libseqlib →
1.2.0+dfsg-8 →
armhf → 2021-11-26 05:50:25
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| libseqlib 1.2.0+dfsg-8 (armhf) Fri, 26 Nov 2021 05:41:25 +0000 |
+==============================================================================+
Package: libseqlib
Version: 1.2.0+dfsg-8
Source Version: 1.2.0+dfsg-8
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-94f08509-9b91-4d96-8980-7a25aeb3e087' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/libseqlib-HQR8c7/resolver-vpr28x' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.5 MB]
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Reading package lists...
+------------------------------------------------------------------------------+
| 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 166 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main libseqlib 1.2.0+dfsg-8 (dsc) [2232 B]
Get:2 http://172.17.0.1/private bookworm-staging/main libseqlib 1.2.0+dfsg-8 (tar) [149 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main libseqlib 1.2.0+dfsg-8 (diff) [14.8 kB]
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I: NOTICE: Log filtering will replace 'build/libseqlib-HQR8c7/libseqlib-1.2.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libseqlib-HQR8c7' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
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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'.
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Install main build dependencies (apt-based resolver)
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The following additional 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 libglib2.0-0 libhts-dev
libhts3 libhtscodecs2 libicu67 libjsoncpp-dev libjsoncpp24 liblzma-dev
libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libssw-dev libssw0 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db media-types pkg-config pkg-kde-tools
po-debconf python3 python3-minimal python3.9 python3.9-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff samtools libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser cdbs libmail-box-perl python3-doc python3-tk python3-venv
python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
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 libglib2.0-0 libhts-dev
libhts3 libhtscodecs2 libicu67 libjsoncpp-dev libjsoncpp24 liblzma-dev
libmagic-mgc libmagic1 libmpdec3 libnghttp2-14 libpipeline1 libpsl5
libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libssw-dev libssw0 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db media-types pkg-config pkg-kde-tools
po-debconf python3 python3-minimal python3.9 python3.9-minimal
sbuild-build-depends-main-dummy zlib1g-dev
0 upgraded, 67 newly installed, 0 to remove and 6 not upgraded.
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Get:48 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
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Get:55 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
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Get:66 http://172.17.0.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:67 http://172.17.0.1/private bookworm-staging/main armhf pkg-kde-tools all 0.15.32 [96.7 kB]
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Processing triggers for libc-bin (2.32-4+rpi1) ...
+------------------------------------------------------------------------------+
| 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_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.12 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3.1 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 d-shlibs_0.104 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+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_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.12 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-4 libbrotli1_1.0.9-2+b1 libbwa-dev_0.7.17-6 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libcurl3-gnutls_7.79.1-2 libcurl4-gnutls-dev_7.79.1-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdeflate-dev_1.8-1 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.186-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.1-1 libfml-dev_0.1+git20190320.b499514-1+rpi1 libfml0_0.1+git20190320.b499514-1+rpi1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libglib2.0-0_2.70.1-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjsoncpp-dev_1.9.4-5 libjsoncpp24_1.9.4-5 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3-1 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.7-1 libpython3.9-minimal_3.9.9-1+rpi1 libpython3.9-stdlib_3.9.9-1+rpi1 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.7-1+rpi1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 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tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: libseqlib
Binary: libseqlib2, libseqlib-dev
Architecture: any
Version: 1.2.0+dfsg-8
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/walaj/SeqLib
Standards-Version: 4.6.0
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
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9e292ad9cd9584648ae4dc0fd7e736c06105284e 14788 libseqlib_1.2.0+dfsg-8.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.8TCIOMNV/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 21 05:51:28 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libseqlib_1.2.0+dfsg-8.dsc
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-8.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=b96ef01d2dac49bab539c44b4e161c4c
JOURNAL_STREAM=8:25110170
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-94f08509-9b91-4d96-8980-7a25aeb3e087
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c132473
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-8
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.m4:121: 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... /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
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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 objdump... objdump
checking how to recognize dependent libraries... pass_all
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checking how to truncate binary pipes... /bin/dd bs=4096 count=1
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checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
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checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
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checking dynamic linker characteristics... (cached) GNU/Linux ld.so
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checking for library containing clock_gettime... none required
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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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -Wformat -Werror=format-security -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o
In file included from /usr/include/c++/11/vector:72,
from ../SeqLib/ReadFilter.h:7,
from ReadFilter.cpp:1:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SeqLib::Filter::AbstractRule&}; _Tp = SeqLib::Filter::AbstractRule; _Alloc = std::allocator<SeqLib::Filter::AbstractRule>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<SeqLib::Filter::AbstractRule>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from ../SeqLib/ReadFilter.h:7,
from ReadFilter.cpp:1:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void SeqLib::Filter::ReadFilter::AddRule(const SeqLib::Filter::AbstractRule&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1198 | _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 -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 -Wformat -Werror=format-security -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void SeqLib::Filter::ReadFilterCollection::CheckHasIncluder()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
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 -Wformat -Werror=format-security -c BamWriter.cpp -o libseqlib_la-BamWriter.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 -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 -Wformat -Werror=format-security -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘SeqLib::Filter::ReadFilterCollection::ReadFilterCollection(const string&, const SeqLib::BamHeader&)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SeqLib::Filter::AbstractRule*, std::vector<SeqLib::Filter::AbstractRule> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from ../SeqLib/BWAWrapper.h:5,
from BWAWrapper.cpp:9:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const mem_aln_t&}; _Tp = mem_aln_t; _Alloc = std::allocator<mem_aln_t>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<mem_aln_t>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from ../SeqLib/BWAWrapper.h:7,
from BWAWrapper.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const mem_aln_t&, const mem_aln_t&)>]’:
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: 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++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from ../SeqLib/BWAWrapper.h:7,
from BWAWrapper.cpp:9:
/usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, std::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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from ../SeqLib/BWAWrapper.h:7,
from BWAWrapper.cpp:9:
/usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<mem_aln_t*, std::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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from ../SeqLib/BWAWrapper.h:5,
from BWAWrapper.cpp:9:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void SeqLib::BWAWrapper::AlignSequence(const string&, const string&, SeqLib::BamRecordVector&, bool, double, int) const’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from ../SeqLib/BWAWrapper.h:7,
from BWAWrapper.cpp:9:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<mem_aln_t*, std::vector<mem_aln_t> >’ changed in GCC 7.1
1871 | 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 -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 -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 -Wformat -Werror=format-security -c ReadFilter.cpp -o libseqlib_la-ReadFilter.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 -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 -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 -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 -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 -Wformat -Werror=format-security -c FermiAssembler.cpp -fPIC -DPIC -o .libs/libseqlib_la-FermiAssembler.o
In file included from /usr/include/c++/11/vector:72,
from ../SeqLib/BamRecord.h:6,
from BamRecord.cpp:1:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<double> SeqLib::BamRecord::GetSmartDoubleTag(const string&) const’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _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 -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 -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 -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 -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 -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 -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/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/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/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/11/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crtn.o -g -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -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 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 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 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 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_fclose 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_init 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_xopen_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 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 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 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 bwa_fill_scmat 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-8_armhf.deb'.
