[med-svn] [Git][med-team/staden-io-lib][master] New version.

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / staden-io-lib


Commits:
b27ab65f by Steffen Moeller at 2020-05-21T00:31:14+02:00
New version.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/usedebianhtscodecs.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,22 @@
-staden-io-lib (1.14.12-1) UNRELEASED; urgency=medium
+staden-io-lib (1.14.12-1) unstable; urgency=medium
 
+  * Team upload.
+
+  [ Michael Crusoe ]
   * New upstream version
   * Standards-Version: 4.5.0 (routine-update)
   * debhelper-compat 12 (routine-update)
   * Remove many patches incorporated upstream
   * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g (routine-update)
 
+  [ Steffen Moeller ]
+  * Fixed FTBFS - added dep on libhtscodecs-dev now distributed
+    as a git submodule of staden-io-lib.
+  * Rules-Requires-Root: no
+  * Adjusted library package name to updated soversion 14
+  * Added extra argument to d-shlibmove to override search for
+    unversioned libhtscodecs-dev package
+
  -- Michael R. Crusoe <michael.crusoe at gmail.com>  Mon, 10 Feb 2020 10:51:13 +0100
 
 staden-io-lib (1.14.11-6) unstable; urgency=medium


=====================================
debian/control
=====================================
@@ -9,11 +9,13 @@ Priority: optional
 Build-Depends: debhelper-compat (= 12),
                zlib1g-dev,
                libcurl4-gnutls-dev | libcurl4-nss-dev,
+               libhtscodecs-dev,
                d-shlibs
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib
 Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git
 Homepage: https://github.com/jkbonfield/io_lib
+Rules-Requires-Root: no
 
 Package: staden-io-lib-utils
 Architecture: any
@@ -34,7 +36,7 @@ Description: programs for manipulating DNA sequencing files
 Package: libstaden-read-dev
 Architecture: any
 Section: libdevel
-Depends: libstaden-read13 (= ${binary:Version}),
+Depends: libstaden-read14 (= ${binary:Version}),
          ${misc:Depends},
 	 ${devlibs:Depends}
 Description: development files for libstaden-read
@@ -46,7 +48,7 @@ Description: development files for libstaden-read
  interface. It has been compiled and tested on a variety of unix systems,
  MacOS X and MS Windows.
 
-Package: libstaden-read13
+Package: libstaden-read14
 Architecture: any
 Multi-Arch: same
 Section: libs


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 pathmax.patch
 fix_fseeko.patch
 spelling
+usedebianhtscodecs.patch


=====================================
debian/patches/usedebianhtscodecs.patch
=====================================
@@ -0,0 +1,26 @@
+Index: staden-io-lib/Makefile.am
+===================================================================
+--- staden-io-lib.orig/Makefile.am
++++ staden-io-lib/Makefile.am
+@@ -32,7 +32,7 @@
+ AUTOMAKE_OPTIONS = foreign no-dependencies
+ ACLOCAL_AMFLAGS = -I m4
+ 
+-SUBDIRS = htscodecs io_lib progs tests
++SUBDIRS = io_lib progs tests
+ 
+ man_MANS = \
+ 	man/man1/srf_index_hash.1 \
+Index: staden-io-lib/io_lib/Makefile.am
+===================================================================
+--- staden-io-lib.orig/io_lib/Makefile.am
++++ staden-io-lib/io_lib/Makefile.am
+@@ -134,6 +134,6 @@ libstaden_read_la_SOURCES = \
+ 	bgzip.h \
+ 	cram_block_compression.h
+ 
+-libstaden_read_la_CPPFLAGS = -I${top_srcdir} -I${top_srcdir}/htscodecs @LIBCURL_CPPFLAGS@
++libstaden_read_la_CPPFLAGS = -I${top_srcdir} -I/usr/include/htscodecs @LIBCURL_CPPFLAGS@
+ libstaden_read_la_LDFLAGS = -version-info @VERS_CURRENT@:@VERS_REVISION@:@VERS_AGE@ 
+-libstaden_read_la_LIBADD = @LIBZ@ @LIBCURL@ ${top_builddir}/htscodecs/htscodecs/libhtscodecs.la
++libstaden_read_la_LIBADD = @LIBZ@ @LIBCURL@ -lhtscodecs


=====================================
debian/rules
=====================================
@@ -27,6 +27,7 @@ override_dh_install-arch:
 		    --devunversioned \
 		    --exclude-la \
 		    --movedev "debian/tmp/usr/include" usr \
+	            --override s/libhtscodecs2-dev/libhtscodecs-dev/ \
 		    debian/tmp/usr/lib/*/$(libpkg).so
 	#
 	# make sure io_lib-config --libs will not return -pie (see  #825461)
@@ -63,6 +64,7 @@ override_dh_fixperms-indep:
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam
+	rm -f config.sub config.guess
 	##
 	## Try to verify correct ABI version right in the beginning
 	## Strangely enough d-shlibmove fails in detecting it in this package



View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/commit/b27ab65ff3033e3a02a0ade35ab5e4c1e33ae765

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View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/commit/b27ab65ff3033e3a02a0ade35ab5e4c1e33ae765
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