[med-svn] [Git][med-team/htqc][master] 2 commits: Merged patches from Andreas and mine
Andreas Tille
gitlab at salsa.debian.org
Wed May 2 14:51:10 BST 2018
Andreas Tille pushed to branch master at Debian Med / htqc
Commits:
6424435f by Leopold Palomo-Avellaneda at 2018-05-02T15:51:02+02:00
Merged patches from Andreas and mine
- - - - -
2ec383ce by Leopold Palomo-Avellaneda at 2018-05-02T15:51:02+02:00
Imported patches with gbp-pq
- - - - -
4 changed files:
- debian/patches/correct_cflags.patch → debian/patches/0001-correct_cflags.patch
- + debian/patches/0002-Added-Debian-specific-SONAMEs.patch.patch
- debian/patches/enable_testing.patch → debian/patches/0003-enable_testing.patch
- debian/patches/series
Changes:
=====================================
debian/patches/correct_cflags.patch → debian/patches/0001-correct_cflags.patch
=====================================
--- a/debian/patches/correct_cflags.patch
+++ b/debian/patches/0001-correct_cflags.patch
@@ -1,13 +1,13 @@
-Author: Gert Wollny <gw.fossdev at gmail.com>
-Last-Update: Mon, 22 Jun 2015 15:49:39 +0200
-Description: Fix cmake file
- The htqc authors might have used a version of cmake that interprets the
- CMAKE_CXX_FLAGS as a list, and Elements of lists in cmake are separated
- by ';'.
- .
- Apparently this is no longer possible so you'll have to (re-)set the
- cxx_flags string directly.
+From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Date: Tue, 23 Jun 2015 13:16:51 +0200
+Subject: correct_cflags
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 73d0f1a..90fadcb 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,7 +22,7 @@ if (CMAKE_BUILD_TYPE STREQUAL "")
=====================================
debian/patches/0002-Added-Debian-specific-SONAMEs.patch.patch
=====================================
--- /dev/null
+++ b/debian/patches/0002-Added-Debian-specific-SONAMEs.patch.patch
@@ -0,0 +1,449 @@
+From: Leopold Palomo-Avellaneda <leopold.palomo at upc.edu>
+Date: Tue, 23 Jun 2015 15:23:35 +0200
+Subject: Added Debian specific SONAMEs.patch
+
+---
+ src/CMakeLists.txt | 80 ++++++++++++++++++++++++++++++++++++++----------------
+ t/CMakeLists.txt | 66 ++++++++++++++++++++++----------------------
+ 2 files changed, 90 insertions(+), 56 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index a3bb0fc..6e0cf3c 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -5,22 +5,54 @@ file(GLOB HTIO_SOURCE_FILES htio2/*.cpp)
+ file(GLOB HTQC_SOURCE_FILES htqc/*.cpp)
+ file(GLOB JUCE_SOURCE_FILES htio2/JUCE-3.0.8/modules/*/*.cpp)
+
+-add_library(htio2 STATIC ${HTIO_SOURCE_FILES} ${JUCE_SOURCE_FILES})
++add_library(htio2_static STATIC ${HTIO_SOURCE_FILES} ${JUCE_SOURCE_FILES})
++set_target_properties(htio2_static PROPERTIES
++ OUTPUT_NAME htio2
++ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
++ CLEAN_DIRECT_OUTPUT 1)
+
+-add_library(ht_common STATIC ${HTQC_SOURCE_FILES})
++#CPACK_PACKAGE_VERSION_MAJOR 1
++#CPACK_PACKAGE_VERSION_MINOR 92
++#CPACK_PACKAGE_VERSION_PATCH 1
++
++add_library(htio2_dynamic SHARED ${HTIO_SOURCE_FILES} ${JUCE_SOURCE_FILES})
++set_target_properties( htio2_dynamic PROPERTIES
++ VERSION
++"${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}"
++ SOVERSION ${CPACK_PACKAGE_VERSION_MAJOR}
++ OUTPUT_NAME htio2
++ LINK_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}"
++ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
++ CLEAN_DIRECT_OUTPUT 1)
++
++add_library(ht_common_static STATIC ${HTQC_SOURCE_FILES})
++set_target_properties(ht_common_static PROPERTIES
++ OUTPUT_NAME ht_common
++ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
++ CLEAN_DIRECT_OUTPUT 1)
++
++add_library(ht_common_dynamic SHARED ${HTQC_SOURCE_FILES})
++set_target_properties( ht_common_dynamic PROPERTIES
++ VERSION
++"${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}"
++ SOVERSION "${CPACK_PACKAGE_VERSION_MAJOR}"
++ OUTPUT_NAME ht_common
++ LINK_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}"
++ INSTALL_NAME_DIR "${CMAKE_INSTALL_LIBDIR}"
++ CLEAN_DIRECT_OUTPUT 1)
+
+ add_executable(ht2-convert ht2-convert.cpp)
+ target_link_libraries(ht2-convert
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-demul ht2-demul.cpp)
+ target_link_libraries(ht2-demul
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -30,71 +62,73 @@ add_executable(ht2-stat ht2-stat.cpp
+ htqc/FastqStat.cpp
+ )
+ target_link_libraries(ht2-stat
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-trim ht2-trim.cpp)
