gentoo resync : 12.05.2022

12 files changed, 29 insertions, 331 deletions

diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
deleted file mode 100644
index 2fcef3b41aff..000000000000
--- a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-MODULE_AUTHOR=LDS
-inherit perl-module webapp
-
-DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser"
-HOMEPAGE="http://gmod.org/wiki/GBrowse"
-KEYWORDS="~amd64 ~x86"
-IUSE="minimal mysql postgres +sqlite"
-
-SLOT="0"
-WEBAPP_MANUAL_SLOT="yes"
-
-CDEPEND="!<sci-biology/GBrowse-2.44-r1
-	>=sci-biology/bioperl-1.6.9
-	>=dev-perl/Bio-Graphics-2.09
-	>=dev-perl/GD-2.07
-	>=dev-perl/CGI-Session-4.02
-	dev-perl/IO-String
-	dev-perl/JSON
-	dev-perl/libwww-perl
-	dev-perl/Statistics-Descriptive
-	!minimal? (
-		dev-perl/Bio-Das
-		>=dev-perl/Bio-SamTools-1.20
-		dev-perl/Crypt-SSLeay
-		dev-perl/DB_File-Lock
-		dev-perl/DBI
-		mysql? ( dev-perl/DBD-mysql )
-		postgres? ( dev-perl/DBD-Pg )
-		sqlite? ( dev-perl/DBD-SQLite )
-		dev-perl/FCGI
-		dev-perl/File-NFSLock
-		dev-perl/GD-SVG
-		dev-perl/Net-OpenID-Consumer
-		dev-perl/Net-SMTP-SSL
-	)"
-#		>=dev-perl/Bio-DB-BigFile-1.00 - requires jklib to compile
-DEPEND="dev-perl/Module-Build
-	dev-perl/Capture-Tiny
-	${CDEPEND}"
-RDEPEND="${CDEPEND}"
-
-PATCHES=( "${FILESDIR}"/GBrowseInstall.pm-2.39.patch )
-
-src_configure() {
-	webapp_src_preinst
-
-#	myconf="--install_base=${D}/usr" or "--install_base=/opt/gbrowse"
-	myconf="--conf=/etc/gbrowse2"
-	myconf="${myconf} --htdocs=${MY_HTDOCSDIR}"
-	myconf="${myconf} --cgibin=${MY_CGIBINDIR}"
-	myconf="${myconf} --tmp=/var/tmp/gbrowse2"
-	myconf="${myconf} --persistent=/var/db/gbrowse2"
-	myconf="${myconf} --databases=/var/db/gbrowse2/databases"
-	myconf="${myconf} --installconf=no"
-	myconf="${myconf} --installetc=no"
-	perl-module_src_configure
-}
-
-src_install() {
-	dodir /var/tmp/gbrowse2
-	dodir /var/db/gbrowse2/sessions
-	dodir /var/db/gbrowse2/userdata
-	webapp_serverowned -R /var/tmp/gbrowse2 /var/db/gbrowse2
-	perl-module_src_install
-	webapp_src_install
-}
diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest
deleted file mode 100644
index ddfd14a7c6fc..000000000000
--- a/sci-biology/GBrowse/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX GBrowseInstall.pm-2.39.patch 2878 BLAKE2B 99ca47ef69aad80322bcc2f0a856a2e0e8d2185189172c842f3bfdc9efbda383f8d00ca5e6a829dbb48f1f668047ec4e66ac83cef433347453a91ee557820c1a SHA512 637dea799290213def1368cdb153463c96964ada99fd6c09d0b95e0d1e42a16942d66ef36282d39b92284ae6eb26c8346d5ad1289b5ec7b2196a1ba5090db85e
-DIST GBrowse-2.48.tar.gz 11958127 BLAKE2B e9527eb47302775d62e37990c42154b677284fff0f0f9624e9173e30e46c5aebbc8a02ee8dec0a1e98761812ef2363e0183008087bce4d283528b7935b4d5f91 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db
-EBUILD GBrowse-2.48-r1.ebuild 1859 BLAKE2B c738aeb5114fc688fea7b2277332530452489c02309926a1acd7a5cde1225577a6c07e432f8aac8515c4d16c97962fbc0833807134292edfc0e3e4b4a768798e SHA512 e763f68e6c3d0d76284a68f918e39c00dfff5be6110852d6f9dde74072d8c1e686157a517c0a15a948bce679a77792d175acf1be1a93326c0e541f544e30086a
