diff options
| author | V3n3RiX <venerix@koprulu.sector> | 2024-04-27 23:59:43 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@koprulu.sector> | 2024-04-27 23:59:43 +0100 |
| commit | 413421048cc2b0df9a218f0ab3cb151846809eb5 (patch) | |
| tree | 3fd887035aa0f5b65d7f147ab77caa98c44c148d /sci-biology/maq | |
| parent | 3e42d1577189af123b773dc0f11e5419035308c8 (diff) | |
gentoo auto-resync : 27:04:2024 - 23:59:42
Diffstat (limited to 'sci-biology/maq')
| -rw-r--r-- | sci-biology/maq/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch | 23 | ||||
| -rw-r--r-- | sci-biology/maq/maq-0.7.1-r4.ebuild (renamed from sci-biology/maq/maq-0.7.1-r3.ebuild) | 5 |
3 files changed, 28 insertions, 3 deletions
diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest index 56728e9a4ce6..28258aa9b4e4 100644 --- a/sci-biology/maq/Manifest +++ b/sci-biology/maq/Manifest @@ -1,8 +1,9 @@ AUX maq-0.7.1-bfr-overfl.patch 527 BLAKE2B 41a4b6bff80faa02158cb4a7884e47c9516394f93e46686483ab9209b2c889ca49c756d4e3516ba58fb2054fcf22828ff94affb877a54ca6cdf6806b5dd0ac8b SHA512 953587e9354f2d3a070aae67ee999105b96678b2b781b9fbe8416d040a594d1db2ed6e7de0516cd29c2020de5129bbc26b78b7bfa5a258ebb5cb9fd4715f8bcf AUX maq-0.7.1-flags.patch 799 BLAKE2B 2f65c9357d8fbbf5cf3450a63b0a6e322472bcc978829d9245e522e2a9d83aaebe52b87e34a231dd8cb319864a8e54761b4f0e98f14e2436eaf8669ccb52caf0 SHA512 f13d8af7884691f2d8c8e9bd9d370c5ca12e863aaf05e156a964ba88053d86dcb63f24169fbc3b2a9264423510061c26d88904b87ea8aeb8bf446b51e190aedb AUX maq-0.7.1-gcc-4.7.patch 1429 BLAKE2B af81651b07186eed305d70534e9f7c41375f60a8376878da80180503daea59a30de5ee726b0b9e87cd45ab6a3e033e5ba1d09a4e02a84c8b723dfec72e6dd068 SHA512 e2936757fff7f32d8dea3da3181839b7b4190a15f4bfb5c3b6cb6a723a10ba8f6e4f762eca32387345a4263c9bf525a425d5e58c78f387a1813508fdc5fb364c +AUX maq-0.7.1-gcc14-build-fix.patch 603 BLAKE2B a1c2722f4bc53014b5281fc8532573d5c0ab3d064fe2e49efb349cd1dfa7e705f045cbe5b5c6125c3703c6699954019c03f9bf2c911ccb5642b47737e9d252b0 SHA512 a1e4c5b896a04fecd50430de14d1e967e78cbf6f499544bbf4259d417c91778a5453de474f8f343b1f63b87e1bad0b842eaeefd30d43bed2a543eac658d7cd23 AUX maq-0.7.1-remove-64bit-flag.patch 787 BLAKE2B 2e94066962194133ccdae4095d3d6bf6f058f7a7d5d04f8737e03fc725508b3e291c76554418c6ff9a15969e332d340b86e11ae3cab90406ec60e9ea63361f5e SHA512 4864453afa79679c253b17a2b125bf0b44c1a05a6ae6341821382991217026b599437288a1c96625cdc2a1fad2cf73c79798a230bbfccef46e1c92012a6c3df1 DIST calib-36.dat.gz 196371 BLAKE2B e4dab71e0830603a7c25bb4c8e15f92e4a5068eeeece451a3e0a2a9e2c4f65b87325e7ff4e4e5543b79f2c3d9dd43c9398cdb32241535bf44e66705bfdf683f7 SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7 DIST maq-0.7.1.tar.bz2 368645 BLAKE2B a7989ae2348a7332f17a75c6fccba55deb8bd9330863d0c5ab3bf997f2f07abd1ca89ebb41d034902f6571ee36365f63db9c8c84c1e5d3d788236279581b989e SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c -EBUILD maq-0.7.1-r3.ebuild 784 BLAKE2B 092e9683af6c7a9248c7336da930947168e937df9bc80829a5a5d7a07046acd9f1d2c6667cfb4d0a62c8f616802c607db8f6926d26166abe8bca5345318bd855 SHA512 52d16dcffa83aba11f6d1a50a0520252ac410b697793dc6f42ca8459d4ae47b56f22fbafe8af8a75a7f522f1e0b94507d1ac6397f19837fc101f8fb866dc3746 +EBUILD maq-0.7.1-r4.ebuild 827 BLAKE2B 1c5389612a5c79df5ab8321c8835b7933abb17136e60c14b85254ea9320b1a9d4b0e433f0df99c5158b3662b8fcb260c283c208e02db4503f47da154fff1a454 SHA512 a7e3ab88ea0b4c51f1f223f3e7c15930345ff614f6e6c468b3195843ff8e6007981bda055949e9c319c417b9fa0b2df0bd08622ea5b93dc7eba63cd7b50e7625 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc diff --git a/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch new file mode 100644 index 000000000000..b92b7711bfe0 --- /dev/null +++ b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch @@ -0,0 +1,23 @@ +Bug: https://bugs.gentoo.org/921137 +--- a/fastq2bfq.c ++++ b/fastq2bfq.c +@@ -15,7 +15,7 @@ int64_t fastq2bfq(FILE *fp_fq, const char *fn_bfq, int n_reads) + char name[256], str[1024]; + int l, is_new = 0, l_prefix = 0; + bit64_t n; +- gzFile *fp = 0; ++ gzFile fp = 0; + INIT_SEQ(seq); INIT_SEQ(qual); + seq_set_block_size(256); + n = 0; +--- a/simulate.c ++++ b/simulate.c +@@ -74,7 +74,7 @@ int maq_simutrain(int argc, char *argv[]) + { + fqc_t *fqc; + FILE *fp; +- gzFile *fpout; ++ gzFile fpout; + if (argc < 3) { + fprintf(stderr, "Usage: maq simutrain <simupars.dat> <known_reads.fastq>\n"); + return 1; diff --git a/sci-biology/maq/maq-0.7.1-r3.ebuild b/sci-biology/maq/maq-0.7.1-r4.ebuild index a64b2b6f4e81..8930c780cfa5 100644 --- a/sci-biology/maq/maq-0.7.1-r3.ebuild +++ b/sci-biology/maq/maq-0.7.1-r4.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 @@ -6,7 +6,7 @@ EAPI=8 inherit autotools DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes" -HOMEPAGE="http://maq.sourceforge.net/" +HOMEPAGE="https://maq.sourceforge.net/" SRC_URI=" mirror://sourceforge/${PN}/${P}.tar.bz2 mirror://sourceforge/${PN}/calib-36.dat.gz" @@ -23,6 +23,7 @@ PATCHES=( "${FILESDIR}"/${P}-bfr-overfl.patch "${FILESDIR}"/${P}-gcc-4.7.patch "${FILESDIR}"/${P}-remove-64bit-flag.patch + "${FILESDIR}"/${P}-gcc14-build-fix.patch ) src_prepare() { |