Date: Sat, 16 Dec 2023 14:00:58 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 0f12812f16d4 - main - biology/py-pybigwig: Update to 0.3.22 Message-ID: <202312161400.3BGE0wJf040726@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=0f12812f16d40ac818faf4123086697a041313d2 commit 0f12812f16d40ac818faf4123086697a041313d2 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-12-16 13:59:37 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-12-16 13:59:37 +0000 biology/py-pybigwig: Update to 0.3.22 No real changes from 0.3.21 Add patch to resolve conflict with roundup() macro in sys/param.h Reported by: pkg-fallout --- biology/py-pybigwig/Makefile | 2 +- biology/py-pybigwig/distinfo | 6 ++--- .../py-pybigwig/files/patch-libBigWig_bwValues.c | 29 ++++++++++++++++++++++ 3 files changed, 33 insertions(+), 4 deletions(-) diff --git a/biology/py-pybigwig/Makefile b/biology/py-pybigwig/Makefile index 131ba5e45ca1..76d160a9e818 100644 --- a/biology/py-pybigwig/Makefile +++ b/biology/py-pybigwig/Makefile @@ -1,5 +1,5 @@ PORTNAME= pyBigWig -DISTVERSION= 0.3.21 +DISTVERSION= 0.3.22 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} diff --git a/biology/py-pybigwig/distinfo b/biology/py-pybigwig/distinfo index 4d8222cfc082..44d8c0b8eead 100644 --- a/biology/py-pybigwig/distinfo +++ b/biology/py-pybigwig/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1680381155 -SHA256 (pyBigWig-0.3.21.tar.gz) = 5bff713fe3f8840e0fbe48cf8c8fe9d92c8af8ba107da0b845076164445d076e -SIZE (pyBigWig-0.3.21.tar.gz) = 73827 +TIMESTAMP = 1681053575 +SHA256 (pyBigWig-0.3.22.tar.gz) = 5d4426f754bd7b7f6dc21d6c3f93b58a96a65b6eb2e578ae03b31a71272d2243 +SIZE (pyBigWig-0.3.22.tar.gz) = 73864 diff --git a/biology/py-pybigwig/files/patch-libBigWig_bwValues.c b/biology/py-pybigwig/files/patch-libBigWig_bwValues.c new file mode 100644 index 000000000000..7b2fc3774b92 --- /dev/null +++ b/biology/py-pybigwig/files/patch-libBigWig_bwValues.c @@ -0,0 +1,29 @@ +--- libBigWig/bwValues.c.orig 2023-12-16 13:51:54 UTC ++++ libBigWig/bwValues.c +@@ -5,7 +5,7 @@ + #include <zlib.h> + #include <errno.h> + +-static uint32_t roundup(uint32_t v) { ++static uint32_t bigwig_roundup(uint32_t v) { + v--; + v |= v >> 1; + v |= v >> 2; +@@ -346,7 +346,7 @@ static bwOverlappingIntervals_t *pushIntervals(bwOverl + //Returns NULL on error, in which case o has been free()d + static bwOverlappingIntervals_t *pushIntervals(bwOverlappingIntervals_t *o, uint32_t start, uint32_t end, float value) { + if(o->l+1 >= o->m) { +- o->m = roundup(o->l+1); ++ o->m = bigwig_roundup(o->l+1); + o->start = realloc(o->start, o->m * sizeof(uint32_t)); + if(!o->start) goto error; + o->end = realloc(o->end, o->m * sizeof(uint32_t)); +@@ -366,7 +366,7 @@ static bbOverlappingEntries_t *pushBBIntervals(bbOverl + + static bbOverlappingEntries_t *pushBBIntervals(bbOverlappingEntries_t *o, uint32_t start, uint32_t end, char *str, int withString) { + if(o->l+1 >= o->m) { +- o->m = roundup(o->l+1); ++ o->m = bigwig_roundup(o->l+1); + o->start = realloc(o->start, o->m * sizeof(uint32_t)); + if(!o->start) goto error; + o->end = realloc(o->end, o->m * sizeof(uint32_t));
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