tjh.dev / nixpkgs
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nixpkgs / pkgs / by-name / mi / minia / no-bundle.patch
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1diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt 2index f48a70b..0e11ece 100644 3--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt 4+++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt 5@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty) 6 # DEPENDENCIES 7 ################################################################################ 8 # we must be sure that hdf5 is built and installed before building gatb-core 9-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild) 10 11 ################################################################################ 12 # DOCUMENTATION GENERATION 13@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) 14 INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL) 15 INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL) 16 INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL) 17- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include) 18 ENDIF() 19 20 ################################################################################ 21diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp 22index dfeee1c..d5553a2 100644 23--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp 24+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp 25@@ -35,7 +35,7 @@ 26 #include <stdint.h> 27 #include <algorithm> 28 #include <iostream> 29-#include <hdf5/hdf5.h> 30+#include <hdf5.h> 31 32 #include <gatb/system/api/Exception.hpp> 33 #include <gatb/system/api/config.hpp> 34diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp 35index 60be5d5..25ae75e 100644 36--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp 37+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp 38@@ -33,7 +33,7 @@ 39 /********************************************************************************/ 40 41 #include <iostream> 42-#include <hdf5/hdf5.h> 43+#include <hdf5.h> 44 45 #include <gatb/system/api/types.hpp> 46 #include <gatb/tools/misc/api/Abundance.hpp> 47diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp 48index 6a71bb0..b9205df 100644 49--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp 50+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp 51@@ -31,7 +31,7 @@ 52 #include <iostream> 53 #include <gatb/system/api/types.hpp> 54 #include <gatb/tools/misc/api/Abundance.hpp> 55-#include <hdf5/hdf5.h> 56+#include <hdf5.h> 57 58 /********************************************************************************/ 59 namespace gatb { 60diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp 61index c22b892..62e6586 100644 62--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp 63+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp 64@@ -31,7 +31,7 @@ 65 #include <iostream> 66 #include <gatb/system/api/types.hpp> 67 #include <gatb/tools/misc/api/Abundance.hpp> 68-#include <hdf5/hdf5.h> 69+#include <hdf5.h> 70 71 /********************************************************************************/ 72 namespace gatb { 73diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp 74index c06aaab..e0befba 100644 75--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp 76+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp 77@@ -31,7 +31,7 @@ 78 #include <iostream> 79 #include <gatb/system/api/types.hpp> 80 #include <gatb/tools/misc/api/Abundance.hpp> 81-#include <hdf5/hdf5.h> 82+#include <hdf5.h> 83 84 extern const unsigned char revcomp_4NT[]; 85 extern const unsigned char comp_NT []; 86diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp 87index 9659874..0c79ff6 100644 88--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp 89+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp 90@@ -31,7 +31,7 @@ 91 #include <iostream> 92 #include <gatb/system/api/types.hpp> 93 #include <gatb/tools/misc/api/Abundance.hpp> 94-#include <hdf5/hdf5.h> 95+#include <hdf5.h> 96 97 /********************************************************************************/ 98 namespace gatb { 99diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 100index 3cb84f8..cd5d382 100644 101--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 102+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 103@@ -31,7 +31,7 @@ 104 /********************************************************************************/ 105 106 #include <sys/types.h> 107-#include <hdf5/hdf5.h> 108+#include <hdf5.h> 109 110 /********************************************************************************/ 111 namespace gatb { 112diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 113index b8f6c79..a040832 100644 114--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 115+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 116@@ -28,7 +28,7 @@ 117 118 #include <gatb/system/api/ISmartPointer.hpp> 119 #include <gatb/tools/storage/impl/Storage.hpp> 120-#include <hdf5/hdf5.h> 121+#include <hdf5.h> 122 123 /********************************************************************************/ 124 namespace gatb { 125diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 126index 2645abd..fad48c0 100644 127--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 128+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 129@@ -40,7 +40,7 @@ 130 #include <string> 131 #include <vector> 132 #include <stdarg.h> 133-#include <hdf5/hdf5.h> 134+#include <hdf5.h> 135 136 /********************************************************************************/ 137 namespace gatb { 138diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 139index a92b729..66d552f 100644 140--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 141+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 142@@ -40,7 +40,7 @@ 143 #include <string> 144 #include <vector> 145 #include <stdarg.h> 146-#include <hdf5/hdf5.h> 147+#include <hdf5.h> 148 149 /********************************************************************************/ 150 namespace gatb { 151diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 152index 29e0949..0565cc4 100644 153--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 154+++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 155@@ -33,7 +33,7 @@ 156 #include <gatb/tools/storage/impl/CollectionHDF5.hpp> 157 #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp> 158 #include <gatb/system/impl/System.hpp> 159-#include <hdf5/hdf5.h> 160+#include <hdf5.h> 161 #include <sstream> 162 163 /********************************************************************************/ 164diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt 165index 6e0b5c4..34aef28 100644 166--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt 167+++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt 168@@ -1,54 +1,3 @@ 169-################################################################################ 170-# HDF5 GENERATION 171-################################################################################ 172- 173-#SET (HDF5_ENABLE_THREADSAFE ON) 174-#SET (H5_HAVE_THREADSAFE 1) 175- 176-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ########## 177-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools") 178-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz") 179- 180-SET (HDF5_EXTERNALLY_CONFIGURED ON) 181- 182-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE}) 183-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE}) 184-SET (HDF5_INSTALL_BIN_DIR bin) 185-SET (HDF5_INSTALL_LIB_DIR lib) 186- 187-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5) 188-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) 189-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) 190- 191-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) 192- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5") 193-ENDIF() 194- 195-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB) 196- OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON) 197-ENDIF() 198- 199-# We don't want warnings from HDF5 compilation 200-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w") 201-add_definitions (${COMPILE_DEFINITIONS}) 202- 203-# add HDF5 generation 204-ADD_SUBDIRECTORY (hdf5) 205- 206-# We add a custom target for copying header files. 207-add_custom_target (hdf5_postbuild ALL) 208- 209-# We build the output directory 210-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR}) 211- 212-# We define all the header files to be copied 213-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h) 214- 215-# We copy each header file 216-foreach (header ${headerfiles}) 217- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} ) 218-endforeach() 219- 220 # include other smaller libraries (json, Boophf) 221 222 add_custom_target (thirdparty_copy ALL)