+ target_link_libraries(ht2-trim
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-filter ht2-filter.cpp)
+ target_link_libraries(ht2-filter
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-rename ht2-rename.cpp)
+ target_link_libraries(ht2-rename
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-sample ht2-sample.cpp)
+ target_link_libraries(ht2-sample
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-overlap ht2-overlap.cpp)
+ target_link_libraries(ht2-overlap
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-primer-trim ht2-primer-trim.cpp)
+ target_link_libraries(ht2-primer-trim
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+ add_executable(ht2-lane-tile ht2-lane-tile.cpp)
+ target_link_libraries(ht2-lane-tile
+- ht_common
+- htio2
++ ht_common_dynamic
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+
+-install(TARGETS ht2-demul ht2-primer-trim ht2-convert ht2-stat ht2-trim ht2-filter ht2-sample ht2-overlap ht2-rename htio2
++install(TARGETS ht2-demul ht2-primer-trim ht2-convert ht2-stat ht2-trim ht2-filter ht2-sample ht2-overlap ht2-rename htio2_dynamic
++ htio2_static ht_common_static ht_common_dynamic
+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+ )
+ install(PROGRAMS ht2-stat-draw.pl DESTINATION bin)
+ install(FILES ${CMAKE_BINARY_DIR}/src/htio2/config.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/htio2)
+diff --git a/t/CMakeLists.txt b/t/CMakeLists.txt
+index 6ca515a..e44b87f 100644
+--- a/t/CMakeLists.txt
++++ b/t/CMakeLists.txt
+@@ -1,12 +1,12 @@
+ include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR})
+ configure_file(TestConfig.h.in TestConfig.h ESCAPE_QUOTES)
+
+-add_library(TestFramework TestFramework.cpp)
++add_library(TestFramework SHARED TestFramework.cpp)
+
+ add_executable(t_text_file_equal t_text_file_equal.cpp)
+ target_link_libraries(t_text_file_equal
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -15,7 +15,7 @@ add_test(text_file_equal t_text_file_equal)
+ add_executable(t_kmer_nt5_16 t_kmer_nt5_16.cpp)
+ target_link_libraries(t_kmer_nt5_16
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -24,7 +24,7 @@ add_test(kmer_nt5_16 t_kmer_nt5_16)
+ add_executable(t_kmer_nt5_32 t_kmer_nt5_32.cpp)
+ target_link_libraries(t_kmer_nt5_32
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -33,7 +33,7 @@ add_test(kmer_nt5_32 t_kmer_nt5_32)
+ add_executable(t_kmer_nt5_64 t_kmer_nt5_64.cpp)
+ target_link_libraries(t_kmer_nt5_64
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -42,7 +42,7 @@ add_test(kmer_nt5_64 t_kmer_nt5_64)
+ add_executable(t_kmer_nt4_16 t_kmer_nt4_16.cpp)
+ target_link_libraries(t_kmer_nt4_16
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -51,7 +51,7 @@ add_test(kmer_nt4_16 t_kmer_nt4_16)
+ add_executable(t_kmer_nt4_32 t_kmer_nt4_32.cpp)
+ target_link_libraries(t_kmer_nt4_32
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -60,7 +60,7 @@ add_test(kmer_nt4_32 t_kmer_nt4_32)
+ add_executable(t_kmer_nt4_64 t_kmer_nt4_64.cpp)
+ target_link_libraries(t_kmer_nt4_64
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -69,7 +69,7 @@ add_test(kmer_nt4_64 t_kmer_nt4_64)
+ add_executable(t_kmer_aa t_kmer_aa.cpp)
+ target_link_libraries(t_kmer_aa
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -78,7 +78,7 @@ add_test(kmer_aa t_kmer_aa)
+ add_executable(t_ref_counted t_ref_counted.cpp)
+ target_link_libraries(t_ref_counted
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -87,7 +87,7 @@ add_test(ref_counted t_ref_counted)
+ add_executable(t_simple_seq t_simple_seq.cpp)
+ target_link_libraries(t_simple_seq
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -96,7 +96,7 @@ add_test(simple_seq t_simple_seq)
+ add_executable(t_plain_file_handle t_plain_file_handle.cpp)
+ target_link_libraries(t_plain_file_handle
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -105,7 +105,7 @@ add_test(plain_file_handle t_plain_file_handle)
+ add_executable(t_gzip_file_handle t_gzip_file_handle.cpp)
+ target_link_libraries(t_gzip_file_handle
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -114,7 +114,7 @@ add_test(gzip_file_handle t_gzip_file_handle)
+ add_executable(t_fastq_io t_fastq_io.cpp)
+ target_link_libraries(t_fastq_io
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -123,7 +123,7 @@ add_test(fastq_io t_fastq_io)
+ add_executable(t_fasta_io t_fasta_io.cpp)
+ target_link_libraries(t_fasta_io
