Date: Sat, 25 Jan 2014 16:48:06 +0000 (UTC) From: Martin Wilke <miwi@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r341053 - in head/biology/ssaha: . files Message-ID: <201401251648.s0PGm6hk097868@svn.freebsd.org>
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Author: miwi Date: Sat Jan 25 16:48:05 2014 New Revision: 341053 URL: http://svnweb.freebsd.org/changeset/ports/341053 QAT: https://qat.redports.org/buildarchive/r341053/ Log: - Fix build on -current - Update MASTER_SITES and WWW: line - Support CXX/CXXFLAGS properly - Support PLIST_FILES - Stage support PR: 184852 Submitted by: Ports Fury Deleted: head/biology/ssaha/pkg-plist Modified: head/biology/ssaha/Makefile head/biology/ssaha/files/patch-GlobalDefinitions.h head/biology/ssaha/files/patch-SSAHAMain.h head/biology/ssaha/files/patch-makefile head/biology/ssaha/pkg-descr Modified: head/biology/ssaha/Makefile ============================================================================== --- head/biology/ssaha/Makefile Sat Jan 25 16:46:40 2014 (r341052) +++ head/biology/ssaha/Makefile Sat Jan 25 16:48:05 2014 (r341053) @@ -3,29 +3,39 @@ PORTNAME= ssaha PORTVERSION= 3.1c -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology -MASTER_SITES= http://www.sanger.ac.uk/Software/analysis/${PORTNAME:U}/ +MASTER_SITES= ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha/ DISTNAME= ${PORTNAME}_v${PORTVERSION:S/.//} MAINTAINER= ports@FreeBSD.org COMMENT= Very fast matching and alignment of DNA sequences NO_WRKSUBDIR= yes +BUILD_WRKSRC= ${WRKSRC}/Binary -USE_GMAKE= yes +USES= gmake +USE_GCC= any +MAKE_ENV= CCC="${CXX}" OPTIM="${CXXFLAGS}" THREAD_LIB="-pthread" MAKEFILE= makefile -BUILD_WRKSRC= ${WRKDIR}/Binary ALL_TARGET= ssaha +PLIST_FILES= bin/ssaha %%DATADIR%%/testSSAHA.csh \ + ${DATA_FILES:S,^,%%DATADIR%%/,} +PLIST_DIRS= %%DATADIR%% + DATA_FILES= test.fasta test_extract.fasta test_filter.fail \ test_filter.fastq test_protein.fasta README -NO_STAGE= yes do-install: - ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/ssaha ${PREFIX}/bin - @${MKDIR} ${DATADIR} - ${INSTALL_SCRIPT} ${BUILD_WRKSRC}/testSSAHA.csh ${DATADIR}/ - ${INSTALL_DATA} ${DATA_FILES:S,^,${BUILD_WRKSRC}/,} ${DATADIR}/ + (cd ${BUILD_WRKSRC} && ${INSTALL_PROGRAM} ssaha \ + ${STAGEDIR}${PREFIX}/bin) + @${MKDIR} ${STAGEDIR}${DATADIR} + (cd ${BUILD_WRKSRC} && ${INSTALL_SCRIPT} testSSAHA.csh \ + ${STAGEDIR}${DATADIR}) +.for i in ${DATA_FILES} + (cd ${BUILD_WRKSRC} && ${INSTALL_DATA} ${i} \ + ${STAGEDIR}${DATADIR}) +.endfor .include <bsd.port.mk> Modified: head/biology/ssaha/files/patch-GlobalDefinitions.h ============================================================================== --- head/biology/ssaha/files/patch-GlobalDefinitions.h Sat Jan 25 16:46:40 2014 (r341052) +++ head/biology/ssaha/files/patch-GlobalDefinitions.h Sat Jan 25 16:48:05 2014 (r341053) @@ -1,6 +1,16 @@ --- ./Global/GlobalDefinitions.h.orig 2004-03-01 13:51:28.000000000 -0300 +++ ./Global/GlobalDefinitions.h 2008-06-12 15:39:31.000000000 -0300 -@@ -726,8 +726,6 @@ +@@ -79,7 +79,8 @@ + #include <map> + #include <utility> + #include <sys/types.h> +-#include <stdio.h> ++#include <cstdio> ++#include <cstring> + #include <sys/file.h> + #include <sys/mman.h> + #include <sys/stat.h> +@@ -726,8 +727,6 @@ template <typename T> class Allocator { public: @@ -9,7 +19,7 @@ Allocator( T** ptr, const string& name, ostream& monStream=cerr ) : ptr_(ptr), name_(name), size_(0), isAllocated_(false), monStream_( monStream ) -@@ -788,32 +786,34 @@ +@@ -788,32 +787,34 @@ virtual void allocate( unsigned long size ) { @@ -53,7 +63,7 @@ } protected: }; -@@ -892,7 +892,7 @@ +@@ -892,7 +893,7 @@ if (isAllocated_) return; mode_ = MemoryMapper::createMap; size_ = size; @@ -62,7 +72,7 @@ isAllocated_ = true; } -@@ -908,7 +908,7 @@ +@@ -908,7 +909,7 @@ if (isAllocated_) return; mode_ = MemoryMapper::readMap; size_ = size; @@ -71,7 +81,7 @@ isAllocated_ = true; } -@@ -921,7 +921,7 @@ +@@ -921,7 +922,7 @@ virtual void deallocate() { if (!isAllocated_) return; Modified: head/biology/ssaha/files/patch-SSAHAMain.h ============================================================================== --- head/biology/ssaha/files/patch-SSAHAMain.h Sat Jan 25 16:46:40 2014 (r341052) +++ head/biology/ssaha/files/patch-SSAHAMain.h Sat Jan 25 16:48:05 2014 (r341053) @@ -1,6 +1,14 @@ --- ./Global/SSAHAMain.h.orig 2004-03-01 13:51:28.000000000 -0300 +++ ./Global/SSAHAMain.h 2008-06-12 15:39:31.000000000 -0300 -@@ -131,7 +131,7 @@ +@@ -41,6 +41,7 @@ + #include <string> + #include <iostream> + #include <memory> ++#include <cstdlib> + class SequenceReaderMulti; + class SequenceReader; + class HashTable; +@@ -131,7 +132,7 @@ -1, // int queryEnd; -1, // int wordLength; -1, // int stepLength; @@ -9,7 +17,7 @@ 1, // int minToPrint; -1, // int maxGap; 0, // int maxInsert; -@@ -174,6 +174,7 @@ +@@ -174,6 +175,7 @@ CommandLineArg( const string& nameLong, const string& nameShort ) : nameLong_( nameLong ), nameShort_( nameShort ) {} Modified: head/biology/ssaha/files/patch-makefile ============================================================================== --- head/biology/ssaha/files/patch-makefile Sat Jan 25 16:46:40 2014 (r341052) +++ head/biology/ssaha/files/patch-makefile Sat Jan 25 16:48:05 2014 (r341053) @@ -13,3 +13,18 @@ GLOBAL_DIR=${SSAHA_TOP_DIR}/Global SEQ_DIR=${SSAHA_TOP_DIR}/SequenceReader +@@ -22,12 +22,12 @@ + QUERY_DIR=${SSAHA_TOP_DIR}/QueryManager + EXEC_DIR=${SSAHA_TOP_DIR}/Executables + +-CCC = g++ ++CCC ?= g++ + # !!!! change -g to -O3 before making deliverable %%%% + # NB use -ggdb to get gdb to work + INCLUDE_PATHS = -I${SSAHA_TOP_DIR} \ + -I${GLOBAL_DIR} -I${SEQ_DIR} -I${HASH_DIR} -I${QUERY_DIR} +-OPTIM = -O3 ++OPTIM ?= -O3 + DEBUG_LEVEL = + # DEBUG_LEVEL = -DEBUG_LEVEL1 + # -D_REENTRANT necessary for thread safety - see pthread man page - TC 24.9.1 Modified: head/biology/ssaha/pkg-descr ============================================================================== --- head/biology/ssaha/pkg-descr Sat Jan 25 16:46:40 2014 (r341052) +++ head/biology/ssaha/pkg-descr Sat Jan 25 16:48:05 2014 (r341053) @@ -8,4 +8,4 @@ SSAHA: a fast search method for large DN Ning Z, Cox AJ, Mullikin JC. Genome Res. 11: 1725-9. PMID: 11591649 -WWW: http://www.sanger.ac.uk/Software/analysis/SSAHA/ +WWW: http://www.sanger.ac.uk/resources/software/ssaha/
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