[med-svn] [bamtools] 07/08: Adapt patches to new upstream version
Andreas Tille
tille at debian.org
Wed Apr 2 13:31:05 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian
in repository bamtools.
commit 87e9ad2f73f924fd30938165d08b1177f0372478
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 2 15:25:36 2014 +0200
Adapt patches to new upstream version
---
.../patches/0002-support-out-of-source-build.patch | 10 ++---
...om-ExportHeader-function-use-install-inst.patch | 46 +++++++++-------------
...bamtools-to-lib.-Installing-libraries-to-.patch | 28 +++++--------
debian/patches/series | 2 +-
4 files changed, 34 insertions(+), 52 deletions(-)
diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch
index 9dcd1c6..9a0c9b9 100644
--- a/debian/patches/0002-support-out-of-source-build.patch
+++ b/debian/patches/0002-support-out-of-source-build.patch
@@ -10,8 +10,8 @@ Subject: support out-of-source build
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -35,8 +35,8 @@
- set( BamTools_VERSION_BUILD 3 )
+@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 3 )
+ set( BamTools_VERSION_BUILD 0 )
# set our library and executable destination dirs
-set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" )
@@ -21,7 +21,7 @@ Subject: support out-of-source build
# define compiler flags for all code
set( CMAKE_BUILD_TYPE Release )
-@@ -60,6 +60,7 @@
+@@ -60,6 +60,7 @@ endif()
# add our includes root path
include_directories( src )
@@ -31,7 +31,7 @@ Subject: support out-of-source build
add_subdirectory( src )
--- a/src/ExportHeader.cmake
+++ b/src/ExportHeader.cmake
-@@ -18,7 +18,7 @@
+@@ -18,7 +18,7 @@ function( ExportHeader MODULE FILE DEST
add_custom_command( TARGET ${MODULE} COMMAND
${CMAKE_COMMAND} -E copy_if_different
"${CMAKE_CURRENT_SOURCE_DIR}/${FILE}"
@@ -42,7 +42,7 @@ Subject: support out-of-source build
install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" )
--- a/src/toolkit/CMakeLists.txt
+++ b/src/toolkit/CMakeLists.txt
-@@ -34,7 +34,7 @@
+@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROP
OUTPUT_NAME "bamtools"
)
# make version info available in application
diff --git a/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch b/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch
index b2aea53..60c8188 100644
--- a/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch
+++ b/debian/patches/0003-remove-custom-ExportHeader-function-use-install-inst.patch
@@ -12,7 +12,7 @@ Subject: remove custom ExportHeader function, use install instead
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -10,7 +10,4 @@
+@@ -10,7 +10,4 @@ add_subdirectory( api )
add_subdirectory( toolkit )
add_subdirectory( utils )
@@ -51,17 +51,23 @@ Subject: remove custom ExportHeader function, use install instead
-
-endfunction( ExportHeader )
-
+--- a/src/toolkit/CMakeLists.txt
++++ b/src/toolkit/CMakeLists.txt
+@@ -35,6 +35,9 @@ set_target_properties( bamtools_cmd PROP
+ )
+ # make version info available in application
+ configure_file( bamtools_version.h.in ${BamTools_BINARY_DIR}/include/bamtools_version.h )
++install( FILES ${BamTools_BINARY_DIR}/include/bamtools_version.h
++ DESTINATION "include/bamtools"
++ COMPONENT Development )
+
+ # define libraries to link
+ target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp )
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
-@@ -54,30 +54,29 @@
- target_link_libraries( BamTools-static ${APILibs} )
-
- # set library install destinations
--install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
--install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
-+install( TARGETS BamTools
-+ LIBRARY DESTINATION "lib/bamtools"
-+ RUNTIME DESTINATION "bin")
+@@ -57,27 +57,23 @@ target_link_libraries( BamTools-static $
+ install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+ install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
-# export API headers
-include(../ExportHeader.cmake)
@@ -84,11 +90,6 @@ Subject: remove custom ExportHeader function, use install instead
-ExportHeader(APIHeaders SamReadGroupDictionary.h ${ApiIncludeDir})
-ExportHeader(APIHeaders SamSequence.h ${ApiIncludeDir})