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -132,7 +132,7 @@ add_test(fasta_io t_fasta_io)
+ add_executable(t_header_util t_header_util.cpp)
+ target_link_libraries(t_header_util
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -141,8 +141,8 @@ add_test(header_util t_header_util)
+ add_executable(t_multi_seq_file_se t_multi_seq_file_se.cpp)
+ target_link_libraries(t_multi_seq_file_se
+ TestFramework
+- ht_common
+- htio2
++ htio2_dynamic
++ ht_common_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -151,8 +151,8 @@ add_test(multi_seq_file_se t_multi_seq_file_se)
+ add_executable(t_multi_seq_file_pe t_multi_seq_file_pe.cpp)
+ target_link_libraries(t_multi_seq_file_pe
+ TestFramework
+- ht_common
+- htio2
++ htio2_dynamic
++ ht_common_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -161,7 +161,7 @@ add_test(multi_seq_file_pe t_multi_seq_file_pe)
+ add_executable(t_ht_sample t_ht_sample.cpp)
+ target_link_libraries(t_ht_sample
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -170,7 +170,7 @@ add_test(ht_sample t_ht_sample)
+ add_executable(t_ht_trim t_ht_trim.cpp)
+ target_link_libraries(t_ht_trim
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -179,7 +179,7 @@ add_test(ht_trim t_ht_trim)
+ add_executable(t_ht_rename t_ht_rename.cpp)
+ target_link_libraries(t_ht_rename
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -188,7 +188,7 @@ add_test(ht_rename t_ht_rename)
+ add_executable(t_ht_overlap t_ht_overlap.cpp)
+ target_link_libraries(t_ht_overlap
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -197,7 +197,7 @@ add_test(ht_overlap t_ht_overlap)
+ add_executable(t_ht_filter t_ht_filter.cpp)
+ target_link_libraries(t_ht_filter
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -206,7 +206,7 @@ add_test(ht_filter t_ht_filter)
+ add_executable(t_ht_convert t_ht_convert.cpp)
+ target_link_libraries(t_ht_convert
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -215,7 +215,7 @@ add_test(ht_convert t_ht_convert)
+ add_executable(t_ht_demul t_ht_demul.cpp)
+ target_link_libraries(t_ht_demul
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -224,7 +224,7 @@ add_test(ht_demul t_ht_demul)
+ add_executable(t_ht_lane_tile t_ht_lane_tile.cpp)
+ target_link_libraries(t_ht_lane_tile
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -233,7 +233,7 @@ add_test(ht_lane_tile t_ht_lane_tile)
+ add_executable(t_string t_string.cpp)
+ target_link_libraries(t_string
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -242,7 +242,7 @@ add_test(string t_string)
+ add_executable(t_cast t_cast.cpp)
+ target_link_libraries(t_cast
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -250,7 +250,7 @@ add_test(cast t_cast)
+
+ add_executable(option_parser option_parser.cpp)
+ target_link_libraries(option_parser
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -258,7 +258,7 @@ target_link_libraries(option_parser
+ add_executable(t_ring_buffer t_ring_buffer.cpp)
+ target_link_libraries(t_ring_buffer
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
+@@ -267,7 +267,7 @@ add_test(ring_buffer t_ring_buffer)
+ add_executable(t_mt19937 t_mt19937.cpp)
+ target_link_libraries(t_mt19937
+ TestFramework
+- htio2
++ htio2_dynamic
+ ${juce_dep_libs}
+ ${ZLIB_LIBRARIES}
+ )
=====================================
debian/patches/enable_testing.patch → debian/patches/0003-enable_testing.patch
=====================================
--- a/debian/patches/enable_testing.patch
+++ b/debian/patches/0003-enable_testing.patch
@@ -1,7 +1,13 @@
-Author: Leopold Palomo-Avellaneda <leo at alaxarxa.net>
-Last-Update: Tue, 23 Jun 2015 09:51:43 +0200
-Description: Enable testing
+From: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Date: Tue, 23 Jun 2015 15:29:55 +0200
+Subject: enable_testing
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 90fadcb..716aad5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,5 +53,6 @@ include_directories(
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
-correct_cflags.patch
-enable_testing.patch
+0001-correct_cflags.patch
+0002-Added-Debian-specific-SONAMEs.patch.patch
+0003-enable_testing.patch
View it on GitLab: https://salsa.debian.org/med-team/htqc/compare/0ced16aaafe95850e0f4d93c1a566c4587912865...2ec383cec13f45f4d8c1bff862060abd47589a35
---
View it on GitLab: https://salsa.debian.org/med-team/htqc/compare/0ced16aaafe95850e0f4d93c1a566c4587912865...2ec383cec13f45f4d8c1bff862060abd47589a35
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