dpkg-deb: building package 'libseqlib2' in '../libseqlib2_1.2.0+dfsg-8_armhf.deb'.
dpkg-deb: building package 'libseqlib-dev' in '../libseqlib-dev_1.2.0+dfsg-8_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../libseqlib_1.2.0+dfsg-8_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 2021-11-26T05:50:18Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libseqlib_1.2.0+dfsg-8_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sun, 21 Nov 2021 06:30:55 +0100
Source: libseqlib
Binary: libseqlib-dev libseqlib2 libseqlib2-dbgsym
Architecture: armhf
Version: 1.2.0+dfsg-8
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@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
Changes:
libseqlib (1.2.0+dfsg-8) unstable; urgency=medium
.
* Provide symbols file only for amd64 to reduce maintenance burden
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+------------------------------------------------------------------------------+
| Buildinfo |
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Build-Architecture: armhf
Build-Date: Fri, 26 Nov 2021 05:50:16 +0000
Build-Path: /<<PKGBUILDDIR>>
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LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1637472655"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libseqlib-dev_1.2.0+dfsg-8_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 194244 bytes: control archive=1752 bytes.
1334 bytes, 25 lines control
1735 bytes, 25 lines md5sums
Package: libseqlib-dev
Source: libseqlib
Version: 1.2.0+dfsg-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1051
Depends: libseqlib2 (= 1.2.0+dfsg-8), 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 2021-11-21 05:30 ./
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/include/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/include/SeqLib/
-rw-r--r-- root/root 3874 2021-11-21 05:30 ./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 2021-11-21 05:30 ./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 2021-11-21 05:30 ./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 2021-11-21 05:30 ./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 2021-11-21 05:30 ./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 2021-11-21 05:30 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 882730 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/libseqlib.a
lrwxrwxrwx root/root 0 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/libseqlib.so -> libseqlib.so.2.0.0
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 301 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libseqlib.pc
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/doc/libseqlib-dev/
-rw-r--r-- root/root 1960 2021-11-21 05:30 ./usr/share/doc/libseqlib-dev/changelog.Debian.gz
-rw-r--r-- root/root 2658 2021-11-21 05:30 ./usr/share/doc/libseqlib-dev/copyright
libseqlib2-dbgsym_1.2.0+dfsg-8_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 2292360 bytes: control archive=556 bytes.
409 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libseqlib2-dbgsym
Source: libseqlib
Version: 1.2.0+dfsg-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2348
Depends: libseqlib2 (= 1.2.0+dfsg-8)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libseqlib2
Build-Ids: bf2fe870a7adde29880a5c62cd541dbb9317bc9e
drwxr-xr-x root/root 0 2021-11-21 05:30 ./
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-11-21 05:30 ./usr/share/doc/libseqlib2-dbgsym -> libseqlib2
libseqlib2_1.2.0+dfsg-8_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 131160 bytes: control archive=1240 bytes.
1330 bytes, 23 lines control
229 bytes, 3 lines md5sums
39 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libseqlib2
Source: libseqlib
Version: 1.2.0+dfsg-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 414
Depends: libc6 (>= 2.32), libfml0 (>= 0.1+git20190320.b499514), libgcc-s1 (>= 3.5), libhts3 (>= 1.10), libjsoncpp24 (>= 1.9.4), libssw0 (>= 1.1), libstdc++6 (>= 11), 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 2021-11-21 05:30 ./
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/libseqlib.so.2 -> libseqlib.so.2.0.0
-rw-r--r-- root/root 407456 2021-11-21 05:30 ./usr/lib/arm-linux-gnueabihf/libseqlib.so.2.0.0
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-11-21 05:30 ./usr/share/doc/libseqlib2/
-rw-r--r-- root/root 1960 2021-11-21 05:30 ./usr/share/doc/libseqlib2/changelog.Debian.gz
-rw-r--r-- root/root 2658 2021-11-21 05:30 ./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: 34432
Build-Time: 136
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 371
Job: libseqlib_1.2.0+dfsg-8
Machine Architecture: armhf
Package: libseqlib
Package-Time: 533
Source-Version: 1.2.0+dfsg-8
Space: 34432
Status: successful
Version: 1.2.0+dfsg-8
--------------------------------------------------------------------------------
Finished at 2021-11-26T05:50:18Z
Build needed 00:08:53, 34432k disk space