gentoo auto-resync : 09:05:2024 - 00:01:03

8 files changed, 152 insertions, 4 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c1eec181be8c..ed0811dd1d57 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index a1e5c6c96c0a..78eb1c46687f 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,5 +1,8 @@
+AUX paml-4.10.7-LDFLAGS.patch 2586 BLAKE2B e77ae705018abccd7acf9bced3c514dee9e1937596e484cdef856a55b746e2d28f6e7dac8a2b55cc2c2c9d6e68107aea600456e7fa93200620f2bbac28c27a70 SHA512 418afede3d3cae5c26ecf5e25b22caf0a9f50e724de92c018df9ccaff52c2f3943f9a1400c8e0a199e5408a8f5aa631a33ff9046b0b4a87e31a5fda1daa222e9
 AUX paml-4.9j-fno-common.patch 521 BLAKE2B 93dda51495e65cde9b3e92379e43756c5efe77953b114ceb88c8dc9ae6453d5b2742e250cf9a2d6feec3e86ff430417a4ecd8fd06b199a899b14d0aeac5199e2 SHA512 c24431264c7a69077f9ea9f511e93d45ac8adc4a5cc41446ca96de4e270b918543fb1a424b9119bc1723b2a9574434321a55a5af88712e0f3d51ef5c964575fb
 AUX paml-4.9j-makefile.patch 1540 BLAKE2B 9ffa0f8fab089d26e325688596975944a10e9e62ba1554b532b3f31c7f508b5b1001f5481ad9b8ae7fa97ffd8bcdffda3c285935c8efa3442175f4686e0a44ad SHA512 51b05e865ff68d58cf0f8cc2bc23e8e90e5d12ac8daceb96ac9cc64fdf75c704b5b16b6b8248a0e3cd03c1b18e5bbb61727c281ad46b4988a197f695b464c80d
+DIST paml-4.10.7.tar.gz 5250841 BLAKE2B 4d2a7fdc8eb93abe200165f7805520a02f4251dc651f26c4e1bf6fb11eee3d0721fd9d6f3c96979bae0f51b77f168e8d8a12f3dd3cbbfec7e8210a70b7c4bb9e SHA512 e450c0a28ecef946279fd92834eb5ddfb50805167655364cc959ef21839a75280a37d79209918373e80dacb0fc35decaccdb1477e53a81fd99fb140a0ce839fe
 DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758
+EBUILD paml-4.10.7.ebuild 860 BLAKE2B 6bafd36fdc346e3d8efb0a1c5b2303f21207854c05c36c39d7b34e0d5a17c815fde3e5492a20265da30b918a5eeb2f5a3d0701bf494ab10ad7851716e6066ce0 SHA512 0f74852064f85a47f3e451630f5c5ed023c9551bbf09fb8e6060b97adbd94677f6ce191240d972388a2cbb1f63b6400b52660e2b5e0878f06c086566337d201c
 EBUILD paml-4.9j.ebuild 843 BLAKE2B 8f92ab034a78571de1bccecc21d04fc9eef7414d98c5a3f4a6d4a96f59ddcd32e0c0c1c82928ed3949f7c64a493fbf5c3962016425ab8bcef6b3718cf50e49ba SHA512 74100d6e6a0913c0c1a56039468b5a78c86fc13fab054a0dc6fe307ba975f84865c999f5472c1e18a5bf28c7f0fe37359f3c557965b251968eba692bec49e607
-MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
+MISC metadata.xml 353 BLAKE2B 1e75fa5d5a443d798ff85ef771cbe8883a0704c88e946064e31f741fae6bf667dda640c3898dc76b3b4112347e656193051642080a7c5a1afb8586d09eba6c9a SHA512 84b85abf47532d11d0aa81c3148a370c99c014093f9c20d28e0ad3aaa6c6d6bb33ab0f4d6eb1e3a10cf7b730dccb58f1044d379255b696a5ca46e529d024411a
diff --git a/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch
new file mode 100644
index 000000000000..492396a0fd83
--- /dev/null
+++ b/sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch
@@ -0,0 +1,60 @@
+https://github.com/abacus-gene/paml/pull/46
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -9,39 +9,39 @@ LIBS = -lm # -lM
+ all : $(PRGS)
+ 
+ baseml : baseml.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ baseml.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ baseml.o tools.o $(LIBS)
+ basemlg : basemlg.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ basemlg.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ basemlg.o tools.o $(LIBS)
+ codeml : codeml.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ codeml.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ codeml.o tools.o $(LIBS)
+ evolver : evolver.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ evolver.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ evolver.o tools.o $(LIBS)
+ pamp : pamp.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ pamp.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ pamp.o tools.o $(LIBS)
+ mcmctree : mcmctree.o tools.o treesub.c treespace.c paml.h
+-	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
+-	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ mcmctree.c tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.o $(LIBS)
+ yn00: yn00.o tools.o paml.h
+-	$(CC) $(CFLAGS) -o $@ yn00.o tools.o $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ yn00.o tools.o $(LIBS)
+ chi2 : chi2.o
+-	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)
++	$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ chi2.c $(LIBS)
+ 
+ tools.o : paml.h tools.c
+-	$(CC) $(CFLAGS) -c tools.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c tools.c
+ baseml.o : paml.h baseml.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c baseml.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c baseml.c
+ basemlg.o : paml.h basemlg.c treesub.c
+-	$(CC) $(CFLAGS) -c basemlg.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c basemlg.c
+ codeml.o : paml.h codeml.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c codeml.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c codeml.c
