Andreas Tille pushed to branch master at Debian Med / libmaus2
Commits: b8f2041e by Andreas Tille at 2019-04-12T12:04:52Z Use d-shlibs - - - - - c72db1d2 by Andreas Tille at 2019-04-12T13:28:37Z Fix installation - - - - - ed125ec5 by Andreas Tille at 2019-04-12T13:58:04Z Start working on d/copyright - needs more work - - - - - 6 changed files: - debian/control - debian/copyright - + debian/libmaus2-2.install - + debian/libmaus2-dev.install - − debian/lintian-overrides - debian/rules Changes: ===================================== debian/control ===================================== @@ -4,13 +4,17 @@ Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 12~), + d-shlibs, + pkg-config, + zlib1g-dev Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/libmaus2 Vcs-Git: https://salsa.debian.org/med-team/libmaus2.git Homepage: https://gitlab.com/german.tischler/libmaus2 -Package: libmaus2 +Package: libmaus2-2 Architecture: any +Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Description: collection of data structures and algorithms for biobambam @@ -22,3 +26,19 @@ Description: collection of data structures and algorithms for biobambam * BAM sequence alignment files input/output (simple and collating) . and many lower level support classes. + +Package: libmaus2-dev +Architecture: any +Section: libdevel +Depends: libmaus2-2 (= ${binary:Version}), + ${shlibs:Depends}, + ${misc:Depends} +Description: collection of data structures and algorithms for biobambam + Libmaus2 is a collection of data structures and algorithms. It contains + . + * I/O classes (single byte and UTF-8) + * bitio classes (input, output and various forms of bit level manipulation) + * text indexing classes (suffix and LCP array, fulltext and minute (FM), ...) + * BAM sequence alignment files input/output (simple and collating) + . + and many lower level support classes. ===================================== debian/copyright ===================================== @@ -3,9 +3,49 @@ Upstream-Name: libmaus2 Source: https://gitlab.com/german.tischler/libmaus2/tags Files: * -Copyright: 20xx-20yy <upstream> -License: <license> +Copyright: 2010-2016 German Tischler +License: GPL-3+ + +Files: src/libmaus2/hashing/hash.hpp +Copyright: 1996, Bob Jenkins <[email protected]> +License: public_domain + You may use this code any way you wish, private, educational, or commercial. + It's free. + +Files: src/libmaus2/lcp/OracleLCP* +Copyright: 2008 Simon Puglisi + 2009-2013 German Tischler + 2011-2013 Genome Research Limited +License: GPL-3+ + +Files: src/libmaus2/rmq/FischerSystematicSuccinctRMQ* +Copyright: 2010 Johannes Fischer + 2010-2013 German Tischler + 2011-2013 Genome Research Limited +License: GPL-3+ + +Files: src/libmaus2/util/NearestNeighbourDictionary.* + src/libmaus2/bp/BalancedParenthesesBase.hpp +Copyright: 2007-2012 Simon Gog (SDSL library) + 2009-2013 German Tischler + 2011-2013 Genome Research Limited +License: GPL-3 + +radixsort code in src/libmaus2/sorting/SerialRadixSort64.hpp adapted from code by Andrew I. Schein (see file for license) +divsufsort code in src/libmaus2/suffixsort/divsufsort* by Yuta Mori (see file for license) +SAIS code in src/libmaus2/suffixsort/SAIS_Mori.hpp by Yuta Mori (see file for license) +md5 code in src/libmaus2/digest/md5.[ch] by L. Peter Deutsch (Aladdin Enterprises) (see file for license) +some code in src/libmaus2/bambam/DuplicationMetrics.hpp is imported from the Picard project (MIT license, see file for copyright) +LZ4 code in src/libmaus2/lz/lz4.[ch] by Yann Collect (BSD 2-Clause licence, see files) +CRC32 code in src/libmaus2/hashing/Crc3.{cpp/hpp} by Stephan Brumme (ZLib type license, see files) +libmaus2/digest/sha(256|512)_*.asm (Intel license, see files) +Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Mark Adler (see file for license) +Part of CRC32{|C} code in src/libmaus2/digest/CRC32{|C}_Core.cpp by Cisco Systems, Inc. and Herbert Xu (GPLv2) +Hash code in src/libmaus2/hashing/MurmurHash3.{cpp|h} and libmaus2/digest/MurmurHash3_x64_128.hpp by Austin Appleby (public domain) +Rest by German Tischler published under GPLv2/GPLv3 (some of it written while at Genome Research Limited/WTSI) + + Files: debian/* Copyright: 2019 Andreas Tille <[email protected]> -License: <license> +License: GPL-3+ ===================================== debian/libmaus2-2.install ===================================== @@ -0,0 +1,2 @@ +usr/lib/*/libmaus2*.so.* +usr/lib/*/libmaus2/2.*/libmaus2_scram_mod.so ===================================== debian/libmaus2-dev.install ===================================== @@ -0,0 +1,2 @@ +usr/lib/*/libmaus2*.a +usr/lib/*/libmaus2*.so ===================================== debian/lintian-overrides deleted ===================================== @@ -1,2 +0,0 @@ -# see https://lists.debian.org/debian-med/2018/06/msg00043.html -#PKGNAME#: script-with-language-extension usr/bin/*.* ===================================== debian/rules ===================================== @@ -3,16 +3,7 @@ # DH_VERBOSE := 1 export LC_ALL=C.UTF-8 -include /usr/share/dpkg/default.mk -# this provides: -# DEB_SOURCE: the source package name -# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision) -# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision -# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch -# DEB_VERSION_UPSTREAM: the package's upstream version -# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog -# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as -# specified by <https://reproducible-builds.org/specs/source-date-epoch/> +# include /usr/share/dpkg/default.mk # for hardening you might like to uncomment this: # export DEB_BUILD_MAINT_OPTIONS=hardening=+all @@ -20,12 +11,27 @@ include /usr/share/dpkg/default.mk %: dh $@ +override_dh_install: + dh_install + d-shlibmove --commit \ + --multiarch \ + --devunversioned \ + --exclude-la \ + --movedev debian/tmp/usr/include/* usr/include \ + --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \ + debian/tmp/usr/lib/*/*.so + # Remove unneeded options from *.pc files + find debian -name "*.pc" -exec sed -i -e 's/-Wdate-time *//' -e 's/-D_FORTIFY_SOURCE=2 *//' \{\} \; + # avoid noise from dh-missing by deleting unneeded files + find debian/tmp -type f -name "*.la" -delete + # Changelog is installed via dh_installchangelogs + rm -f debian/tmp/usr/share/doc/libmaus2/changelog.gz + +override_dh_installchangelogs: + dh_installchangelogs ChangeLog + ### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected #override_dh_auto_test: #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) # do_stuff_for_testing #endif - -### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script -#get-orig-source: -# . debian/get-orig-source View it on GitLab: https://salsa.debian.org/med-team/libmaus2/compare/89b8e7a8f9697789fc0ced18e0780617f4903dd9...ed125ec56451e5d0fb0404173a72630c0810fe8d -- View it on GitLab: https://salsa.debian.org/med-team/libmaus2/compare/89b8e7a8f9697789fc0ced18e0780617f4903dd9...ed125ec56451e5d0fb0404173a72630c0810fe8d You're receiving this email because of your account on salsa.debian.org.
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