gentoo resync : 12.05.2022

5 files changed, 28 insertions, 170 deletions

diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
index 8f7c05fc8c7f..74eeb0bb4086 100644
--- a/sci-biology/STAR/Manifest
+++ b/sci-biology/STAR/Manifest
@@ -1,7 +1,5 @@
-AUX STAR-2.5.3a-fix-build-system.patch 5318 BLAKE2B 28a839eb61a5b1adef804249328c7917dca2ec765f00a48b90aa42d7da3ca393f7726b7aafdb6d0429a55fe696bd51b0e06d85ef6e50a3a4f5874c731b194f1e SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441
 AUX STAR-2.7.10a-fix-build-system.patch 7176 BLAKE2B 24a14d2d8af26565a3a7f754e9633c54c2cdaf72bf4e3b4fe3390a3790be16620117f576abf82d91e8816478fc1a012e7424ab6d93bb6161b975acd08627d3f0 SHA512 4d854336b2e0c61ca1ac604cded7f08e484974e1ec6d78928e5eb21eb7adb0ae3f6ec9deb3dc050dcffe1732f9076f2b4cddad7aa18ccad20f9232c9e11d1856
-DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf
+AUX STAR-2.7.10a-missing-include.patch 568 BLAKE2B 90d86e5bde440771edc60fb61f7d2f6ed2cd6cfbaff795725dfafe33213fa6eac86ac5cb90ba4df98e72b55fccd68bb6e1b6512cde3843fea05da53e271d8d5e SHA512 5ee3c977af62038014cf4aee31a03c534579a9e6846ad12ab32cd548ac18167816d7f4facedffae20a3e2f61b08c5325fea16969b9b1107a8bd0837d94453b7c
 DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9
-EBUILD STAR-2.5.3a.ebuild 881 BLAKE2B 692466b512aaa3da2e2323f90576d47c2f5e694a4ac8ee8ce2d887435a1ef964dcab9adbdb3c3f88b43cc5463b258635be0f2b542485ee16bc9ec32b655fcf65 SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663
-EBUILD STAR-2.7.10a.ebuild 970 BLAKE2B 63bc2b4656d4e672faf819f83bd2a930851e0b5c2d1ff422c5a72b655d5c68515a317675c59df2ff9256e4653351f1f180d9c94dbd256c89810d31ca3940b9ad SHA512 76841ebb6bb3a7c15da15c2124287959938beeb1c6e1a5fa362c476283b51dca49bcca83be9e10d5f39702f23b01ee131f8ab2f568b986e529fc006e65a25ffb
+EBUILD STAR-2.7.10a.ebuild 1022 BLAKE2B bfd279163ccdd54b834a5ca50b8ee5b09548a7370dbaa632d01f6cf7b2b9d013aa40419790f1b558dbc27dabd1ad55b3c8eb833321084925125db55647b6e020 SHA512 6a86e78d98ea727598cfcc281713caaacd910c1f48c9d711af47ca44b1f51e5c880a3490910f9547517c7bb783d817e32436f86e35e166661bc41f57492f6314
 MISC metadata.xml 341 BLAKE2B 5cf54dcbc5013bbebd80edd8d03456553ec6f7f52527d076f921916ebe9b862c97aae6f641741b81ac44cfc84356ca13e19dd3be2b63c075923a701c22e695c1 SHA512 888d00d5873390206f21aa9daaf78fc8c3f9b88e528c38ca7696779b221fd21acc6beadf543c14e16f74cb600cab479bc3f9bba8625214480583f369e6ea67a8
diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.5.3a.ebuild
deleted file mode 100644
index 73743cbb4e59..000000000000
--- a/sci-biology/STAR/STAR-2.5.3a.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
-HOMEPAGE="https://github.com/alexdobin/STAR"
-SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="sci-libs/htslib:="
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch )
-DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-src_configure() {
-	tc-export CC CXX PKG_CONFIG
-}
-
-src_compile() {
-	emake -C source STAR
-}
-
-src_install() {
-	dobin source/STAR
-	einstalldocs
-}
diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild
index 7239efcfe45c..c3deb5a94b0a 100644
--- a/sci-biology/STAR/STAR-2.7.10a.ebuild
+++ b/sci-biology/STAR/STAR-2.7.10a.ebuild
@@ -17,7 +17,10 @@ RDEPEND="sci-libs/htslib:="
 DEPEND="${RDEPEND}"
 BDEPEND="virtual/pkgconfig"
 
-PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch )
+PATCHES=(
+	"${FILESDIR}"/${PN}-2.7.10a-fix-build-system.patch
+	"${FILESDIR}"/${PN}-2.7.10a-missing-include.patch
+)
 DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
 
 pkg_pretend() {
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{