Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

sci-biology/maq: Fix assignment to incompatible pointer type #36459

Closed
wants to merge 1 commit into from
Closed

sci-biology/maq: Fix assignment to incompatible pointer type #36459

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
23 changes: 23 additions & 0 deletions sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 changes: 3 additions & 2 deletions sci-biology/maq/maq-0.7.1-r3.ebuild → sci-biology/maq/maq-0.7.1-r4.ebuild
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
# Copyright 1999-2022 Gentoo Authors
# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2

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/${PN}/calib-36.dat.gz"
Expand All @@ -23,6 +23,7 @@ PATCHES=(
"${FILESDIR}"/${P}-bfr-overfl.patch
"${FILESDIR}"/${P}-gcc-4.7.patch
"${FILESDIR}"/${P}-remove-64bit-flag.patch
"${FILESDIR}"/${P}-gcc14-build-fix.patch
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

just bump the other ebuild, dont add a new one

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

All of these fixes require a new revision ("revbump") for the reasons described above. Also, developers want to know quickly if the fix is somehow insufficient, and a new revision helps to weed out any problems.

From https://wiki.gentoo.org/wiki/Modern_C_porting#Fixes_.28C99.29

Also since I'm doing a runtime change, thought a revision bump would be needed.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

yes, but just add the patch and rename -r3 -> -r4

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Ooh ... sure.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Did the same for #36460

)

src_prepare() {
Expand Down