-MISC metadata.xml 328 BLAKE2B ce5ed72774e7d696776952832799cd960fae4bc4034e69d38db80fb3e9eceb77c538b0d6f15c0602582003cfe5e214124714e2e385d3d5707d2df8927b2a46ba SHA512 9bd9535f41bcb395c1d59abdbd4c9e0499aa6d945bf5a8fb79b1fe1b7d2e2864e3276878546160e238f1b04ecdfe95551f32f5d53587d85a8628f90d36ffdbc0
diff --git a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch b/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
deleted file mode 100644
index 5aa0be9df918..000000000000
--- a/sci-biology/GBrowse/files/GBrowseInstall.pm-2.39.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff -durr GBrowse-2.39-orig/install_util/GBrowseInstall.pm GBrowse-2.39/install_util/GBrowseInstall.pm
---- GBrowse-2.39-orig/install_util/GBrowseInstall.pm	2011-07-19 20:14:52.434608020 +0000
-+++ GBrowse-2.39/install_util/GBrowseInstall.pm	2011-07-19 21:02:13.685107753 +0000
-@@ -454,33 +454,33 @@
-     $gid =~ /^(\d+)$/;
-     $gid = $1;
-     
--    unless (chown $uid,$gid,$tmp) {
--	$self->ownership_warning($tmp,$user);
--    }
-+#    unless (chown $uid,$gid,$tmp) {
-+#	$self->ownership_warning($tmp,$user);
-+#    }
- 
-     my $htdocs_i = File::Spec->catfile($self->install_path->{htdocs},'i');
-     my $images   = File::Spec->catfile($tmp,'images');
-     my $htdocs = $self->install_path->{htdocs};
--    chown $uid,-1,$htdocs;
-+#    chown $uid,-1,$htdocs;
-     {
- 	local $> = $uid;
--	symlink($images,$htdocs_i);  # so symlinkifowner match works!
-+#	symlink($images,$htdocs_i);  # so symlinkifowner match works!
-     }
--    chown $>,-1,$self->install_path->{htdocs};
-+#    chown $>,-1,$self->install_path->{htdocs};
- 
-     my $persistent = $self->install_path->{'persistent'};
-     my $sessions   = File::Spec->catfile($persistent,'sessions');
-     my $userdata   = File::Spec->catfile($persistent,'userdata');
--    mkpath([$sessions,$userdata],0711);
-+#    mkpath([$sessions,$userdata],0711);
- 
-     my $databases = $self->install_path->{'databases'};
-     
--    unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) {
--	$self->ownership_warning($databases,$user);
--    }
-+#    unless (chown $uid,$gid,glob(File::Spec->catfile($databases,'').'*')) {
-+#	$self->ownership_warning($databases,$user);
-+#    }
- 
--    chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
--    $self->fix_selinux;
-+    # chmod 0755,File::Spec->catfile($self->install_path->{'etc'},'init.d','gbrowse-slave');
-+    # $self->fix_selinux;
- 
-     my $base = basename($self->install_path->{htdocs});
- 
-@@ -489,14 +489,14 @@
-     my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
-     my $perl          = $self->perl;
-     my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
--    system $perl,@inc,$metadb_script;
--    system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
-+#    system $perl,@inc,$metadb_script;
-+#    system 'sudo','chown','-R',"$uid.$gid",$sessions,$userdata;
- 
--    if (Module::Build->y_n(
--	    "It is recommended that you restart Apache. Shall I try this for you?",'y'
--	)) {
--	system "sudo /etc/init.d/apache2 restart";
--    }
-+#    if (Module::Build->y_n(
-+#	    "It is recommended that you restart Apache. Shall I try this for you?",'y'
-+#	)) {
-+#	system "sudo /etc/init.d/apache2 restart";
-+#    }
-     
-     print STDERR "\n***INSTALLATION COMPLETE***\n";
