Andreas Tille pushed to branch master at Debian Med / htslib
Commits: 2f390879 by Andreas Tille at 2019-12-17T12:19:32Z for some very strange reason /usr/include/htslib/cram/cram.h is using the private interface header.h. This is provided now in the libhts-private-dev package rather than htslib-test - - - - - 32684fbc by Andreas Tille at 2019-12-17T12:23:40Z debhelper-compat 12 - - - - - e6d55aaf by Andreas Tille at 2019-12-17T12:24:09Z R-U: DEB_BUILD_OPTIONS allow override_dh_auto_test - - - - - 98615441 by Andreas Tille at 2019-12-17T12:25:32Z Remove trailing whitespace in debian/rules - - - - - 59a725c6 by Andreas Tille at 2019-12-17T12:26:33Z Set upstream metadata fields: Bug-Database, Repository, Repository-Browse. - - - - - d4a63315 by Andreas Tille at 2019-12-17T13:29:46Z Fix more verbose error reporting in case of failed tests - - - - - 498fdd91 by Andreas Tille at 2019-12-17T13:34:03Z Fix Perl interpreter path - - - - - 61e050b9 by Andreas Tille at 2019-12-17T13:35:36Z Fix permissions of script - - - - - 6 changed files: - debian/changelog - − debian/compat - debian/control - debian/libhts-private-dev.install - debian/rules - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,17 @@ +htslib (1.10-3) UNRELEASED; urgency=medium + + * for some very strange reason /usr/include/htslib/cram/cram.h is using the + private interface header.h. This is provided now in the + libhts-private-dev package rather than htslib-test + * debhelper-compat 12 + * DEB_BUILD_OPTIONS allow override_dh_auto_test + * Remove trailing whitespace in debian/rules + * More verbose error reporting in case of failed tests + * Fix Perl interpreter path + * Fix permissions of script + + -- Andreas Tille <[email protected]> Tue, 17 Dec 2019 11:31:46 +0100 + htslib (1.10-2) unstable; urgency=medium * Fix check for config.mk. ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -5,7 +5,7 @@ Uploaders: Charles Plessy <[email protected]>, Michael R. Crusoe <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 12), dh-exec, libbz2-dev, libcurl4-gnutls-dev, ===================================== debian/libhts-private-dev.install ===================================== @@ -1 +1,2 @@ cram/*.h usr/include/htslib/cram +header.h usr/include/htslib/cram ===================================== debian/rules ===================================== @@ -26,7 +26,7 @@ endif cp -a test test_backup autoconf dh_auto_configure -- --enable-libcurl --enable-gcs --enable-s3 - + override_dh_auto_build-arch: dh_auto_build -- \ CFLAGS="$$(dpkg-buildflags --get CFLAGS)" \ @@ -51,18 +51,44 @@ override_dh_auto_install-arch: override_dh_auto_install-indep: override_dh_auto_test-arch: - dh_auto_test || for file in $$(find . -name "FAIL*"); do echo $${file}; cat $${file}; done && false +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + dh_auto_test || \ + if find . -name "FAIL*" > /dev/null ; then \ + for file in $$(find . -name "FAIL*"); do echo $${file}; cat $${file}; done && false ; \ + fi +endif override_dh_auto_test-indep: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + echo "Suppress test for Architecture independant builds." +endif override_dh_install-indep: dh_install --indep sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk +override_dh_installdocs: + dh_installdocs + # Fix Perl interpreter path + for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ + sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \ + done + override_dh_installchangelogs: dh_installchangelogs NEWS +override_dh_link: + dh_link + # for some very strange reason /usr/include/htslib/cram/cram.h is using the private interface header.h + # this is provided now in the libhts-private-dev package rather than htslib-test so we need a symlink here + find debian/htslib-test -name header.h + dh_link -phtslib-test usr/include/htslib/cram/header.h usr/share/htslib-test/header.h + +override_dh_fixperms + dh_fixperms + find debian -name simple_test_driver.sh -exec chmod +x \{\} \; + override_dh_auto_clean: ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386)) ifneq (,$(wildcard debian/htslib.pc.in)) ===================================== debian/upstream/metadata ===================================== @@ -1,21 +1,22 @@ Reference: - Author: "Heng Li" - Title: > - Tabix: fast retrieval of sequence features from generic TAB-delimited - files - Journal: Bioinformatics - Year: 2011 - Volume: 27 - Number: 5 - Pages: 718-719 - DOI: 10.1093/bioinformatics/btq671 - PMID: 21208982 - URL: "https://academic.oup.com/bioinformatics/article/27/5/718/262743/\ - Tabix-fast-retrieval-of-sequence-features-from" - ePrint: "https://academic.oup.com/bioinformatics/article-pdf/\ - 27/5/718/5504485/btq671.pdf" + Author: Heng Li + Title: > + Tabix: fast retrieval of sequence features from generic TAB-delimited + files + Journal: Bioinformatics + Year: 2011 + Volume: 27 + Number: 5 + Pages: 718-719 + DOI: 10.1093/bioinformatics/btq671 + PMID: 21208982 + URL: https://academic.oup.com/bioinformatics/article/27/5/718/262743/Tabix-fast-retrieval-of-sequence-features-from + ePrint: https://academic.oup.com/bioinformatics/article-pdf/27/5/718/5504485/btq671.pdf Registry: - - Name: OMICtools - Entry: OMICS_13459 - - Name: conda:bioconda - Entry: htslib +- Name: OMICtools + Entry: OMICS_13459 +- Name: conda:bioconda + Entry: htslib +Bug-Database: https://github.com/samtools/htslib/issues +Repository: https://github.com/samtools/htslib.git +Repository-Browse: https://github.com/samtools/htslib View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/16482427526166bc5224fdf3a84bdd05ef9c9871...61e050b9d3d5e587cb5a4628fa61111b344ee4ed -- View it on GitLab: https://salsa.debian.org/med-team/htslib/compare/16482427526166bc5224fdf3a84bdd05ef9c9871...61e050b9d3d5e587cb5a4628fa61111b344ee4ed You're receiving this email because of your account on salsa.debian.org.
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