diff options
| author | V3n3RiX <venerix@koprulu.sector> | 2024-05-09 00:01:03 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@koprulu.sector> | 2024-05-09 00:01:03 +0100 |
| commit | a0ce545d52f231499bf9f3644493113d8af58ec9 (patch) | |
| tree | 4d67c09eed0c2ae28d1317f72d7f7b08b4f6aeea /sci-biology/velvet | |
| parent | 5181ced3f3566a9610b85922b083c8f84f20d78f (diff) | |
gentoo auto-resync : 09:05:2024 - 00:01:03
Diffstat (limited to 'sci-biology/velvet')
| -rw-r--r-- | sci-biology/velvet/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch | 26 | ||||
| -rw-r--r-- | sci-biology/velvet/velvet-1.2.10.ebuild | 22 |
3 files changed, 48 insertions, 3 deletions
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 |