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Message-Id: <20131217024642.6fe5abc1185b51ceb6399d3b@yahoo.com>
Date: Tue, 17 Dec 2013 02:46:42 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: biology/ssaha: Fix build on -current

>Number:         184852
>Category:       ports
>Synopsis:       biology/ssaha: Fix build on -current
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    miwi
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Dec 16 18:10:14 UTC 2013
>Closed-Date:    Sat Jan 25 16:48:16 UTC 2014
>Last-Modified:  Sat Jan 25 16:50:00 UTC 2014
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p4 i386
>Organization:
>Environment:
>Description:
- Fix build on -current
- Update MASTER_SITES and WWW: line
- Support CXX/CXXFLAGS properly
- Support PLIST_FILES

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/ssaha/Makefile biology/ssaha/Makefile
--- /usr/ports/biology/ssaha/Makefile	2013-11-06 22:05:41.000000000 +0900
+++ biology/ssaha/Makefile	2013-12-17 00:00:00.000000000 +0900
@@ -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>
diff -urN /usr/ports/biology/ssaha/files/patch-GlobalDefinitions.h biology/ssaha/files/patch-GlobalDefinitions.h
--- /usr/ports/biology/ssaha/files/patch-GlobalDefinitions.h	2013-11-06 22:05:41.000000000 +0900
+++ biology/ssaha/files/patch-GlobalDefinitions.h	2013-12-17 00:00:00.000000000 +0900
@@ -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;
diff -urN /usr/ports/biology/ssaha/files/patch-SSAHAMain.h biology/ssaha/files/patch-SSAHAMain.h
--- /usr/ports/biology/ssaha/files/patch-SSAHAMain.h	2013-11-06 22:05:41.000000000 +0900
+++ biology/ssaha/files/patch-SSAHAMain.h	2013-12-17 00:00:00.000000000 +0900
@@ -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 ) {}
diff -urN /usr/ports/biology/ssaha/files/patch-makefile biology/ssaha/files/patch-makefile
--- /usr/ports/biology/ssaha/files/patch-makefile	2013-11-06 22:05:41.000000000 +0900
+++ biology/ssaha/files/patch-makefile	2013-12-17 00:00:00.000000000 +0900
@@ -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
diff -urN /usr/ports/biology/ssaha/pkg-descr biology/ssaha/pkg-descr
--- /usr/ports/biology/ssaha/pkg-descr	2013-11-06 22:05:41.000000000 +0900
+++ biology/ssaha/pkg-descr	2013-12-17 00:00:00.000000000 +0900
@@ -8,4 +8,4 @@
 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/
diff -urN /usr/ports/biology/ssaha/pkg-plist biology/ssaha/pkg-plist
--- /usr/ports/biology/ssaha/pkg-plist	2013-11-06 22:05:41.000000000 +0900
+++ biology/ssaha/pkg-plist	1970-01-01 09:00:00.000000000 +0900
@@ -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%%
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: miwi 
Responsible-Changed-When: Thu Jan 23 15:45:51 UTC 2014 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=184852 
State-Changed-From-To: open->closed 
State-Changed-By: miwi 
State-Changed-When: Sat Jan 25 16:48:16 UTC 2014 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=184852 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/184852: commit references a PR
Date: Sat, 25 Jan 2014 16:48:14 +0000 (UTC)

 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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>Unformatted:
