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| author |   David Seifert <soap@gentoo.org> | 2016-06-05 17:18:04 +0200 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2016-06-05 17:22:05 +0200 |
| commit | 0947afa365abf88670172058186a1ff22de84a07 (patch) | |
| tree | 28abe932cc12f586c5ba58b91358a14180ea3f89 /sci-chemistry/ball/files | |
| parent | p/p/l-s/arm: add arm profile for prefix-standalone. (diff) | |
| download | gentoo-0947afa365abf88670172058186a1ff22de84a07.tar.gz gentoo-0947afa365abf88670172058186a1ff22de84a07.tar.bz2 gentoo-0947afa365abf88670172058186a1ff22de84a07.zip | |
sci-chemistry/ball: Fix Swig bug, qualify std::isnan
Gentoo-Bug: 583932
* EAPI=6
* Also fix GCC warning pollution due to
misplaced attributes
* Add subslot operator for dev-libs/boost
* Remove USE=webkit, as webkit is no longer supported
Package-Manager: portage-2.3.0_rc1
Diffstat (limited to 'sci-chemistry/ball/files')
3 files changed, 118 insertions, 0 deletions
diff --git a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch new file mode 100644 index 000000000000..a13ea2f36ec0 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch @@ -0,0 +1,22 @@ +From 38a955ad9588817073a330c79d4b4476afcf69d5 Mon Sep 17 00:00:00 2001 +From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de> +Date: Thu, 14 Apr 2016 19:30:04 +0200 +Subject: [PATCH] Fix Python bindings for Box + +--- + source/PYTHON/EXTENSIONS/VIEW/box.sip | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/source/PYTHON/EXTENSIONS/VIEW/box.sip b/source/PYTHON/EXTENSIONS/VIEW/box.sip +index 341b1a4..592765e 100644 +--- a/source/PYTHON/EXTENSIONS/VIEW/box.sip ++++ b/source/PYTHON/EXTENSIONS/VIEW/box.sip +@@ -6,7 +6,7 @@ + + class Box + : GeometricObject, +- Vertex2 ++ Box3 + { + %TypeHeaderCode + #include <BALL/VIEW/PRIMITIVES/box.h> diff --git a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch new file mode 100644 index 000000000000..cea6377b6a20 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch @@ -0,0 +1,16 @@ +Fix C++11 changes to isnan(): +* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/source/MOLMEC/MINIMIZATION/shiftedLVMM.C:769:46: required from here +* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] +* return (isnan(t) != 0); + +--- BALL-1.4.2/include/BALL/MATHS/common.h ++++ BALL-1.4.2/include/BALL/MATHS/common.h +@@ -172,7 +172,7 @@ + #elif defined(BALL_OS_DARWIN) + return ( __inline_isnand(t) != 0); + #else +- return (isnan(t) != 0); ++ return (std::isnan(t) != 0); + #endif + } + diff --git a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch new file mode 100644 index 000000000000..da334915f410 --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch @@ -0,0 +1,80 @@ +Silence warning pollution due to misplaced attributes: +* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/COMMON/logStream.h:165:22: note: attribute for ‘struct BALL::LogStreamBuf::StreamStruct’ must follow the ‘struct’ keyword + +--- BALL-1.4.2/include/BALL/COMMON/logStream.h ++++ BALL-1.4.2/include/BALL/COMMON/logStream.h +@@ -162,7 +162,7 @@ + virtual int overflow(int c = -1); + //@} + +- BALL_EXPORT struct StreamStruct ++ struct BALL_EXPORT StreamStruct + { + std::ostream* stream; + string prefix; +--- BALL-1.4.2/include/BALL/FORMAT/MOL2File.h ++++ BALL-1.4.2/include/BALL/FORMAT/MOL2File.h +@@ -33,7 +33,7 @@ + public: + + /// A class used for storing TRIPOS sets +- BALL_EXPORT struct SetStruct ++ struct BALL_EXPORT SetStruct + { + String name; + bool is_static; +@@ -136,7 +136,7 @@ + + bool containsAtomChilds_(AtomContainerConstIterator& frag_it); + +- BALL_EXPORT struct AtomStruct ++ struct BALL_EXPORT AtomStruct + { + String name; + Vector3 position; +@@ -146,14 +146,14 @@ + float charge; + }; + +- BALL_EXPORT struct BondStruct ++ struct BALL_EXPORT BondStruct + { + Position atom1; + Position atom2; + String type; + }; + +- BALL_EXPORT struct MoleculeStruct ++ struct BALL_EXPORT MoleculeStruct + { + String name; + Size number_of_atoms; +@@ -166,7 +166,7 @@ + String comment; + }; + +- BALL_EXPORT struct SubstructureStruct ++ struct BALL_EXPORT SubstructureStruct + { + String name; + Size root_atom; +@@ -178,7 +178,7 @@ + String comment; + }; + +- BALL_EXPORT struct CommentStruct ++ struct BALL_EXPORT CommentStruct + { + String name; + String value; +--- BALL-1.4.2/include/BALL/FORMAT/MOLFile.h ++++ BALL-1.4.2/include/BALL/FORMAT/MOLFile.h +@@ -41,7 +41,7 @@ + @see PropertyManager::setProperty + @see PropertyManager::getProperty + */ +- BALL_EXPORT struct Property ++ struct BALL_EXPORT Property + { + /// + static const String ATOM_MASS_DIFFERENCE; |