-     print STDERR "Load http://localhost/$base for demo and documentation.\n";
-Only in GBrowse-2.39/install_util: GBrowseInstall.pm~
diff --git a/sci-biology/GBrowse/metadata.xml b/sci-biology/GBrowse/metadata.xml
deleted file mode 100644
index 08238dd44f7a..000000000000
--- a/sci-biology/GBrowse/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<maintainer type="project">
-  <email>sci-biology@gentoo.org</email>
-  <name>Gentoo Biology Project</name>
-</maintainer>
-<upstream>
-  <remote-id type="cpan">GBrowse</remote-id>
-</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index b726b826cf1a..52b23c3b700c 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
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{
diff --git a/sci-biology/tree-puzzle/Manifest b/sci-biology/tree-puzzle/Manifest
index 95db460be96a..d13157e1d6c1 100644
--- a/sci-biology/tree-puzzle/Manifest
+++ b/sci-biology/tree-puzzle/Manifest
@@ -1,5 +1,5 @@
 AUX tree-puzzle-5.2-MPI-3.0.patch 15029 BLAKE2B 368eb7e3d209515a94f1049da80ebf9f14824e44e8c0b1996ba9c5ac7bfd58c167c01582bbc0d058a57d9797d844ad32e8bf45ce921a13c6e217d7728564a4d7 SHA512 576ed6c4a96225d55a1def0c4912cf908d0225d9ad9f9e0974a98f24d8bce172406a11202b9656c23661f6bb27b51a0b4e3bf95634b3c11aa10c20cd9d68e648
 AUX tree-puzzle-impl-dec.patch 380 BLAKE2B 22c00e2e0b4682a98212ec0b6e941ac37eff4cdeb8f684dc607e80a1617a35e209d23ac739af0e69af91deb8122fe04c3f9e7bdbd0c54edd8e603a817bdf0848 SHA512 092743fff8a305a41ef55afde3e058c1892d9c608bd05cb87de38a451c2b9cafc7749825347d5c245f1c6b1e84cf9d28b63bd4e7389440da5604766412290110
 DIST tree-puzzle-5.2.tar.gz 875142 BLAKE2B aa13e9a7aa403c12aebefb94a1931baa8b17cbee56d20011cb06db5a7b1b7f78c719ed6c6bfb0b79e47dc652d7b984415694907fc6cd56bdbe9eebca4aaa96a8 SHA512 5b9a729b120cba59f59ba426acd439cf396826ea01e75361b23387ccb9baf295d2512f21af96071a5f7b7507db4ff4d6b135cf6c5b6233a8b438532d31abe751
-EBUILD tree-puzzle-5.2.ebuild 1122 BLAKE2B 98582441713aa9afc4bdb69311f219588954046e759a680c936ef2174ef3b0e6ec572feab87aaf3f1cd9bb02db497a5df19a4bef0a096c961fc3f8e3b579a8f5 SHA512 7db6341bc1a12a2278fbcca1a8ca5080249c6453c497c6493923b295a971f168eeb2e1c8796444ae23872e362347151366c3243f8c786e9bf7a6ede48832af4f
+EBUILD tree-puzzle-5.2.ebuild 1097 BLAKE2B 3012cc63ec7ab38158729e754af531c5e09d11c993ae7abc9ba6d8be7aad98e800b3f9d442767afcb2fc4b71a0470698e68ebdf0eedc45435ba317801e36b932 SHA512 595de2081f21863d030382450d26a8677191b4e573258ef4ea185969df0b6a9868491c5c9b7d35517f8699ebcaa1e946b501622efbc1cccb3264c763c0c83f11
 MISC metadata.xml 1556 BLAKE2B 1f8b1d4719d156e9a9783adce70d8f4c0c17a7c855e5590bc796e16062066883a27f780946edaffdc04eb6f640ac7e81d71b075ebc5ed9759c2a5d4da20ac46e SHA512 07bd436f7616301172b07fefd72390a46778098baa3e9db949169850a60cd40e27a0e58dcafe5689923bc1e7cebb4e317a291f5caf2750651b76c447f5799215
diff --git a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
index 06fc28376ff5..e5093420d6a8 100644
--- a/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
+++ b/sci-biology/tree-puzzle/tree-puzzle-5.2.ebuild
@@ -3,8 +3,6 @@
 
 EAPI=8
 
-inherit toolchain-funcs
-
 DESCRIPTION="Maximum likelihood analysis for nucleotide, amino acid, and two-state data"
 HOMEPAGE="http://www.tree-puzzle.de"
 SRC_URI="http://www.tree-puzzle.de/${P}.tar.gz"