[med-svn] [Git][med-team/htslib][master] 8 commits: for some very strange reason /usr/include/htslib/cram/cram.h is using the...

Andreas Tille gitlab at salsa.debian.org
Tue Dec 17 13:35:48 GMT 2019 


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 <tille at debian.org>  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 <plessy at debian.org>,
            Michael R. Crusoe <michael.crusoe at gmail.com>
 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
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