commit: d11fa811ea39d044575471f7c4006bab88e23bfe Author: NHOrus <jy6x2b32pie9 <AT> yahoo <DOT> com> AuthorDate: Fri Mar 29 20:44:26 2024 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Wed May 8 10:43:28 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d11fa811
sci-biology/velvet: Fix incompatible pointer types in 1.2.10 * C99 porting. Split multi-assignments of NULLs into multiple lines * Also added dependencies on OpenMP if USE=openmp is enabled [sam: Formatting tweaks to commit msg.] Closes: https://bugs.gentoo.org/919223 Signed-off-by: NHOrus <jy6x2b32pie9 <AT> yahoo.com> Closes: https://github.com/gentoo/gentoo/pull/35993 Signed-off-by: Sam James <sam <AT> gentoo.org> .../velvet-1.2.10-incompatible-pointers.patch | 27 ++++++++++++++++++++++ sci-biology/velvet/velvet-1.2.10.ebuild | 13 +++++++++-- 2 files changed, 38 insertions(+), 2 deletions(-) diff --git a/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch new file mode 100644 index 000000000000..e736655ae5bc --- /dev/null +++ b/sci-biology/velvet/files/velvet-1.2.10-incompatible-pointers.patch @@ -0,0 +1,27 @@ +diff --git a/velvet_1.2.10.orig/src/readSet.c b/velvet_1.2.10/src/readSet.c +index f58122e..26e579c 100644 +--- a/src/readSet.c ++++ b/src/readSet.c +@@ -638,7 +638,8 @@ static void readFastXFile(int fileType, SequencesWriter *seqWriteInfo, char *fil + FileGZOrAuto file; + IDnum counter = 0; + +- file.gzFile = file.autoFile = NULL; ++ file.autoFile = NULL; ++ file.gzFile = NULL; + if (fileType == AUTO) { + file.autoFile = openFileAuto(filename); + if (!file.autoFile) +@@ -677,8 +678,10 @@ static void readFastXPair(int fileType, SequencesWriter *seqWriteInfo, char *fil + if (cat==REFERENCE) + exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode"); + +- file1.gzFile = file1.autoFile = NULL; +- file2.gzFile = file2.autoFile = NULL; ++ file1.autoFile = NULL; ++ file2.autoFile = NULL; ++ file1.autoFile = NULL; ++ file2.autoFile = NULL; + if (fileType == AUTO) { + file1.autoFile = openFileAuto(filename1); + if (!file1.autoFile) diff --git a/sci-biology/velvet/velvet-1.2.10.ebuild b/sci-biology/velvet/velvet-1.2.10.ebuild index ea0b3630b78b..bb1a0b441b1e 100644 --- a/sci-biology/velvet/velvet-1.2.10.ebuild +++ b/sci-biology/velvet/velvet-1.2.10.ebuild @@ -16,7 +16,16 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="doc openmp" -BDEPEND="doc? ( virtual/latex-base )" +BDEPEND="doc? ( virtual/latex-base ) + openmp? ( + || ( + sys-devel/gcc[openmp] + sys-devel/clang-runtime[openmp] + ) + ) +" + +PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" ) src_prepare() { default @@ -49,7 +58,7 @@ src_prepare() { CFLAGS="${CFLAGS}" OPT="${CFLAGS}" ) - use openmp && MAKE_XOPTS+=( OPENMP=1 ) + use openmp && MAKE_XOPTS+=( OPENMP=1 ) && tc-check-openmp [[ ! -z "${VELVET_MAXKMERLENGTH}" ]] && MAKE_XOPTS+=( MAXKMERLENGTH=${VELVET_MAXKMERLENGTH} ) [[ ! -z "${VELVET_CATEGORIES}" ]] && MAKE_XOPTS+=( CATEGORIES=${VELVET_CATEGORIES} ) [[ ! -z "${VELVET_BIGASSEMBLY}" ]] && MAKE_XOPTS+=( BIGASSEMBLY=${VELVET_BIGASSEMBLY} )
