Date: Thu, 17 Aug 2023 16:05:07 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: a382bcefaf86 - main - biology/star: Update to 2.7.11a Message-ID: <202308171605.37HG57qF096470@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a382bcefaf863b6a253ea49758b67de6995e9ca2 commit a382bcefaf863b6a253ea49758b67de6995e9ca2 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2023-08-17 16:01:09 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2023-08-17 16:01:09 +0000 biology/star: Update to 2.7.11a A few bug fixes and new features Add USE_GCC as a temporary hack for input read issue This was also an issue in 2.7.10b Changes: https://github.com/alexdobin/STAR/releases --- biology/star/Makefile | 5 ++++- biology/star/distinfo | 6 +++--- biology/star/files/patch-SpliceGraph.cpp | 10 ---------- biology/star/files/patch-opal_opal.cpp | 13 ------------- 4 files changed, 7 insertions(+), 27 deletions(-) diff --git a/biology/star/Makefile b/biology/star/Makefile index fc32ddebc58b..dd8137dee91f 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -1,5 +1,5 @@ PORTNAME= STAR -DISTVERSION= 2.7.10b +DISTVERSION= 2.7.11a CATEGORIES= biology PKGNAMEPREFIX= rna- @@ -16,9 +16,12 @@ NOT_FOR_ARCHS_REASON= Requires 64-bit processor BROKEN= requires OpenMP support that is missing on this architecture .endif +BUILD_DEPENDS= xxd:sysutils/xxd LIB_DEPENDS= libhts.so:biology/htslib USES= compiler:c++11-lang gmake localbase:ldflags +# FIXME: When built with clang, number of input reads = 0 +USE_GCC= yes USE_GITHUB= yes GH_ACCOUNT= alexdobin diff --git a/biology/star/distinfo b/biology/star/distinfo index 6f7048071c63..395c98a981c1 100644 --- a/biology/star/distinfo +++ b/biology/star/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1689939622 -SHA256 (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5 -SIZE (alexdobin-STAR-2.7.10b_GH0.tar.gz) = 12443703 +TIMESTAMP = 1692285897 +SHA256 (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a +SIZE (alexdobin-STAR-2.7.11a_GH0.tar.gz) = 12463429 diff --git a/biology/star/files/patch-SpliceGraph.cpp b/biology/star/files/patch-SpliceGraph.cpp deleted file mode 100644 index b839bfe7e802..000000000000 --- a/biology/star/files/patch-SpliceGraph.cpp +++ /dev/null @@ -1,10 +0,0 @@ ---- SpliceGraph.cpp.orig 2023-07-21 15:27:26 UTC -+++ SpliceGraph.cpp -@@ -1,7 +1,6 @@ - /* - * Created by Fahimeh Mirhaj on 6/10/19. - */ --using namespace std; - - #include "SpliceGraph.h" - #include "GTF.h" diff --git a/biology/star/files/patch-opal_opal.cpp b/biology/star/files/patch-opal_opal.cpp deleted file mode 100644 index dcda064df27a..000000000000 --- a/biology/star/files/patch-opal_opal.cpp +++ /dev/null @@ -1,13 +0,0 @@ ---- opal/opal.cpp.orig 2021-11-26 16:14:46 UTC -+++ opal/opal.cpp -@@ -5,10 +5,8 @@ - #include <limits> - #include <vector> - --extern "C" { - #define SIMDE_ENABLE_NATIVE_ALIASES - #include <simde_avx2.h> // AVX2 and lower --} - - #include "opal.h" -
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