a79eee2c4e 135228 libs optional libseqlib2_1.2.0+dfsg-11_armhf.deb
0d830d9cafe38457ed95d975befc8dbc 7724 science optional libseqlib_1.2.0+dfsg-11_armhf.buildinfo
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: libseqlib
Binary: libseqlib-dev libseqlib2 libseqlib2-dbgsym
Architecture: armhf
Version: 1.2.0+dfsg-11
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Wed, 20 Dec 2023 10:49:10 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
adduser (= 3.137),
apt (= 2.7.6),
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.2),
bash (= 5.2.15-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-2),
bsdutils (= 1:2.39.3-2),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
d-shlibs (= 0.105),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.8),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dirmngr (= 2.2.40-1.1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
gcc-13-base (= 13.2.0-5+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
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 (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libapt-pkg6.0 (= 2.7.6),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-5+rpi1),
libassuan0 (= 2.5.6-1),
libatomic1 (= 13.2.0-5+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.3-2),
libbrotli1 (= 1.1.0-2),
libbwa-dev (= 0.7.17-7),
libbz2-1.0 (= 1.0.8-5+b2),
libbz2-dev (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-5+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.4.0-2+rpi1),
libcurl4-gnutls-dev (= 8.4.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.8),
libdeflate-dev (= 1.18-1),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libffi8 (= 3.4.4-1),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libfml-dev (= 0.1+git20190320.b499514-1+rpi1),
libfml0 (= 0.1+git20190320.b499514-1+rpi1),
libgcc-12-dev (= 12.3.0-10+rpi1),
libgcc-13-dev (= 13.2.0-5+rpi1),
libgcc-s1 (= 13.2.0-5+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 (= 13.2.0-5+rpi1),
libgpg-error0 (= 1.47-2),
libgssapi-krb5-2 (= 1.20.1-5),
libhogweed6 (= 3.9.1-2),
libhts-dev (= 1.18+ds-1),
libhts3 (= 1.18+ds-1),
libhtscodecs2 (= 1.5.2-1),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjsoncpp-dev (= 1.9.5-6),
libjsoncpp25 (= 1.9.5-6),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
libksba8 (= 1.6.4-2),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.5-0.1),
liblzma5 (= 5.4.5-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.3-2),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.4+20231016-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.58.0-1),
libnpth0 (= 1.6-3),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
libp11-kit0 (= 0.25.0-5),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpkgconf3 (= 1.8.1-1),
libpsl5 (= 0.21.2-1+b1),
libpython3-stdlib (= 3.11.4-5),
libpython3.11-minimal (= 3.11.7-2),
libpython3.11-stdlib (= 3.11.7-2),
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),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-2),
libsqlite3-0 (= 3.43.2-1),
libssh2-1 (= 1.11.0-3),
libssl3 (= 3.0.11-1),
libssw-dev (= 1.1-14),
libssw0 (= 1.1-14),
libstdc++-13-dev (= 13.2.0-5+rpi1),
libstdc++6 (= 13.2.0-5+rpi1),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtext-glob-perl (= 0.11-3),
libtinfo6 (= 6.4+20231016-1),
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 (= 13.2.0-5+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-2),
libxml2 (= 2.9.14+dfsg-1.3),
libxxhash0 (= 0.8.2-2),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
lsb-base (= 11.6+rpi1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-1),
mawk (= 1.3.4.20230808-1),
media-types (= 10.1.0),
ncurses-base (= 6.4+20231016-1),
ncurses-bin (= 6.4+20231016-1),
netbase (= 6.4),
passwd (= 1:4.13+dfsg1-3),
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),
pkg-config (= 1.8.1-1),
pkg-kde-tools (= 0.15.38),
pkgconf (= 1.8.1-1),
pkgconf-bin (= 1.8.1-1),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.11.4-5),
python3-minimal (= 3.11.4-5),
python3.11 (= 3.11.7-2),
python3.11-minimal (= 3.11.7-2),
raspbian-archive-keyring (= 20120528.2),
readline-common (= 8.2-1.3),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-3),
tar (= 1.34+dfsg-1.2),
tzdata (= 2023c-10),
usrmerge (= 38),
util-linux (= 2.39.3-2),
xz-utils (= 5.4.5-0.1),
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"
SOURCE_DATE_EPOCH="1702591266"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libseqlib-dev_1.2.0+dfsg-11_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 196576 bytes: control archive=1752 bytes.
