Date: Mon, 27 Feb 2017 14:08:30 +0000 (UTC) From: Jan Beich <jbeich@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r434940 - in head/biology/bowtie2: . files Message-ID: <201702271408.v1RE8Uom001593@repo.freebsd.org>
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Author: jbeich Date: Mon Feb 27 14:08:30 2017 New Revision: 434940 URL: https://svnweb.freebsd.org/changeset/ports/434940 Log: biology/bowtie2: update to 2.3.0 - Unbreak with Clang 4.0 Changes: https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0 PR: 216619 Submitted by: Jason Bacon <bacon4000@gmail.com> (maintainer) Added: head/biology/bowtie2/files/patch-aligner__result.cpp (contents, props changed) Modified: head/biology/bowtie2/Makefile (contents, props changed) head/biology/bowtie2/distinfo (contents, props changed) head/biology/bowtie2/files/patch-Makefile (contents, props changed) Modified: head/biology/bowtie2/Makefile ============================================================================== --- head/biology/bowtie2/Makefile Mon Feb 27 13:58:16 2017 (r434939) +++ head/biology/bowtie2/Makefile Mon Feb 27 14:08:30 2017 (r434940) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= bowtie2 -PORTVERSION= 2.2.9 +PORTVERSION= 2.3.0 DISTVERSIONPREFIX= v CATEGORIES= biology @@ -12,6 +12,8 @@ COMMENT= Ultrafast, memory-efficient sho LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE +LIB_DEPENDS+= libtbb.so:devel/tbb + # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 USES= gmake perl5 python shebangfix Modified: head/biology/bowtie2/distinfo ============================================================================== --- head/biology/bowtie2/distinfo Mon Feb 27 13:58:16 2017 (r434939) +++ head/biology/bowtie2/distinfo Mon Feb 27 14:08:30 2017 (r434940) @@ -1,3 +1,3 @@ -TIMESTAMP = 1475861880 -SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee -SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106 +TIMESTAMP = 1487550143 +SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221 +SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016 Modified: head/biology/bowtie2/files/patch-Makefile ============================================================================== --- head/biology/bowtie2/files/patch-Makefile Mon Feb 27 13:58:16 2017 (r434939) +++ head/biology/bowtie2/files/patch-Makefile Mon Feb 27 14:08:30 2017 (r434940) @@ -1,4 +1,4 @@ ---- Makefile.orig 2016-02-11 17:20:57 UTC +--- Makefile.orig 2016-12-30 15:40:06 UTC +++ Makefile @@ -21,8 +21,8 @@ # Makefile for bowtie, bowtie2-build, bowtie2-inspect @@ -11,7 +11,34 @@ INC = GCC_PREFIX = $(shell dirname `which gcc`) -@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 +@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY)) + INC += -I third_party + endif + ++INC += -I ${LOCALBASE}/include ++ + MM_DEF = + + ifeq (1,$(BOWTIE_MM)) +@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM)) + endif + + PTHREAD_PKG = +-PTHREAD_LIB = ++PTHREAD_LIB = + + #if we're not using TBB, then we can't use queuing locks + ifeq (1,$(NO_TBB)) +@@ -94,7 +96,7 @@ endif + + #default is to use Intel TBB + ifneq (1,$(NO_TBB)) +- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy ++ LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc + override EXTRA_FLAGS += -DWITH_TBB + else + LIBS = $(PTHREAD_LIB) +@@ -185,7 +187,7 @@ SSE_FLAG=-msse2 DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" Added: head/biology/bowtie2/files/patch-aligner__result.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/bowtie2/files/patch-aligner__result.cpp Mon Feb 27 14:08:30 2017 (r434940) @@ -0,0 +1,13 @@ +https://github.com/BenLangmead/bowtie2/issues/81 + +--- aligner_result.cpp.orig 2016-12-30 15:40:06 UTC ++++ aligner_result.cpp +@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool + else if(!nfilt_ ) flag = "NS"; + else if(!scfilt_ ) flag = "SC"; + else if(!qcfilt_ ) flag = "QC"; +- if(flag > 0) { ++ if(*flag != '\0') { + if(!first) o.append('\t'); + o.append("YF:Z:"); + o.append(flag);
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