[gentoo-commits] repo/gentoo:master commit in: sci-biology/bamtools/files/, sci-biology/bamtools/

[David Seifert]

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()) );
-     }
- }
-