svn commit: r554390 - in head/biology/bowtie2: . files

[Jason W. Bacon]

Author: jwb
Date: Sat Nov  7 13:47:41 2020
New Revision: 554390
URL: https://svnweb.freebsd.org/changeset/ports/554390

Log:
  biology/bowtie2: Upgrade to 2.4.2
  
  Minor bug fix release
  
  Reported by:    portscout

Modified:
  head/biology/bowtie2/Makefile
  head/biology/bowtie2/distinfo
  head/biology/bowtie2/files/patch-Makefile

Modified: head/biology/bowtie2/Makefile
==============================================================================
--- head/biology/bowtie2/Makefile	Sat Nov  7 12:02:11 2020	(r554389)
+++ head/biology/bowtie2/Makefile	Sat Nov  7 13:47:41 2020	(r554390)
@@ -2,8 +2,7 @@
 
 PORTNAME=		bowtie2
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.4.1
-PORTREVISION=		2
+DISTVERSION=		2.4.2
 CATEGORIES=		biology perl5 python
 
 MAINTAINER=	jwb at FreeBSD.org

Modified: head/biology/bowtie2/distinfo
==============================================================================
--- head/biology/bowtie2/distinfo	Sat Nov  7 12:02:11 2020	(r554389)
+++ head/biology/bowtie2/distinfo	Sat Nov  7 13:47:41 2020	(r554390)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1583075948
-SHA256 (BenLangmead-bowtie2-v2.4.1_GH0.tar.gz) = 9fb25513886bf294217dd9c5ca26d18dd5e02e0ae999935ac7ba5700befc492e
-SIZE (BenLangmead-bowtie2-v2.4.1_GH0.tar.gz) = 10588621
+TIMESTAMP = 1604617529
+SHA256 (BenLangmead-bowtie2-v2.4.2_GH0.tar.gz) = ea33a1562faf759b21b3a905e20b87a3524ac4e53af8cd723d9a9f31ee159c8a
+SIZE (BenLangmead-bowtie2-v2.4.2_GH0.tar.gz) = 10590144

Modified: head/biology/bowtie2/files/patch-Makefile
==============================================================================
--- head/biology/bowtie2/files/patch-Makefile	Sat Nov  7 12:02:11 2020	(r554389)
+++ head/biology/bowtie2/files/patch-Makefile	Sat Nov  7 13:47:41 2020	(r554390)
@@ -1,7 +1,16 @@
---- Makefile.orig	2020-03-01 15:16:08 UTC
+--- Makefile.orig	2020-11-05 23:04:50 UTC
 +++ Makefile
-@@ -200,22 +200,22 @@ endif
+@@ -24,7 +24,7 @@
+ PREFIX := /usr/local
+ bindir := $(PREFIX)/bin
  
+-ARCH := $(shell uname -m)
++ARCH := $(shell uname -p)
+ LDLIBS := -lz
+ GCC_PREFIX := $(shell dirname `which gcc`)
+ GCC_SUFFIX :=
+@@ -201,22 +201,22 @@ endif
+ 
  BITS := 32
  SSE_FLAG := -msse2
 -ifeq (x86_64,$(shell uname -m))
@@ -14,17 +23,17 @@
 +else ifeq (aarch64,$(shell uname -p))
    BITS := 64
    SSE_FLAG :=
-   CXXFLAGS := -fopenmp-simd
-   CPPFLAGS := -Ithird_party/simde
+   CXXFLAGS += -fopenmp-simd
+   CPPFLAGS += -Ithird_party/simde
 -else ifeq (s390x,$(shell uname -m))
 +else ifeq (s390x,$(shell uname -p))
    BITS := 64
    SSE_FLAG :=
-   CXXFLAGS := -fopenmp-simd
-   CPPFLAGS := -Ithird_party/simde
+   CXXFLAGS += -fopenmp-simd
+   CPPFLAGS += -Ithird_party/simde
    SANITIZER_FLAGS :=
 -else ifeq (ppc64le,$(shell uname -m))
 +else ifeq (ppc64le,$(shell uname -p))
    BITS := 64
    SSE_FLAG :=
-   CXXFLAGS := -fopenmp-simd
+   CXXFLAGS += -fopenmp-simd