mirror of
https://anongit.gentoo.org/git/repo/gentoo.git
synced 2025-06-10 15:19:09 +02:00
4aa71fb389
Filter LTO too, and no-SA. Not reported upstream as it has a lot of open bugs already and seems low activity. Closes: https://bugs.gentoo.org/862273 Signed-off-by: Sam James <sam@gentoo.org>
79 lines
2.8 KiB
Diff
79 lines
2.8 KiB
Diff
Fix building and don't use bundled uchime.
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--- a/Makefile
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+++ b/Makefile
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@@ -104,12 +104,19 @@ endif
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# INCLUDE directories for mothur
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#
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#
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- VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
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+ VPATH=source:source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
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+ source := source
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skipUchime := source/uchime_src/
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+ skipTestMothur := source/TestMothur/
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+ skipSeqnoise := seqnoise.cpp
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subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
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+ subdirs := $(filter-out $(skipTestMothur), $(subdirs))
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subDirIncludes = $(patsubst %, -I %, $(subdirs))
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+ subDirIncludes += $(patsubst %, -I %, $(source))
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subDirLinking = $(patsubst %, -L%, $(subdirs))
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- CXXFLAGS += -I. $(subDirIncludes)
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+ subDirLinking += $(patsubst %, -L%, $(source))
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+ subdirs := $(dir source) $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))
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+ CXXFLAGS += -Isource -I. $(subDirIncludes)
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LDFLAGS += $(subDirLinking)
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@@ -118,15 +125,14 @@ endif
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#
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OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
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OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
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+ OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.cpp)))
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+ OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.c)))
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OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
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OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
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-mothur : $(OBJECTS) uchime
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+mothur : $(OBJECTS)
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$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
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-uchime :
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- cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd ..
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-
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install : mothur
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ifeq ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"")
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--- a/makefile-internal
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+++ b/makefile-internal
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@@ -115,7 +115,6 @@ endif
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mothur : $(OBJECTS)
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$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
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- strip mothur
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%.o : %.c %.h
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$(COMPILE.c) $(OUTPUT_OPTION) $<
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--- a/source/uchime_src/makefile
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+++ b/source/uchime_src/makefile
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@@ -1,4 +1,4 @@
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-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
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+CXXFLAGS = -std=c++11 -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
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LDFLAGS = -g
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#
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@@ -26,4 +26,4 @@ install : uchime
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clean :
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@rm -f $(OBJECTS)
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-
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\ No newline at end of file
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+
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--- a/source/writer.h
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+++ b/source/writer.h
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@@ -9,6 +9,7 @@
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#ifndef writer_h
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#define writer_h
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+#include <memory>
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#include "sharedwriter.hpp"
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/***********************************************************************/
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