[med-svn] [bamtools] 04/05: gbp pq import/export to refresh package queue
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Sep 24 07:41:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository bamtools.
commit f964536dc168320362f26eddd0777814bf09c235
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Thu Sep 24 17:26:07 2015 +1000
gbp pq import/export to refresh package queue
---
.../0001-ignore-thirdparty-and-fix-jsoncpp.patch | 33 +++++++++-------
.../patches/0002-support-out-of-source-build.patch | 18 ++++++---
...om-ExportHeader-function-use-install-inst.patch | 45 +++++++++++++---------
...ls-statically-with-libbamtools-utils-as-w.patch | 22 -----------
...bamtools-to-lib.-Installing-libraries-to-.patch | 14 +++++--
debian/patches/0006-Doxygen-reproducibility | 15 +++++---
debian/patches/series | 1 -
7 files changed, 79 insertions(+), 69 deletions(-)
diff --git a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
index abfbc76..321e91d 100644
--- a/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
+++ b/debian/patches/0001-ignore-thirdparty-and-fix-jsoncpp.patch
@@ -3,10 +3,13 @@ Date: Wed, 7 Nov 2012 18:44:06 -0700
Subject: ignore-thirdparty-and-fix-jsoncpp
---
- src/CMakeLists.txt | 2 +-
- src/toolkit/bamtools_filter.cpp | 2 +-
- 2 files changed, 238 insertions(+), 2 deletions(-)
+ src/CMakeLists.txt | 2 +-
+ src/toolkit/CMakeLists.txt | 1 -
+ src/toolkit/bamtools_filter.cpp | 2 +-
+ 3 files changed, 2 insertions(+), 3 deletions(-)
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index e359695..636bd62 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -6,7 +6,7 @@
@@ -18,6 +21,20 @@ Subject: ignore-thirdparty-and-fix-jsoncpp
add_subdirectory( toolkit )
add_subdirectory( utils )
+diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
+index c781148..d074870 100644
+--- a/src/toolkit/CMakeLists.txt
++++ b/src/toolkit/CMakeLists.txt
+@@ -8,7 +8,6 @@
+ # set include path
+ include_directories( ${BamTools_SOURCE_DIR}/src/api
+ ${BamTools_SOURCE_DIR}/src/utils
+- ${BamTools_SOURCE_DIR}/src/third_party
+ )
+
+ # compile main bamtools application
+diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp
+index 2f17242..521e7c2 100644
--- a/src/toolkit/bamtools_filter.cpp
+++ b/src/toolkit/bamtools_filter.cpp
@@ -16,7 +16,7 @@
@@ -29,13 +46,3 @@ Subject: ignore-thirdparty-and-fix-jsoncpp
using namespace Json;
#include <cstdio>
---- a/src/toolkit/CMakeLists.txt
-+++ b/src/toolkit/CMakeLists.txt
-@@ -8,7 +8,6 @@
- # set include path
- include_directories( ${BamTools_SOURCE_DIR}/src/api
- ${BamTools_SOURCE_DIR}/src/utils
-- ${BamTools_SOURCE_DIR}/src/third_party
- )
-
- # compile main bamtools application
diff --git a/debian/patches/0002-support-out-of-source-build.patch b/debian/patches/0002-support-out-of-source-build.patch
index 9a0c9b9..e5d1eb0 100644
--- a/debian/patches/0002-support-out-of-source-build.patch
+++ b/debian/patches/0002-support-out-of-source-build.patch
@@ -3,14 +3,16 @@ Date: Fri, 21 Sep 2012 11:16:28 -0400
Subject: support out-of-source build
---
- CMakeLists.txt | 5 +++--
- src/ExportHeader.cmake | 2 +-
- src/toolkit/CMakeLists.txt | 2 +-
+ CMakeLists.txt | 5 +++--
+ src/ExportHeader.cmake | 2 +-
+ src/toolkit/CMakeLists.txt | 2 +-
3 files changed, 5 insertions(+), 4 deletions(-)
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index dade1e3..c4f5ab7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 3 )
+@@ -35,8 +35,8 @@ set( BamTools_VERSION_MINOR 4 )
set( BamTools_VERSION_BUILD 0 )
# set our library and executable destination dirs
@@ -29,9 +31,11 @@ Subject: support out-of-source build
# list subdirectories to build in
add_subdirectory( src )
+diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake
+index ec62573..ddfe410 100644
--- a/src/ExportHeader.cmake
+++ b/src/ExportHeader.cmake
-@@ -18,7 +18,7 @@ function( ExportHeader MODULE FILE DEST
+@@ -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}/${FILE}"
@@ -40,9 +44,11 @@ Subject: support out-of-source build
# make sure files are properly 'installed'
install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" )
+diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
+index d074870..e6a2da9 100644
--- a/src/toolkit/CMakeLists.txt
+++ b/src/toolkit/CMakeLists.txt
-@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROP
+@@ -34,7 +34,7 @@ set_target_properties( bamtools_cmd PROPERTIES
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 60c8188..a465e85 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
@@ -3,13 +3,15 @@ Date: Fri, 19 Oct 2012 11:35:52 -0400
Subject: remove custom ExportHeader function, use install instead
---
- src/CMakeLists.txt | 5 +----
- src/ExportHeader.cmake | 27 ------------------------
- src/api/CMakeLists.txt | 49 ++++++++++++++++++++++----------------------