-ExportHeader(APIHeaders SamSequenceDictionary.h ${ApiIncludeDir})
-+install( TARGETS BamTools-static
-+ ARCHIVE DESTINATION "lib/bamtools")
-
--set( AlgorithmsIncludeDir "api/algorithms" )
--ExportHeader( AlgorithmsHeaders algorithms/Sort.h ${AlgorithmsIncludeDir} )
+install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development )
+install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development )
+install( FILES BamAlignment.h DESTINATION "include/bamtools/api" COMPONENT Development )
@@ -107,16 +108,7 @@ Subject: remove custom ExportHeader function, use install instead
+install( FILES SamReadGroupDictionary.h DESTINATION "include/bamtools/api" COMPONENT Development )
+install( FILES SamSequence.h DESTINATION "include/bamtools/api" COMPONENT Development )
+install( FILES SamSequenceDictionary.h DESTINATION "include/bamtools/api" COMPONENT Development )
-+install( FILES algorithms/Sort.h DESTINATION "include/bamtools/api/algorithms" COMPONENT Development )
---- a/src/toolkit/CMakeLists.txt
-+++ b/src/toolkit/CMakeLists.txt
-@@ -35,6 +35,9 @@
- )
- # make version info available in application
- configure_file( bamtools_version.h.in ${BamTools_BINARY_DIR}/include/bamtools_version.h )
-+install( FILES ${BamTools_BINARY_DIR}/include/bamtools_version.h
-+ DESTINATION "include/bamtools"
-+ COMPONENT Development )
- # define libraries to link
- target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp )
+-set( AlgorithmsIncludeDir "api/algorithms" )
+-ExportHeader( AlgorithmsHeaders algorithms/Sort.h ${AlgorithmsIncludeDir} )
++install( FILES algorithms/Sort.h DESTINATION "include/bamtools/api/algorithms" COMPONENT Development )
diff --git a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
index a9b76f0..c63c60a 100644
--- a/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
+++ b/debian/patches/0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
@@ -1,29 +1,19 @@
From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
Date: Wed, 7 Nov 2012 19:11:51 -0700
-Subject: =?UTF-8?q?Install=20libbamtools=20to=20/lib.=20Installing=20librari?=
- =?UTF-8?q?es=20to=20/lib/bamtools=20requires=20setting=0ALD=5FLIBRARY=5FPAT?=
- =?UTF-8?q?H=20or=20the=20executable's=20rpath.=20Installing=20libraries=20t?=
- =?UTF-8?q?o=0A/lib=20is=20cleaner.?=
+Subject: Install libbamtools to /usr/lib. Installing libraries to
+ /usr/lib/bamtools requires setting LD_LIBRARY_PATH or the
+ executable's rpath. Installing libraries to /usr/lib is cleaner.
----
- src/api/CMakeLists.txt | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
-index 8234e78..b1b372a 100644
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
-@@ -55,11 +55,11 @@ target_link_libraries( BamTools-static ${APILibs} )
+@@ -54,8 +54,8 @@ target_link_libraries( BamTools $
+ target_link_libraries( BamTools-static ${APILibs} )
# set library install destinations
- install( TARGETS BamTools
-- LIBRARY DESTINATION "lib/bamtools"
-+ LIBRARY DESTINATION "lib"
- RUNTIME DESTINATION "bin")
-
- install( TARGETS BamTools-static
-- ARCHIVE DESTINATION "lib/bamtools")
-+ ARCHIVE DESTINATION "lib")
+-install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
+-install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
++install( TARGETS BamTools LIBRARY DESTINATION "lib" RUNTIME DESTINATION "bin")
++install( TARGETS BamTools-static ARCHIVE DESTINATION "lib")
install( FILES api_global.h DESTINATION "include/bamtools/api" COMPONENT Development )
install( FILES BamAlgorithms.h DESTINATION "include/bamtools/api" COMPONENT Development )
diff --git a/debian/patches/series b/debian/patches/series
index d623b9a..794a5a2 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,5 @@
0001-ignore-thirdparty-and-fix-jsoncpp.patch
0002-support-out-of-source-build.patch
0003-remove-custom-ExportHeader-function-use-install-inst.patch
-0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch
+# 0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch
0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bamtools.git
More information about the debian-med-commit
mailing list