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-rw-r--r--sci-biology/Manifest.gzbin19007 -> 19010 bytes
-rw-r--r--sci-biology/hmmer/Manifest3
-rw-r--r--sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch18
-rw-r--r--sci-biology/hmmer/hmmer-2.3.2-r6.ebuild (renamed from sci-biology/hmmer/hmmer-2.3.2-r5.ebuild)3
-rw-r--r--sci-biology/paml/Manifest5
-rw-r--r--sci-biology/paml/files/paml-4.10.7-LDFLAGS.patch60
-rw-r--r--sci-biology/paml/metadata.xml3
-rw-r--r--sci-biology/paml/paml-4.10.7.ebuild37
-rw-r--r--sci-biology/velvet/Manifest3
-rw-r--r--sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch26
-rw-r--r--sci-biology/velvet/velvet-1.2.10.ebuild22
11 files changed, 174 insertions, 6 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c1eec181be8c..90ea37bf4b0d 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
Binary files differ
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index 79c67879328d..4b622aa2a7dc 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -1,9 +1,10 @@
AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 BLAKE2B 46264f43ed43a567c1f650710e1485942eb48a0b7ed3860424f00ca06cf04f9e923318c5df3d56eb312ed773bf2d42e22880b4ac6c2f81ac6c65bf2cebf44008 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f
+AUX hmmer-2.3.2-fix-missing-include-in-configure.patch 526 BLAKE2B 5b382c4d827a3287349d4f4f4969e9d46339ccb065fd5f9eedcd855b8f830d3625c42a7df5f40476c16d00113038ebb658d510135e42b337d00f2fcfee7ac36d SHA512 aac277e7a8f5eed78b72b841f520f6792d327b7f2cc2173e526ce33fb25069d674f9875997fb0bf8e585cd9a645e88501e30f22aa43bacb29127fc380efc40de
AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 BLAKE2B 1afca014901d79416dac2c1d41e20371ef970aa3691a6b414e9a96adf8331c619753df7a42e1d9af63aab12a3fc8b8c7d2251129dd581bfb33a0d7c3e50970b2 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9
AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 BLAKE2B c0c78fed780b43df960dc24914e5dabe161243cec015deaf058d7eebf79c5e1633ded4f1305bb37b9766d74588009142fd58886e67810940e9601ef138647c21 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff
AUX hmmer-3.1_beta2-makefile.patch 3679 BLAKE2B e258b23bda9d0515891f1d571b94f9ef48499f25ce6cb52c3d1bcd0a28bc527f335cb25ece944afb33e4824438315cc9986243fb13e07eb128d7859e0a77f4b1 SHA512 bebd36deee48d4a043a1d84233ccbc93de8e44b5f7f57bf24a551b53a6f3dbfb3166861555755744d0abb4fce871d7c19fa8887c08115b7d8f61ca5ad38c3cc6
DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7
DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771
-EBUILD hmmer-2.3.2-r5.ebuild 1843 BLAKE2B ecea0f3370698641b3ddc5c572f9386bacc2547fab72889d79fd910052edd14bd4a2447b8a9183290a5c0be4f313735bbab8e1bd67d1c4275a6d036fe2fae3dc SHA512 3109f304c6f48b7d924eeadd416fa3e9c3e662f2380b4ce1da283d80a47de9fda4585966e8f29c47dd89914e7e03bf0f9966f828d45a13befb0f035e89cb2978
+EBUILD hmmer-2.3.2-r6.ebuild 1902 BLAKE2B caf57622e095891b70b95838ded043a530c0160e53da84dc1d93ecdd7c65e08ee7abb05c98c835c64d6aea4d9b064f511e34cd1d5cee2c33493a957e31b5991f SHA512 c68017cec913425eed52350638bf1f9408f1fb65e1ada8209da60acb533944e1ec3b6ffd035692844d53ac069999023b54da937f7fa6d51c3e212220bf8950c9
EBUILD hmmer-3.1_beta2-r1.ebuild 1140 BLAKE2B a5a0a26f2461edc08101505fa600383952501083111e828b4a0484a2c895acb63b3784247ea3a9b4fb10a13089a84f09f9721b4835cbb7b5479f0877e62c84aa SHA512 65889b5afe47d60abdd7ebb4d098510e8f25979e442df2a88d6327ab2fffc6d056fa6f96f32c0d37614473bc961c1e60fc3e194e535c5b6816b3c420816c5ea9
MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
new file mode 100644
index 000000000000..37683d425edb
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
@@ -0,0 +1,18 @@
+--- a/squid/configure 2024-05-08 09:21:15.751063495 -0000
++++ b/squid/configure 2024-05-08 09:22:50.491502934 -0000
+@@ -2493,6 +2493,7 @@
+ cat confdefs.h >>conftest.$ac_ext
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
++#include <stdlib.h>
+ int
+ main ()
+ {
+@@ -3500,6 +3501,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h. */
+ #include <ctype.h>
++#include <stdlib.h>
+ #if ((' ' & 0x0FF) == 0x020)
+ # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+ # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
index b305820faff3..74a8a151b0c4 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -20,6 +20,7 @@ BDEPEND="test? ( dev-lang/perl )"
PATCHES=(
"${FILESDIR}/${P}-fix-perl-shebangs.patch"
"${FILESDIR}/${P}-fix-build-system-destdir.patch"
+ "${FILESDIR}/${P}-fix-missing-include-in-configure.patch"
)
src_configure() {
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
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-08 05:06:50 +0000