1336 bytes, 25 lines control
1735 bytes, 25 lines md5sums
Package: libseqlib-dev
Source: libseqlib
Version: 1.2.0+dfsg-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1061
Depends: libseqlib2 (= 1.2.0+dfsg-11), libfml-dev, libhts-dev, libjsoncpp-dev, libssw-dev, zlib1g-dev, libbwa-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/walaj/SeqLib
Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence data (dev)
C++ API and command line tool that provides a rapid and user-friendly
interface to BAM/SAM/CRAM files, global sequence alignment operations
and sequence assembly. Four C libraries perform core operations in
SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment
and Fermi for error correction and sequence assembly. Benchmarking
indicates that SeqLib has lower CPU and memory requirements than leading
C++ sequence analysis APIs. Minimal SeqLib code can extract, error-correct
and assemble reads from a CRAM file and then align with BWA-MEM.
SeqLib also provides additional capabilities, including chromosome-aware
interval queries and read plotting. Command line tools are available for
performing integrated error correction, micro-assemblies and alignment.
.
This package contains the header files and static library.
drwxr-xr-x root/root 0 2023-12-14 22:01 ./
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/include/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/include/SeqLib/
-rw-r--r-- root/root 3874 2023-12-14 22:01 ./usr/include/SeqLib/BFC.h
-rw-r--r-- root/root 7129 2021-01-07 04:18 ./usr/include/SeqLib/BWAWrapper.h
-rw-r--r-- root/root 3605 2023-12-14 22:01 ./usr/include/SeqLib/BamHeader.h
-rw-r--r-- root/root 9275 2021-01-07 04:18 ./usr/include/SeqLib/BamReader.h
-rw-r--r-- root/root 32406 2023-12-14 22:01 ./usr/include/SeqLib/BamRecord.h
-rw-r--r-- root/root 1979 2021-01-07 04:18 ./usr/include/SeqLib/BamWalker.h
-rw-r--r-- root/root 3473 2021-01-07 04:18 ./usr/include/SeqLib/BamWriter.h
-rw-r--r-- root/root 1170 2021-01-07 04:18 ./usr/include/SeqLib/FastqReader.h
-rw-r--r-- root/root 4281 2023-12-14 22:01 ./usr/include/SeqLib/FermiAssembler.h
-rw-r--r-- root/root 6354 2021-01-07 04:18 ./usr/include/SeqLib/GenomicRegion.h
-rw-r--r-- root/root 19869 2021-01-07 04:18 ./usr/include/SeqLib/GenomicRegionCollection.cpp
-rw-r--r-- root/root 11804 2021-01-07 04:18 ./usr/include/SeqLib/GenomicRegionCollection.h
-rw-r--r-- root/root 7320 2021-01-07 04:18 ./usr/include/SeqLib/IntervalTree.h
-rw-r--r-- root/root 17538 2021-01-07 04:18 ./usr/include/SeqLib/ReadFilter.h
-rw-r--r-- root/root 1387 2023-12-14 22:01 ./usr/include/SeqLib/RefGenome.h
-rw-r--r-- root/root 3832 2021-01-07 04:18 ./usr/include/SeqLib/SeqLibCommon.h
-rw-r--r-- root/root 4176 2021-01-07 04:18 ./usr/include/SeqLib/SeqLibUtils.h
-rw-r--r-- root/root 2455 2021-01-07 04:18 ./usr/include/SeqLib/SeqPlot.h
-rw-r--r-- root/root 577 2021-01-07 04:18 ./usr/include/SeqLib/ThreadPool.h
-rw-r--r-- root/root 2421 2021-01-07 04:18 ./usr/include/SeqLib/UnalignedSequence.h
-rw-r--r-- root/root 17078 2021-01-07 04:18 ./usr/include/SeqLib/aho_corasick.hpp
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 893944 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/libseqlib.a
lrwxrwxrwx root/root 0 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/libseqlib.so -> libseqlib.so.2.0.0
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 301 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libseqlib.pc
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/doc/libseqlib-dev/
-rw-r--r-- root/root 1718 2023-12-14 22:01 ./usr/share/doc/libseqlib-dev/changelog.Debian.gz
-rw-r--r-- root/root 2658 2023-12-14 22:01 ./usr/share/doc/libseqlib-dev/copyright
libseqlib2-dbgsym_1.2.0+dfsg-11_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 2169204 bytes: control archive=556 bytes.
