commit: 061394aeecb50cf5301012467a02d1ada1e1be01 Author: Brahmajit Das <brahmajit.xyz <AT> gmail <DOT> com> AuthorDate: Sat Apr 27 19:15:05 2024 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Apr 27 19:15:05 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=061394ae
sci-biology/maq: Fix assignment to incompatible pointer type Closes: https://github.com/gentoo/gentoo/pull/36459 Closes: https://bugs.gentoo.org/921137 Signed-off-by: Brahmajit Das <brahmajit.xyz <AT> gmail.com> Signed-off-by: David Seifert <soap <AT> gentoo.org> .../maq/files/maq-0.7.1-gcc14-build-fix.patch | 23 ++++++++++++++++++++++ .../{maq-0.7.1-r3.ebuild => maq-0.7.1-r4.ebuild} | 5 +++-- 2 files changed, 26 insertions(+), 2 deletions(-) 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 similarity index 85% rename from sci-biology/maq/maq-0.7.1-r3.ebuild rename to 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() {
