git: a382bcefaf86 - main - biology/star: Update to 2.7.11a
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Thu, 17 Aug 2023 16:05:07 UTC
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"
-