411 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libseqlib2-dbgsym
Source: libseqlib
Version: 1.2.0+dfsg-11
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2225
Depends: libseqlib2 (= 1.2.0+dfsg-11)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libseqlib2
Build-Ids: 5e36eb8b4ebcfb1b23af44a6f38f185851ff7088
drwxr-xr-x root/root 0 2023-12-14 22:01 ./
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/debug/.build-id/5e/
-rw-r--r-- root/root 2267472 2023-12-14 22:01 ./usr/lib/debug/.build-id/5e/36eb8b4ebcfb1b23af44a6f38f185851ff7088.debug
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-12-14 22:01 ./usr/share/doc/libseqlib2-dbgsym -> libseqlib2
libseqlib2_1.2.0+dfsg-11_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 135228 bytes: control archive=1236 bytes.
1333 bytes, 23 lines control
229 bytes, 3 lines md5sums
39 bytes, 1 lines shlibs
68 bytes, 2 lines triggers
Package: libseqlib2
Source: libseqlib
Version: 1.2.0+dfsg-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 430
Depends: libc6 (>= 2.33), libfml0 (>= 0.1+git20190320.b499514), libgcc-s1 (>= 3.5), libhts3 (>= 1.17), libjsoncpp25 (>= 1.9.5), libssw0 (>= 1.1), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/walaj/SeqLib
Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence data
C++ API and command line tool that provides a rapid and user-friendly
interface to BAM/SAM/CRAM files, global sequence alignment operations
and sequence assembly. Four C libraries perform core operations in
SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment
and Fermi for error correction and sequence assembly. Benchmarking
indicates that SeqLib has lower CPU and memory requirements than leading
C++ sequence analysis APIs. Minimal SeqLib code can extract, error-correct
and assemble reads from a CRAM file and then align with BWA-MEM.
SeqLib also provides additional capabilities, including chromosome-aware
interval queries and read plotting. Command line tools are available for
performing integrated error correction, micro-assemblies and alignment.
drwxr-xr-x root/root 0 2023-12-14 22:01 ./
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/libseqlib.so.2 -> libseqlib.so.2.0.0
-rw-r--r-- root/root 423840 2023-12-14 22:01 ./usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-12-14 22:01 ./usr/share/doc/libseqlib2/
-rw-r--r-- root/root 1718 2023-12-14 22:01 ./usr/share/doc/libseqlib2/changelog.Debian.gz
-rw-r--r-- root/root 2658 2023-12-14 22:01 ./usr/share/doc/libseqlib2/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 32960
Build-Time: 121
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 597
Job: libseqlib_1.2.0+dfsg-11
Machine Architecture: armhf
Package: libseqlib
Package-Time: 754
Source-Version: 1.2.0+dfsg-11
Space: 32960
Status: successful
Version: 1.2.0+dfsg-11
--------------------------------------------------------------------------------
Finished at 2023-12-20T10:49:11Z
Build needed 00:12:34, 32960k disk space