diff options
| author | V3n3RiX <venerix@koprulu.sector> | 2025-04-08 08:43:12 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@koprulu.sector> | 2025-04-08 08:43:12 +0100 |
| commit | e81d2dd033df3a61b874a9a37f951ca05eead86f (patch) | |
| tree | 82bfb1314b75b6c04de41a378a4838b7a18b0d68 /sci-biology | |
| parent | 288d9455931660abb6dfa534a78d45c7fb901477 (diff) | |
gentoo auto-resync : 08:04:2025 - 08:43:11
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/Manifest.gz | bin | 19009 -> 19009 bytes | |||
| -rw-r--r-- | sci-biology/bfast/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/bfast/bfast-0.7.0a-r1.ebuild | 30 | ||||
| -rw-r--r-- | sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch | 13 |
4 files changed, 45 insertions, 0 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz Binary files differindex 178954ee8e4a..1d8d1a5596ea 100644 --- a/sci-biology/Manifest.gz +++ b/sci-biology/Manifest.gz diff --git a/sci-biology/bfast/Manifest b/sci-biology/bfast/Manifest index 9ea43db42657..880438f67a22 100644 --- a/sci-biology/bfast/Manifest +++ b/sci-biology/bfast/Manifest @@ -1,6 +1,8 @@ AUX bfast-0.7.0a-C99-inline.patch 2316 BLAKE2B 744908af002c5d5af57358baffbaff75a6299b7d0467573e5416c78ab2d4c9fc35dddbdcf308ada17583ca0e732412d1293152240748e84ac5eea243a944e8a1 SHA512 13144864d6a758d6dc0cba59e2a4458242ce33ab77108aafc33967a5343d1f0e2d59f872822e13df8a2f77f1eba2f58c5cc14060a48900509726e48fe6061177 AUX bfast-0.7.0a-autotools.patch 1268 BLAKE2B b5da950d0230322f0a95b7c1417aec5fc4774a7d40ce4576b10bbc66d21f8d4907e17f3020679f3074cfdbe10f7e69bc3d8b62371ad381a2fb7b17854f146e46 SHA512 d1b00230ef35e82fb633a063c32e48a50866d8c40889cb0e13fddb0866a5b5447ed0f41cc948811f7e50918544ed3d0758ace3e1060a97a33ff5a0c3ee12b29c +AUX bfast-0.7.0a-gzeof.patch 398 BLAKE2B 16ad56feda55aea56d515b9834a01b7a9dd0bb8bafcba2dae66072f8bb1e97c5614f6a949dde25ca496c2c93be8e8d8a3fdfba847a3b16ee76cf21bfa6c72e82 SHA512 c5ea9aa636982e94340abc1a54003da813ce077447300745895d911f23ee443943ada8b75c3637211302946b5f03cfd05d553d0c0cb0b2736820d926d3321fb9 AUX bfast-0.7.0a-test-sourcing.patch 1399 BLAKE2B 2cc246d437da36a28d6fd86fe8c4acb78ba06120672158c16305c108298f46f4cabf37193f793e9b32ecb8fddc022f076bc845d06564f23ed9f412f5d7c22378 SHA512 3257038564997ae1b2bdd814e893825951c9cc72934cc204d6a3cd1dd31c796d26b76b6801dca4722be3e10ac309e0d177ddf725a6b6a2c5fe01106bd35d5a5f DIST bfast-0.7.0a.tar.gz 2456617 BLAKE2B a841e7651e731dbb3faf22eb03dce5d2008c84f9a6198204d3c41aea26626058e3a23375bc0e7e8fc142d4898e09ddbb168016c71a7b79527e602e06ec329151 SHA512 16e7ec5101c478f0dfc171016cbacb2b9240773e43b2d40eeb42d0e47afcee50a6dd5838e043a0326fc1ca9a87d3e55b42326a7f17b7c5654ef9825913860836 +EBUILD bfast-0.7.0a-r1.ebuild 640 BLAKE2B ef21cc3a4c3eed6f5ae672b6f84030d350ff10a47ef9989782748b164f0d14230bb56e1e27144d5c298ce0c6d5a51562f2d959ecb62893f8f97fe267fed593d8 SHA512 401a79d1ebc2c597f3bc0012d4b504bc258dd374b4ea37c23cdfa6ba70da7553f62676570a9189136003fedb43ef2b2b33d93e64d92b231f8c6821951057ae8c EBUILD bfast-0.7.0a.ebuild 608 BLAKE2B eea76ad72a8017eddf0926670727b9f19c6f7e84ac3c1d1f74470e95c07a696769ad33c8393342b5d5132c8cf87a8df954180d17b7b6a6f1617764e26fc05b3e SHA512 a2e7c794d0e02240fefac07fa29ddece91010ee0677c2b5474c5541a24c4c33d5e33efcc07b9f16a2dc041eece726396f0eff54e53fd79f28e52facdc408982a MISC metadata.xml 347 BLAKE2B fda3b1b1f01d1cadeae82a76b136ff36dca51aa87133f2413169e8e42f9551a5982aa865638d0fcd62aacac988bfca1cb273b4fc631f645a017be4242c481f66 SHA512 56e5f098713a53961f0967972197ee5eee51175964a4299c4aa647f66a47abf882304384a5dac51134ab1f806d300c7278c4479912b723f0a7ab5d19b0fe0834 diff --git a/sci-biology/bfast/bfast-0.7.0a-r1.ebuild b/sci-biology/bfast/bfast-0.7.0a-r1.ebuild new file mode 100644 index 000000000000..56c2f6035994 --- /dev/null +++ b/sci-biology/bfast/bfast-0.7.0a-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit autotools + +DESCRIPTION="Blat-like Fast Accurate Search Tool" +HOMEPAGE="https://sourceforge.net/projects/bfast/" +SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="test" # tests broken, upstream unresponsive + +RDEPEND="dev-perl/XML-Simple" + +PATCHES=( + "${FILESDIR}"/${P}-autotools.patch + "${FILESDIR}"/${P}-test-sourcing.patch + "${FILESDIR}"/${P}-C99-inline.patch + "${FILESDIR}"/${P}-gzeof.patch +) + +src_prepare() { + default + eautoreconf +} diff --git a/sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch b/sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch new file mode 100644 index 000000000000..b0b992abf1bc --- /dev/null +++ b/sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch @@ -0,0 +1,13 @@ +Use correct gzip function to check for the end of file +https://bugs.gentoo.org/919254 +--- a/bfast/RGMatch.c ++++ b/bfast/RGMatch.c +@@ -20,7 +20,7 @@ + /* Read in the read length */ + if(gzread64(fp, &m->readLength, sizeof(int32_t))!=sizeof(int32_t)|| + gzread64(fp, &m->qualLength, sizeof(int32_t))!=sizeof(int32_t)) { +- if(feof(fp) != 0) { ++ if(gzeof(fp) != 0) { + return EOF; + } + else { |