git: 0e8f22496e31 - main - biology/star: Fix SIMD issue on non-amd64
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Date: Mon, 21 Aug 2023 14:35:01 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=0e8f22496e314bf6c0f863722217eb8bebef9cf2
commit 0e8f22496e314bf6c0f863722217eb8bebef9cf2
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-08-21 14:33:20 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-08-21 14:33:20 +0000
biology/star: Fix SIMD issue on non-amd64
Also remove some extraneous build flags from upstream Makefile
PR: 273240
Reported by: dizzy
---
biology/star/Makefile | 9 ++-------
biology/star/files/patch-Makefile | 12 +++++++-----
2 files changed, 9 insertions(+), 12 deletions(-)
diff --git a/biology/star/Makefile b/biology/star/Makefile
index 6172318b1e7d..968caa762551 100644
--- a/biology/star/Makefile
+++ b/biology/star/Makefile
@@ -1,5 +1,6 @@
PORTNAME= STAR
DISTVERSION= 2.7.11a
+PORTREVISION= 1
CATEGORIES= biology
PKGNAMEPREFIX= rna-
@@ -26,7 +27,7 @@ USE_GITHUB= yes
GH_ACCOUNT= alexdobin
WRKSRC_SUBDIR= source
-MAKE_FLAGS= HTSLIB=''
+MAKE_FLAGS= HTSLIB='' CXXFLAGS_SIMD=""
PLIST_FILES= bin/STAR
@@ -44,12 +45,6 @@ post-patch:
${WRKSRC}/bam_cat.h \
${WRKSRC}/signalFromBAM.h
-.include <bsd.port.options.mk>
-
-.if ${ARCH} != amd64
-MAKE_FLAGS+= CXXFLAGS_SIMD=""
-.endif
-
do-install:
${INSTALL_PROGRAM} ${WRKSRC}/STAR ${STAGEDIR}${PREFIX}/bin
diff --git a/biology/star/files/patch-Makefile b/biology/star/files/patch-Makefile
index c9943e2e73bc..55d592e70c2f 100644
--- a/biology/star/files/patch-Makefile
+++ b/biology/star/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig 2022-11-01 14:50:35 UTC
+--- Makefile.orig 2023-08-15 19:21:58 UTC
+++ Makefile
-@@ -11,6 +11,10 @@ CXXFLAGSextra ?=
+@@ -11,14 +11,19 @@ CXXFLAGSextra ?=
# user may define the compiler
CXX ?= g++
@@ -9,9 +9,11 @@
+HTSLIB ?= htslib
+
# pre-defined flags
- LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
- LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
-@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
++LDFLAGS_shared := -pthread -lhts -lz
++LDFLAGS_static := -static -pthread -lhts -lz
+ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
LDFLAGS_gdb := $(LDFLAGS_shared)