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sci-biology/maq: Fix assignment to incompatible pointer type

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Closes: https://github.com/gentoo/gentoo/pull/36459
Closes: https://bugs.gentoo.org/921137
Signed-off-by: Brahmajit Das <brahmajit.xyz@gmail.com>
Signed-off-by: David Seifert <soap@gentoo.org>
This commit is contained in:
Brahmajit Das
2024-04-27 21:15:05 +02:00
committed by David Seifert
parent 27cb9ea633
commit 061394aeec
2 changed files with 26 additions and 2 deletions
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23
sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch Normal file
View File

@@ -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;

5
sci-biology/maq/maq-0.7.1-r3.ebuild → sci-biology/maq/maq-0.7.1-r4.ebuild
View File

@@ -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() {