[med-svn] [libseqlib] 02/05: Explicitly use -I/usr/include/htslib instead of pkg-config in libhts-dev since upstream insisted that the cram headers are private (see bug #881359)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository libseqlib.

commit b1e4d662944e1a7b53add146d048a91a2f96a03b
Author: Andreas Tille <tille at debian.org>
Date:   Sun Dec 10 09:30:14 2017 +0100

    Explicitly use -I/usr/include/htslib instead of pkg-config in libhts-dev since upstream insisted that the cram headers are private (see bug #881359)
---
 debian/changelog                                 | 3 +++
 debian/patches/dynamic_lib.patch                 | 2 +-
 debian/patches/use_debian_packaged_jsoncpp.patch | 4 ++--
 debian/patches/use_debian_packaged_ssw.patch     | 2 +-
 debian/rules                                     | 5 -----
 5 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index c21d148..110fa67 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,9 @@ libseqlib (1.1.1+dfsg-3) UNRELEASED; urgency=medium
   * Remove liblzma-dev again since it is only used for dist target
   * Build-Depends: libhts-private-dev since libhts-dev does not provide
     private cran headers any more (see bug #881170)
+  * Explicitly use -I/usr/include/htslib instead of pkg-config in libhts-dev
+    since upstream insisted that the cram headers are private
+    (see bug #881359)
 
  -- Andreas Tille <tille at debian.org>  Sun, 18 Jun 2017 10:28:01 +0200
 
diff --git a/debian/patches/dynamic_lib.patch b/debian/patches/dynamic_lib.patch
index 0917c5c..08e4930 100644
--- a/debian/patches/dynamic_lib.patch
+++ b/debian/patches/dynamic_lib.patch
@@ -9,7 +9,7 @@ Description: Create dynamic library
 +lib_LTLIBRARIES  = libseqlib.la
  
 -libseqlib_a_CPPFLAGS = -I../ -I../htslib -I/usr/include/fml -Wno-sign-compare
-+libseqlib_la_CPPFLAGS = -I/usr/include `pkg-config --cflags htslib` -I/usr/include/fml -Wno-sign-compare
++libseqlib_la_CPPFLAGS = -I/usr/include -I/usr/include/htslib -I/usr/include/fml -Wno-sign-compare
  
 -libseqlib_a_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
 +libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
diff --git a/debian/patches/use_debian_packaged_jsoncpp.patch b/debian/patches/use_debian_packaged_jsoncpp.patch
index f9ef394..9755128 100644
--- a/debian/patches/use_debian_packaged_jsoncpp.patch
+++ b/debian/patches/use_debian_packaged_jsoncpp.patch
@@ -7,8 +7,8 @@ Description: Do not use code copy of jsoncpp
 @@ -1,8 +1,8 @@
  lib_LTLIBRARIES  = libseqlib.la
  
--libseqlib_la_CPPFLAGS = -I/usr/include `pkg-config --cflags htslib` -I/usr/include/fml -Wno-sign-compare
-+libseqlib_la_CPPFLAGS = -I/usr/include `pkg-config --cflags htslib` -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare
+-libseqlib_la_CPPFLAGS = -I/usr/include -I/usr/include/htslib -I/usr/include/fml -Wno-sign-compare
++libseqlib_la_CPPFLAGS = -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare
  
 -libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
 +libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp ssw_cpp.cpp ssw.c \
diff --git a/debian/patches/use_debian_packaged_ssw.patch b/debian/patches/use_debian_packaged_ssw.patch
index 3912174..653eae6 100644
--- a/debian/patches/use_debian_packaged_ssw.patch
+++ b/debian/patches/use_debian_packaged_ssw.patch
@@ -14,7 +14,7 @@ Description: Do not use code copy of libssw
 +++ b/src/Makefile.am
 @@ -2,7 +2,7 @@ lib_LTLIBRARIES  = libseqlib.la
  
- libseqlib_la_CPPFLAGS = -I/usr/include `pkg-config --cflags htslib` -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare
+ libseqlib_la_CPPFLAGS = -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare
  
 -libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp ssw_cpp.cpp ssw.c \
 +libseqlib_la_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp \
diff --git a/debian/rules b/debian/rules
index 1357d26..2fd11d7 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,11 +11,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 	dh $@
 
 override_dh_auto_build:
-	# FIXME
-	# upstream is using code from htslib-test which is made
-	# available via this hackish link.  The proper solution
-	# would surely be to move cram/cram.h to libhts-dev
-	ln -s /usr/share/htslib-test/cram/ htslib
 	dh_auto_build
 	rm htslib/cram
 

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libseqlib.git