commit: 70aa79d9e30fc3338314000c13b71ab66bf8552b Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Thu Nov 2 03:19:41 2017 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Thu Nov 2 03:19:41 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=70aa79d9
sci-biology/bamtools: Remove old Package-Manager: Portage-2.3.11, Repoman-2.3.3 sci-biology/bamtools/Manifest | 1 - sci-biology/bamtools/bamtools-2.4.1.ebuild | 25 --- .../files/bamtools-2.4.1-fix-build-system.patch | 209 --------------------- .../bamtools/files/bamtools-2.4.1-fix-c++14.patch | 78 -------- 4 files changed, 313 deletions(-) diff --git a/sci-biology/bamtools/Manifest b/sci-biology/bamtools/Manifest index 45492cd4dca..855871fa7e3 100644 --- a/sci-biology/bamtools/Manifest +++ b/sci-biology/bamtools/Manifest @@ -1,2 +1 @@ -DIST bamtools-2.4.1.tar.gz 540482 SHA256 933a0c1a83c88c1dac8078c0c0e82f6794c75cb927265399404bc2cc2611204b SHA512 ee674014f27b2dc0aa7c0415e8654ee7c39cfdecafbd9983d970fad6ad29f070a7ff372ee05765956cf7c8f8bb3b9763b6e537e693a0d2d64680148b1a23cfee WHIRLPOOL 6ef73f0713ebf993123eac7095061e32fe6a53db383e28a5dd8967afee92fb211ce56611de9718ce4cce84bdee14157ff968e0a6edcaead4e06b44008b78b84c DIST bamtools-2.4.2.tar.gz 548095 SHA256 04165bf8a7566f4be1a6e68f69bfdd9f08364ba7b0d2f6687302434641408102 SHA512 244a63609c0b10a85bba7cac210a27ea9abafba136e9c91fc789c7aa21a6cdaa7622afebc50ec8d30d4446872d5206dbd3d679ca03e95ac90771c87359cb69a0 WHIRLPOOL e1ed40d1ec47cbe97c4de160671f34095bf56f5786ebcc0cf7fb7b5e4b129d9c562b1cf19fb1d22e3ef20fa21d45f1fe50640b9d9919c01fabed044f82c9c2de diff --git a/sci-biology/bamtools/bamtools-2.4.1.ebuild b/sci-biology/bamtools/bamtools-2.4.1.ebuild deleted file mode 100644 index 2196c66790d..00000000000 --- a/sci-biology/bamtools/bamtools-2.4.1.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2016 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit cmake-utils - -DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files" -HOMEPAGE="https://github.com/pezmaster31/bamtools"; -SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - >=dev-libs/jsoncpp-1.8.0 - sys-libs/zlib" -DEPEND="${RDEPEND}" - -PATCHES=( - "${FILESDIR}"/${PN}-2.4.1-fix-build-system.patch - "${FILESDIR}"/${PN}-2.4.1-fix-c++14.patch -) diff --git a/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch b/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch deleted file mode 100644 index 79597233030..00000000000 --- a/sci-biology/bamtools/files/bamtools-2.4.1-fix-build-system.patch +++ /dev/null @@ -1,209 +0,0 @@ -* Unbundle jsoncpp -* Remove forcing C++98 -* Remove forcing CMAKE_BUILD_TYPE -* Remove -fPIC globally -* Fix LFS macro definitions -* Make building static library optional -* Use GNUInstallDirs conventions -* Install .pc file -See also: https://bugs.gentoo.org/show_bug.cgi?id=550144 - -Taken from https://github.com/pezmaster31/bamtools/pull/139 - ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -9,7 +9,14 @@ - project( BamTools ) - - # Cmake requirements --cmake_minimum_required( VERSION 2.6.4 ) -+cmake_minimum_required( VERSION 3.0 ) -+ -+# on macOS, MACOSX_RPATH is enabled by default on more recent versions -+# of CMake. Disable this behaviour, and let user enable it if need be. -+cmake_policy( SET CMP0042 OLD ) -+ -+# Adhere to GNU filesystem layout conventions -+include( GNUInstallDirs ) - - # Force the build directory to be different from source directory - macro( ENSURE_OUT_OF_SOURCE_BUILD MSG ) -@@ -34,18 +41,21 @@ - set( BamTools_VERSION_MINOR 4 ) - set( BamTools_VERSION_BUILD 1 ) - --# set our library and executable destination dirs --set( EXECUTABLE_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/bin" ) --set( LIBRARY_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/lib" ) -- - # define compiler flags for all code --set( CMAKE_BUILD_TYPE Release ) --set( CMAKE_CXX_FLAGS_RELEASE "-std=c++98 ${CMAKE_CXX_FLAGS_RELEASE}" ) --add_definitions( -Wall -D_FILE_OFFSET_BITS=64 ) -+add_definitions( -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE ) -+add_compile_options( -Wall ) - - # ----------------------------------------------- - # handle platform-/environment-specific defines - -+# Make building the static library