gentoo resync : 12.05.2022

2 files changed, 22 insertions, 123 deletions

diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
deleted file mode 100644
index 8e504fa429e0..000000000000
--- a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-* unbundle htslib
-* honour all user flags
-* use pkg-config for linking
-
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -8,24 +8,12 @@
- LDFLAGSextra ?=
- CXXFLAGSextra ?=
- 
--# user may define the compiler
--CXX ?= g++
--
- # pre-defined flags
--LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
--LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
--LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
--LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
--LDFLAGS_gdb := $(LDFLAGS_shared)
--
- COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
- 
--CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
--CXXFLAGS_main := -O3 $(CXXFLAGS_common)
--CXXFLAGS_gdb :=  -O0 -g $(CXXFLAGS_common)
--
--CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
--
-+CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib`
-+CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE)
-+LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt
- 
- ##########################################################################################################
- 
-@@ -54,10 +42,10 @@
- 
- 
- %.o : %.cpp
--	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
-+	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $<
- 
- %.o : %.c
--	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
-+	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $<
- 
- all: STAR
- 
-@@ -84,7 +72,7 @@
- ifneq ($(MAKECMDGOALS),CLEAN)
- ifneq ($(MAKECMDGOALS),STARforMac)
- ifneq ($(MAKECMDGOALS),STARforMacGDB)
--Depend.list: $(SOURCES) parametersDefault.xxd htslib
-+Depend.list: $(SOURCES) parametersDefault.xxd
- 	echo $(SOURCES)
- 	/bin/rm -f ./Depend.list
- 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -95,57 +83,34 @@
- endif
- endif
- 
--htslib : htslib/libhts.a
--
--htslib/libhts.a :
--	$(MAKE) -C htslib lib-static
--
- parametersDefault.xxd: parametersDefault
- 	xxd -i parametersDefault > parametersDefault.xxd
- 
--STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
--STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- STAR : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
--POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
--STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
- STARstatic : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- STARlong : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
- STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
--gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
- gdb : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
- gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
--STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
- STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
- 
--STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
--STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
- STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
--	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
- 
- 
diff --git a/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch b/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch
new file mode 100644
index 000000000000..c056a8aad887
--- /dev/null
+++ b/sci-biology/STAR/files/STAR-2.7.10a-missing-include.patch
@@ -0,0 +1,22 @@
+From f5ad94329db4fd81fc6ae30684c298772002e30b Mon Sep 17 00:00:00 2001
+From: David Seifert <soap@gentoo.org>
+Date: Sat, 7 May 2022 15:06:11 +0200
+Subject: [PATCH] Add missing `#include <array>` (GCC 12)
+
+Bug: https://bugs.gentoo.org/840586
+---
+ source/SoloCommon.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/source/SoloCommon.h b/source/SoloCommon.h
+index 2a1d5fcf..5adc5040 100644
+--- a/source/SoloCommon.h
++++ b/source/SoloCommon.h
+@@ -1,6 +1,7 @@
+ #ifndef H_SoloCommon
+ #define H_SoloCommon
+ 
++#include <array>
+ #include <unordered_map>
+ 
+ typedef struct{