- 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

biology/ssaha/Makefile

@@ -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>

biology/ssaha/files/patch-GlobalDefinitions.h

@@ -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;

biology/ssaha/files/patch-SSAHAMain.h

@@ -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 ) {}

biology/ssaha/files/patch-makefile

@@ -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

biology/ssaha/pkg-descr

@@ -8,4 +8,4 @@ SSAHA: a fast search method for large DNA databases (2001).
 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/

biology/ssaha/pkg-plist

@@ -1,9 +0,0 @@
-bin/ssaha
-%%DATADIR%%/testSSAHA.csh
-%%DATADIR%%/test.fasta
-%%DATADIR%%/test_extract.fasta
-%%DATADIR%%/test_filter.fail
-%%DATADIR%%/test_filter.fastq
-%%DATADIR%%/test_protein.fasta
-%%DATADIR%%/README
-@dirrmtry %%DATADIR%%