optional -+option( BUILD_STATIC "Build static libbamtools archive" OFF ) -+if( BUILD_STATIC ) -+ set( BAMTOOLS_CMD_LDFLAGS BamTools-static ) -+else() -+ set( BAMTOOLS_CMD_LDFLAGS BamTools ) -+endif() -+ - # If planning to run in Node.js environment, run: - # cmake -DEnableNodeJS=true - if( EnableNodeJS ) -@@ -57,6 +67,11 @@ - add_definitions( -DSUN_OS ) - endif() - -+# find system JsonCpp -+find_package( PkgConfig ) -+pkg_search_module( JSONCPP jsoncpp>=1 ) -+ -+ - # ------------------------------------------- - - # add our includes root path ---- a/src/api/CMakeLists.txt -+++ b/src/api/CMakeLists.txt -@@ -10,7 +10,6 @@ - - # add compiler definitions - add_definitions( -DBAMTOOLS_API_LIBRARY ) # (for proper exporting of library symbols) --add_definitions( -fPIC ) # (attempt to force PIC compiling on CentOS, not being set on shared libs by CMake) - - # fetch all internal source files - add_subdirectory( internal ) -@@ -31,18 +30,6 @@ - ${InternalSources} - ) - --# create main BamTools API shared library --add_library( BamTools SHARED ${BamToolsAPISources} ) --set_target_properties( BamTools PROPERTIES -- SOVERSION "2.4.1" -- OUTPUT_NAME "bamtools" ) -- --# create main BamTools API static library --add_library( BamTools-static STATIC ${BamToolsAPISources} ) --set_target_properties( BamTools-static PROPERTIES -- OUTPUT_NAME "bamtools" -- PREFIX "lib" ) -- - # link libraries automatically with zlib (and Winsock2, if applicable) - if( WIN32 ) - set( APILibs z ws2_32 ) -@@ -50,12 +37,23 @@ - set( APILibs z ) - endif() - --target_link_libraries( BamTools ${APILibs} ) --target_link_libraries( BamTools-static ${APILibs} ) -+# create main BamTools API shared library -+add_library( BamTools SHARED ${BamToolsAPISources} ) -+set_target_properties( BamTools PROPERTIES -+ SOVERSION "2.4.1" -+ OUTPUT_NAME "bamtools" ) -+target_link_libraries( BamTools ${APILibs} ) -+install( TARGETS BamTools LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ) - --# set library install destinations --install( TARGETS BamTools LIBRARY DESTINATION "lib/bamtools" RUNTIME DESTINATION "bin") --install( TARGETS BamTools-static ARCHIVE DESTINATION "lib/bamtools") -+# create main BamTools API static library -+if( BUILD_STATIC ) -+ add_library( BamTools-static STATIC ${BamToolsAPISources} ) -+ set_target_properties( BamTools-static PROPERTIES -+ OUTPUT_NAME "bamtools" -+ PREFIX "lib" ) -+ target_link_libraries( BamTools-static ${APILibs} ) -+ install( TARGETS BamTools-static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" ) -+endif() - - # export API headers - include(../ExportHeader.cmake) ---- a/src/bamtools.pc.in -+++ b/src/bamtools.pc.in -@@ -0,0 +1,11 @@ -+prefix=@CMAKE_INSTALL_PREFIX@ -+exec_prefix=${prefix} -+libdir=${exec_prefix}/@CMAKE_INSTALL_LIBDIR@ -+includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@ -+ -+Name: BamTools -+Description: BamTools is a C++ library for reading and manipulating BAM files -+Version: @BamTools_VERSION_MAJOR@.@BamTools_VERSION_MINOR@.@BamTools_VERSION_BUILD@ -+ -+Libs: -L${libdir} -lbamtools -+Cflags: -I${includedir} ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -14,3 +14,7 @@ - include( ExportHeader.cmake ) - set( SharedIncludeDir "shared" ) - ExportHeader( SharedHeaders shared/bamtools_global.h ${SharedIncludeDir} ) -+ -+# configure and install pkg-config file -+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools.pc.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc @ONLY ) -+install( FILES ${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig ) ---- a/src/ExportHeader.cmake -+++ b/src/ExportHeader.cmake -@@ -18,10 +18,10 @@ - add_custom_command( TARGET ${MODULE} COMMAND - ${CMAKE_COMMAND} -E copy_if_different - "${CMAKE_CURRENT_SOURCE_DIR}/${FILE}" -- "${CMAKE_SOURCE_DIR}/include/${DEST}/${FILENAME}" ) -+ "${CMAKE_CURRENT_BINARY_DIR}/include/${DEST}/${FILENAME}" ) - - # make sure files are properly 'installed' -- install( FILES "${FILE}" DESTINATION "include/bamtools/${DEST}" ) -+ install( FILES "${FILE}" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/bamtools/${DEST}" ) - - endfunction( ExportHeader ) - ---- a/src/third_party/CMakeLists.txt -+++ b/src/third_party/CMakeLists.txt -@@ -5,5 +5,3 @@ - # src/third-party/ - # ========================== - --# list third-party subdirectories to build in --add_subdirectory( jsoncpp ) ---- a/src/toolkit/CMakeLists.txt -+++ b/src/toolkit/CMakeLists.txt -@@ -35,10 +35,14 @@ - OUTPUT_NAME "bamtools" - ) - # make version info available in application --configure_file( bamtools_version.h.in ${BamTools_SOURCE_DIR}/src/toolkit/bamtools_version.h ) -+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/bamtools_version.h.in ${CMAKE_CURRENT_BINARY_DIR}/bamtools_version.h ) -+include_directories( ${CMAKE_CURRENT_BINARY_DIR} ) -+ -+# set include paths for system JsonCpp -+target_include_directories( bamtools_cmd PRIVATE ${JSONCPP_INCLUDE_DIRS} ) - - # define libraries to link --target_link_libraries( bamtools_cmd BamTools BamTools-utils jsoncpp ) -+target_link_libraries( bamtools_cmd BamTools-utils ${BAMTOOLS_CMD_LDFLAGS} ${JSONCPP_LDFLAGS} ) - - # set application install destinations --install( TARGETS bamtools_cmd DESTINATION "bin") -+install( TARGETS bamtools_cmd DESTINATION "${CMAKE_INSTALL_BINDIR}" ) ---- a/src/utils/CMakeLists.txt -+++ b/src/utils/CMakeLists.txt -@@ -8,9 +8,8 @@ - # list include paths - include_directories( ${BamTools_SOURCE_DIR}/src/api ) - --# add compiler definitions -+# add compiler definitions - add_definitions( -DBAMTOOLS_UTILS_LIBRARY ) # (for proper exporting of library symbols) --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 STATIC diff --git a/sci-biology/bamtools/files/bamtools-2.4.1-fix-c++14.patch b/sci-biology/bamtools/files/bamtools-2.4.1-fix-c++14.patch deleted file mode 100644 index 8d9b1e02c19..00000000000 --- a/sci-biology/bamtools/files/bamtools-2.4.1-fix-c++14.patch +++ /dev/null @@ -1,78 +0,0 @@ -* Fix building in C++11/C++14 modes -See also: https://bugs.gentoo.org/show_bug.cgi?id=596208 - -Taken from https://github.com/pezmaster31/bamtools/pull/139 - ---- a/src/api/BamConstants.h -+++ b/src/api/BamConstants.h -@@ -126,10 +126,10 @@ - - // zlib & BGZF constants - const char GZIP_ID1 = 31; --const char GZIP_ID2 = 139; -+const char GZIP_ID2 = static_cast<char>(139); - const char CM_DEFLATE = 8; - const char FLG_FEXTRA = 4; --const char OS_UNKNOWN = 255; -+const char OS_UNKNOWN = static_cast<char>(255); - const char BGZF_XLEN = 6; - const char BGZF_ID1 = 66; - const char BGZF_ID2 = 67; ---- a/src/toolkit/bamtools_filter.cpp -+++ b/src/toolkit/bamtools_filter.cpp -@@ -16,7 +16,7 @@ - #include <utils/bamtools_utilities.h> - using namespace BamTools; - --#include <jsoncpp/json.h> -+#include <json/json.h> - using namespace Json; - - #include <cstdio> -@@ -647,7 +647,7 @@ - if ( !reader.parse(document, root) ) { - // use built-in error reporting mechanism to alert user what was wrong with the script - cerr << "bamtools filter ERROR: failed to parse script - see error message(s) below" << endl -- << reader.getFormatedErrorMessages(); -+ << reader.getFormattedErrorMessages(); - return false; - } - ---- a/src/toolkit/bamtools_resolve.cpp -+++ b/src/toolkit/bamtools_resolve.cpp -@@ -410,7 +410,7 @@ - ReadGroupResolver& resolver = (*rgIter).second; - - // store read name with resolver -- resolver.ReadNames.insert( make_pair<string,bool>(fields[1], true) ) ; -+ resolver.ReadNames.insert( make_pair(fields[1], true) ) ; - } - - // if here, return success -@@ -607,7 +607,7 @@ - resolver.IsAmbiguous = ( fields.at(6) == TRUE_KEYWORD ); - - // store RG entry and return success -- readGroups.insert( make_pair<string, ReadGroupResolver>(name, resolver) ); -+ readGroups.insert( make_pair(name, resolver) ); - return true; - } - -@@ -1014,7 +1014,7 @@ - } - - // if read name not found, store new entry -- else resolver.ReadNames.insert( make_pair<string, bool>(al.Name, isCurrentMateUnique) ); -+ else resolver.ReadNames.insert( make_pair(al.Name, isCurrentMateUnique) ); - } - - // close files -@@ -1046,7 +1046,7 @@ - SamReadGroupConstIterator rgEnd = header.ReadGroups.ConstEnd(); - for ( ; rgIter != rgEnd; ++rgIter ) { - const SamReadGroup& rg = (*rgIter); -- m_readGroups.insert( make_pair<string, ReadGroupResolver>(rg.ID, ReadGroupResolver()) ); -+ m_readGroups.insert( make_pair(rg.ID, ReadGroupResolver()) ); - } - } -