+ evolver.o: evolver.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c evolver.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c evolver.c
+ mcmctree.o : paml.h mcmctree.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c mcmctree.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c mcmctree.c
+ pamp.o : paml.h pamp.c treesub.c treespace.c
+-	$(CC) $(CFLAGS) -c pamp.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c pamp.c
+ yn00.o : paml.h yn00.c
+-	$(CC) $(CFLAGS) -c yn00.c
++	$(CC) $(CPPFLAGS) $(CFLAGS) -c yn00.c
+ 
+ clean :
+ 	-rm *.o $(PRGS)
diff --git a/sci-biology/paml/metadata.xml b/sci-biology/paml/metadata.xml
index ccdff086e20b..1407729820e0 100644
--- a/sci-biology/paml/metadata.xml
+++ b/sci-biology/paml/metadata.xml
@@ -5,4 +5,7 @@
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
+  <upstream>
+    <remote-id type="github">abacus-gene/paml</remote-id>
+  </upstream>
 </pkgmetadata>
diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild
new file mode 100644
index 000000000000..3291f74efcad
--- /dev/null
+++ b/sci-biology/paml/paml-4.10.7.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="https://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-4.10.7-LDFLAGS.patch
+)
+
+src_compile() {
+	emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
+
+	dodoc -r README.md doc/.
+
+	insinto /usr/share/${PN}/control
+	doins examples/*.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins -r examples/stewart* examples/*.dat dat/.
+
+	insinto /usr/share/${PN}
+	doins -r examples
+}
diff --git a/sci-biology/velvet/Manifest b/sci-biology/velvet/Manifest
index 2edf4614a91f..ba54f2f0765a 100644
--- a/sci-biology/velvet/Manifest
+++ b/sci-biology/velvet/Manifest
@@ -1,3 +1,4 @@
+AUX velvet-1.2.10-incompatible-pointers.patch 1006 BLAKE2B a3e3ded8de6b71d284eb41f9c3663f6cdb5daab5fdb6a7c4c01244e5fe3173db545b8543d37b39adefb9c33e31a40a0809f4b06f570de3bab2c84112b51b1729 SHA512 31cc0c77aaf54b63fdce5084af8d2a28b683e9898f425766dd8fe08bc665f15c345a7f80d0a13ec39d27a29cc3f078ebc3fcf829b79ed4f9c3b92841b3bbbc9d
 DIST velvet_1.2.10.tgz 18818559 BLAKE2B 5723c9c040e570cd88b774e5b0044dd04def88778fe2b137ec7c007ab83fc98e5423ad1d9d0499780cf6d3152347ca1a4e4e6b6c1900ce4adfc4930f1f6d3c34 SHA512 a6f3e35cebceb22cc10e83088b8cd9758492da78866237cae63d8826d6f5cfb44d82dd8bfcb1185d37cd434d4c7a0f2ac7135bb80a51db86e754afd6156ea874
-EBUILD velvet-1.2.10.ebuild 2085 BLAKE2B f0aa88a145341553ad74006189dec738a05a29620a4f90843daf4f4e3fd2bce857836b1332c2fee4764db63a202c6b5a908f97dd7ae1e654f24c51e04c865065 SHA512 4a61a2df8715691deba0dfb22b6e8ca049e655e55e82e620a25af4de625b6e43757963942304983145c9b7a29751dbc90aa3854fdb9496a50622d4b5b0d677ed
+EBUILD velvet-1.2.10.ebuild 2397 BLAKE2B 651a319f3e0b49a330a8317afb2e5fb3848a3f657ed6d564f70bdc815d266ff3030045f0846c952fd1895cef3413d36f9dca922e72c2dd23de8a47663912b80e SHA512 62018be7826cac6417b49b04c5a3e47915ab2f0d8ca3d6d3d65413dbfa3ca00eb1c09b6996c6d8c7453b88f5ed828898b2b69d563bf8c359a35b16722131da56
 MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch
new file mode 100644
index 000000000000..22cd48ee814f
--- /dev/null
+++ b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch
@@ -0,0 +1,26 @@
+https://bugs.gentoo.org/919223
+--- a/src/readSet.c
++++ b/src/readSet.c
+@@ -638,7 +638,8 @@ static void readFastXFile(int fileType, SequencesWriter *seqWriteInfo, char *fil
+ 	FileGZOrAuto file;
+ 	IDnum counter = 0;
+ 
+-        file.gzFile = file.autoFile = NULL;
++        file.autoFile = NULL;
++        file.gzFile = NULL;
+         if (fileType == AUTO) {
+         	file.autoFile = openFileAuto(filename);
+                 if (!file.autoFile)
+@@ -677,8 +678,10 @@ static void readFastXPair(int fileType, SequencesWriter *seqWriteInfo, char *fil
+ 	if (cat==REFERENCE)
+ 		exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode");
+ 
+-        file1.gzFile = file1.autoFile = NULL;
+-        file2.gzFile = file2.autoFile = NULL;
++        file1.autoFile = NULL;
++        file2.autoFile = NULL;
++        file1.autoFile = NULL;
++        file2.autoFile = NULL;
+         if (fileType == AUTO) {
+         	file1.autoFile = openFileAuto(filename1);
+                 if (!file1.autoFile)
diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild
index ea0b3630b78b..07b44eb65254 100644
--- a/sci-biology/velvet/velvet-1.2.10.ebuild
+++ b/sci-biology/velvet/velvet-1.2.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -16,7 +16,25 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc openmp"
 
-BDEPEND="doc? ( virtual/latex-base )"
+BDEPEND="
+	doc? ( virtual/latex-base )
+	openmp? (
+		|| (
+			sys-devel/gcc[openmp]
+			sys-devel/clang-runtime[openmp]
+		)
+	)
+"
+
+PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" )
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
 
 src_prepare() {
 	default