- src/toolkit/CMakeLists.txt | 3 +++
- 4 files changed, 28 insertions(+), 56 deletions(-)
+ src/CMakeLists.txt | 5 +----
+ src/ExportHeader.cmake | 27 ---------------------------
+ src/api/CMakeLists.txt | 42 +++++++++++++++++++-----------------------
+ src/toolkit/CMakeLists.txt | 3 +++
+ 4 files changed, 23 insertions(+), 54 deletions(-)
delete mode 100644 src/ExportHeader.cmake
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index 636bd62..3298ff9 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -10,7 +10,4 @@ add_subdirectory( api )
@@ -21,6 +23,9 @@ Subject: remove custom ExportHeader function, use install instead
-set( SharedIncludeDir "shared" )
-ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} )
+install( FILES shared/bamtools_global.h DESTINATION "include/bamtools/shared" COMPONENT Development )
+diff --git a/src/ExportHeader.cmake b/src/ExportHeader.cmake
+deleted file mode 100644
+index ddfe410..0000000
--- a/src/ExportHeader.cmake
+++ /dev/null
@@ -1,27 +0,0 @@
@@ -51,21 +56,11 @@ 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 )
+diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt
+index 32edcff..91ce1a2 100644
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
-@@ -57,27 +57,23 @@ target_link_libraries( BamTools-static $
+@@ -57,27 +57,23 @@ target_link_libraries( BamTools-static ${APILibs} )
install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin")
install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools")
@@ -112,3 +107,17 @@ Subject: remove custom ExportHeader function, use install instead
-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/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt
+index e6a2da9..d4a221f 100644
+--- a/src/toolkit/CMakeLists.txt
++++ b/src/toolkit/CMakeLists.txt
+@@ -35,6 +35,9 @@ set_target_properties( bamtools_cmd PROPERTIES
+ )
+ # 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 )
diff --git a/debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch b/debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch
deleted file mode 100644
index cd35a58..0000000
--- a/debian/patches/0004-Link-bamtools-statically-with-libbamtools-utils-as-w.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
-Date: Wed, 7 Nov 2012 19:07:43 -0700
-Subject: Link bamtools statically with libbamtools-utils as we aren't
- distributing it seperately
-
----
- src/utils/CMakeLists.txt | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt
-index 2d91ca3..b38859c 100644
---- a/src/utils/CMakeLists.txt
-+++ b/src/utils/CMakeLists.txt
-@@ -13,7 +13,7 @@ add_definitions( -DBAMTOOLS_UTILS_LIBRARY ) # (for proper exporting of library s
- add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake)
-
- # create BamTools utils library
--add_library( BamTools-utils SHARED
-+add_library( BamTools-utils STATIC
- bamtools_fasta.cpp
- bamtools_options.cpp
- bamtools_pileup_engine.cpp
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 c63c60a..1a35403 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
@@ -1,12 +1,18 @@
From: "Michael R. Crusoe" <michael.crusoe at gmail.com>
Date: Wed, 7 Nov 2012 19:11:51 -0700
-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.
+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 91ce1a2..b6fa538 100644
--- a/src/api/CMakeLists.txt
+++ b/src/api/CMakeLists.txt
-@@ -54,8 +54,8 @@ target_link_libraries( BamTools $
+@@ -54,8 +54,8 @@ target_link_libraries( BamTools ${APILibs} )
target_link_libraries( BamTools-static ${APILibs} )
# set library install destinations
diff --git a/debian/patches/0006-Doxygen-reproducibility b/debian/patches/0006-Doxygen-reproducibility
index 58229dd..d6710c8 100644
--- a/debian/patches/0006-Doxygen-reproducibility
+++ b/debian/patches/0006-Doxygen-reproducibility
@@ -1,11 +1,16 @@
-Description: Turns off timestamps in documentation generated by Doxygen
-Author: Michael R. Crusoe <mcrusoe at msu.edu>
-Forwarded: no
-Last-Update: 2015-02-21
+From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Date: Thu, 24 Sep 2015 17:25:24 +1000
+Subject: Doxygen-reproducibility
+---
+ docs/Doxyfile | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/docs/Doxyfile b/docs/Doxyfile
+index 7c21624..2a0f578 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
-@@ -853,7 +853,7 @@
+@@ -853,7 +853,7 @@ HTML_STYLESHEET =
# page will contain the date and time when the page was generated. Setting
# this to NO can help when comparing the output of multiple runs.
diff --git a/debian/patches/series b/debian/patches/series
index f3a85fb..32d122c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +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
0005-Install-libbamtools-to-lib.-Installing-libraries-to-.patch
0006-Doxygen-reproducibility
--
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