diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/amap/files |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/amap/files')
-rw-r--r-- | sci-biology/amap/files/amap-2.2-includes.patch | 44 | ||||
-rw-r--r-- | sci-biology/amap/files/amap-2.2-makefile.patch | 35 |
2 files changed, 79 insertions, 0 deletions
diff --git a/sci-biology/amap/files/amap-2.2-includes.patch b/sci-biology/amap/files/amap-2.2-includes.patch new file mode 100644 index 000000000000..77c4261db5cf --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-includes.patch @@ -0,0 +1,44 @@ +Fixes build with gcc 4.3 and 4.6 + +http://bugs.gentoo.org/217921 +http://bugs.gentoo.org/360517 + +--- amap-align/align/Amap.cc ++++ amap-align/align/Amap.cc +@@ -12,6 +12,8 @@ + #include "ProbabilisticModel.h" + #include "EvolutionaryTree.h" + #include "SparseMatrix.h" ++#include <limits> ++#include <climits> + #include <string> + #include <sstream> + #include <iomanip> +@@ -23,6 +25,7 @@ + #include <cstdlib> + #include <cerrno> + #include <iomanip> ++#include <cstring> + + string parametersInputFilename = ""; + string parametersOutputFilename = "no training"; +--- amap-align/align/MultiSequenceDag.h ++++ amap-align/align/MultiSequenceDag.h +@@ -13,6 +13,7 @@ + #include <map> + #include <queue> + #include <iostream> ++#include <limits> + #include "MultiSequence.h" + #include "SparseMatrix.h" + +--- amap-align/align/SafeVector.h.org 2011-03-26 11:50:11.935069583 +0100 ++++ amap-align/align/SafeVector.h 2011-03-26 11:50:21.112553151 +0100 +@@ -9,6 +9,7 @@ + #define SAFEVECTOR_H + + #include <cassert> ++#include <cstddef> + #include <vector> + + ///////////////////////////////////////////////////////////////// diff --git a/sci-biology/amap/files/amap-2.2-makefile.patch b/sci-biology/amap/files/amap-2.2-makefile.patch new file mode 100644 index 000000000000..5a9841c98255 --- /dev/null +++ b/sci-biology/amap/files/amap-2.2-makefile.patch @@ -0,0 +1,35 @@ +Respect {CXX,LD}FLAGS + +http://bugs.gentoo.org/332009 + +--- amap-align/align/Makefile ++++ amap-align/align/Makefile +@@ -15,6 +15,8 @@ + # c) RELEASE mode + ################################################################################ + ++OPT_CXXFLAGS = -O3 -W -Wall -pedantic -funroll-loops ++ + OTHERFLAGS = -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' + + # debug mode +@@ -26,8 +28,7 @@ + + # release mode + #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer +-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops +- ++CXXFLAGS = $(OPT_CXXFLAGS) -DNDEBUG $(OTHERFLAGS) + ################################################################################ + # 3) Dependencies + ################################################################################ + +@@ -38,7 +37,7 @@ + all : $(TARGETS) + + amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc +- $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc ++ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o amap Amap.cc -lm + + .PHONY : clean + clean: |