commit: 50d985100206472488c09036e81b226b3757f279 Author: NHOrus <jy6x2b32pie9 <AT> yahoo <DOT> com> AuthorDate: Thu Mar 27 16:30:19 2025 +0000 Commit: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> CommitDate: Mon Apr 7 18:59:20 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=50d98510
sci-biology/bfast: update EAPI 7 -> 8, fix build with C99 Closes: https://bugs.gentoo.org/919254 Signed-off-by: NHOrus <jy6x2b32pie9 <AT> yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/41322 Signed-off-by: Arthur Zamarin <arthurzam <AT> gentoo.org> sci-biology/bfast/bfast-0.7.0a-r1.ebuild | 30 ++++++++++++++++++++++++ sci-biology/bfast/files/bfast-0.7.0a-gzeof.patch | 13 ++++++++++ 2 files changed, 43 insertions(+) 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 {
