[med-svn] [Git][med-team/libseqlib][master] 4 commits: Make sure also private headers of htslib will be installed and usable since…

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / libseqlib


Commits:
d9ecf04c by Andreas Tille at 2018-03-05T16:24:05+01:00
Make sure also private headers of htslib will be installed and usable since these are used in libseqlib-dev

- - - - -
a46d8dfe by Andreas Tille at 2018-03-05T16:24:32+01:00
Standards-Version: 4.1.3

- - - - -
38ebebcb by Andreas Tille at 2018-03-05T16:24:51+01:00
debhelper 11

- - - - -
d15d1594 by Andreas Tille at 2018-03-05T16:45:10+01:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/patches/series
- + debian/patches/use_private_htslib_headers.patch


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+libseqlib (1.1.1+dfsg-4) unstable; urgency=medium
+
+  * Make sure also private headers of htslib will be installed and usable
+    since these are used in libseqlib-dev
+    Closes: #891745
+  * Standards-Version: 4.1.3
+  * debhelper 11
+
+ -- Andreas Tille <tille at debian.org>  Mon, 05 Mar 2018 16:25:15 +0100
+
 libseqlib (1.1.1+dfsg-3) unstable; urgency=medium
 
   * Remove liblzma-dev again since it is only used for dist target


=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                d-shlibs,
                pkg-config,
                libhts-private-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 10),
                libbwa-dev (>= 0.7.15-3),
                libjsoncpp-dev,
                libssw-dev
-Standards-Version: 4.1.2
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libseqlib.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/libseqlib.git
 Homepage: https://github.com/walaj/SeqLib
@@ -43,6 +43,7 @@ Depends: libseqlib0 (= ${binary:Version}),
          ${shlibs:Depends},
          ${misc:Depends},
          libhts-dev (>= 1.3.2-3),
+         libhts-private-dev,
          libjsoncpp-dev,
          libbwa-dev,
          libfml-dev


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -7,3 +7,4 @@ dynamic_lib.patch
 use_debian_packaged_jsoncpp.patch
 use_debian_packaged_ssw.patch
 pkg-config.patch
+use_private_htslib_headers.patch


=====================================
debian/patches/use_private_htslib_headers.patch
=====================================
--- /dev/null
+++ b/debian/patches/use_private_htslib_headers.patch
@@ -0,0 +1,27 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 05 Mar 2018 15:39:42 +0100
+Bug-Debian: https://bugs.debian.org/891745
+Description: Hack around improper use of private files of htslib
+
+--- a/SeqLib/BamWalker.h
++++ b/SeqLib/BamWalker.h
+@@ -12,8 +12,8 @@
+ #endif
+ 
+ extern "C" {
+-#include "htslib/cram/cram.h"
+-#include "htslib/cram/cram_io.h"
++#include <htslib/cram/cram.h>
++#include <htslib/cram/cram_io.h>
+ }
+ 
+ struct idx_delete {
+--- a/libseqlib.pc.in
++++ b/libseqlib.pc.in
+@@ -7,5 +7,5 @@ Name: libseqlib
+ Version: @VERSION@
+ Description: C++ htslib/bwa-mem/fermi interface for interrogating sequence data
+ Libs: -L${libdir} -lseqlib -lfml -lbwa -lssw
+-Cflags: -I${includedir}
++Cflags: -I${includedir} -I/usr/include/htslib
+ 



View it on GitLab: https://salsa.debian.org/med-team/libseqlib/compare/b03053066a1afb6b25ae0c560584105c8908e3c6...d15d15945f046b947d4218719ae56fede19eaa44

---
View it on GitLab: https://salsa.debian.org/med-team/libseqlib/compare/b03053066a1afb6b25ae0c560584105c8908e3c6...d15d15945f046b947d4218719ae56fede19eaa44
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