From tkato432@yahoo.com  Sun Jan 12 18:30:36 2014
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Message-Id: <20140113031854.3ac83abbf020c8b9ba956520@yahoo.com>
Date: Mon, 13 Jan 2014 03:18:54 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: biology/fasta3: Fix build

>Number:         185698
>Category:       ports
>Synopsis:       biology/fasta3: Fix build
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    miwi
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Sun Jan 12 18:40:02 UTC 2014
>Closed-Date:    Thu Feb 27 09:57:53 UTC 2014
>Last-Modified:  Thu Feb 27 09:57:53 UTC 2014
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE-p4 i386
>Organization:
>Environment:
>Description:
- Fix build

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile	2014-01-04 16:31:29.000000000 +0900
+++ biology/fasta3/Makefile	2014-01-13 00:00:00.000000000 +0900
@@ -6,12 +6,11 @@
 CATEGORIES=	biology
 MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
 DISTNAME=	fasta-${PORTVERSION}
+DIST_SUBDIR=	repacked
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Collection of programs for searching DNA and protein databases
 
-BROKEN=		Invalid checksum, seems like the software was rerolled
-
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
 NO_CDROM=	May not be sold or incorporated into a commercial product
diff -urN /usr/ports/biology/fasta3/distinfo biology/fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo	2013-11-06 22:05:44.000000000 +0900
+++ biology/fasta3/distinfo	2014-01-13 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730
-SIZE (fasta-36.3.6d.tar.gz) = 997714
+SHA256 (repacked/fasta-36.3.6d.tar.gz) = a4c81e95f013f71c428d01e72e344a5eded87a5c4402a6d92efaad7bee928d8f
+SIZE (repacked/fasta-36.3.6d.tar.gz) = 998195
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: miwi 
Responsible-Changed-When: Thu Jan 23 15:48:32 UTC 2014 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=185698 
State-Changed-From-To: open->feedback 
State-Changed-By: miwi 
State-Changed-When: Tue Jan 28 04:58:58 UTC 2014 
State-Changed-Why:  
checksum mismatch 
http://pkgdev.miwibox.org/latest-per-pkg/fasta3/36.3.6d/ 

http://www.freebsd.org/cgi/query-pr.cgi?pr=185698 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/185698: biology/fasta3: Fix build
Date: Wed, 29 Jan 2014 03:00:01 +0900

 This is a multi-part message in MIME format.
 
 --Multipart=_Wed__29_Jan_2014_03_00_01_+0900_=.BDnBIKxysL2vWt
 Content-Type: text/plain; charset=US-ASCII
 Content-Transfer-Encoding: 7bit
 
 It seems the tarball has been rerolled again just after the
 submission of this PR.
 
 --Multipart=_Wed__29_Jan_2014_03_00_01_+0900_=.BDnBIKxysL2vWt
 Content-Type: text/x-diff;
  name="biology_fasta3.diff"
 Content-Disposition: attachment;
  filename="biology_fasta3.diff"
 Content-Transfer-Encoding: 7bit
 
 diff -urN /usr/ports/biology/fasta3/Makefile biology/fasta3/Makefile
 --- /usr/ports/biology/fasta3/Makefile	2014-01-04 16:31:29.000000000 +0900
 +++ biology/fasta3/Makefile	2014-01-29 00:00:00.000000000 +0900
 @@ -6,14 +6,11 @@
  CATEGORIES=	biology
  MASTER_SITES=	http://faculty.virginia.edu/wrpearson/fasta/fasta36/
  DISTNAME=	fasta-${PORTVERSION}
 +DIST_SUBDIR=	fasta3/20140126
  
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Collection of programs for searching DNA and protein databases
  
 -BROKEN=		Invalid checksum, seems like the software was rerolled
 -
 -OPTIONS_DEFINE=	DOCS EXAMPLES
 -
  NO_CDROM=	May not be sold or incorporated into a commercial product
  
  WRKSRC=		${WRKDIR}/${DISTNAME}
 @@ -38,6 +35,21 @@
  DATA=		data/*.mat
  EXAMPLES=	seq/*.aa seq/*.lc seq/*.seq seq/*.lib
  
 +OPTIONS_DEFINE=		DOCS EXAMPLES
 +OPTIONS_RADIO=		SQL
 +OPTIONS_RADIO_SQL=	MYSQL PGSQL
 +
 +MYSQL_USE=		MYSQL=yes
 +MYSQL_MAKE_ARGS=	LIB_M="$$(mysql_config --libs)" \
 +			NCBL_LIB="ncbl2_mlib.o mysql_lib.o"
 +MYSQL_CPPFLAGS=		$$(mysql_config --include) -DMYSQL_DB
 +PGSQL_USE=		PGSQL=yes
 +PGSQL_MAKE_ARGS=	LIB_M="-L${LOCALBASE}/lib -lpq -lm" \
 +			NCBL_LIB="ncbl2_mlib.o pgsql_lib.o"
 +PGSQL_CPPFLAGS=		-I${LOCALBASE}/include -DPGSQL_DB
 +
 +.include <bsd.port.options.mk>
 +
  post-patch:
  	@${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC}
  
 diff -urN /usr/ports/biology/fasta3/distinfo biology/fasta3/distinfo
 --- /usr/ports/biology/fasta3/distinfo	2013-11-06 22:05:44.000000000 +0900
 +++ biology/fasta3/distinfo	2014-01-29 00:00:00.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (fasta-36.3.6d.tar.gz) = 6392741abecc8b25daeee53389584f48cee8a8ea7340c7f8cc97e149720a5730
 -SIZE (fasta-36.3.6d.tar.gz) = 997714
 +SHA256 (fasta3/20140126/fasta-36.3.6d.tar.gz) = 7d30b829e26d2ba7fdacaaf143627706ee1faaec0f6caaadb13f09f3cb3119e8
 +SIZE (fasta3/20140126/fasta-36.3.6d.tar.gz) = 970941
 diff -urN /usr/ports/biology/fasta3/files/patch-Makefile.freebsd biology/fasta3/files/patch-Makefile.freebsd
 --- /usr/ports/biology/fasta3/files/patch-Makefile.freebsd	2013-11-06 22:05:44.000000000 +0900
 +++ biology/fasta3/files/patch-Makefile.freebsd	2014-01-29 00:00:00.000000000 +0900
 @@ -8,8 +8,12 @@
   
   # Compiler executable, and optional flags
   CC?=		gcc
 -@@ -38,7 +39,7 @@
 - CFLAGS+=	${COMMON_CFLAGS} ${STANDARD_CFLAGS}
 +@@ -35,10 +36,10 @@
 + # optional flags that define our intended use.
 + # The default standard flags are selected by default, although the user
 + # can override this if s/he wants
 +-CFLAGS+=	${COMMON_CFLAGS} ${STANDARD_CFLAGS}
 ++CFLAGS+=	${COMMON_CFLAGS} ${STANDARD_CFLAGS} ${CPPFLAGS}
   
   BIN = ../bin
  -XDIR =		/usr/local/bin
 
 --Multipart=_Wed__29_Jan_2014_03_00_01_+0900_=.BDnBIKxysL2vWt--
State-Changed-From-To: feedback->closed 
State-Changed-By: miwi 
State-Changed-When: Thu Feb 27 09:57:23 UTC 2014 
State-Changed-Why:  
I am closing this, because the checksum got again rerolled: 

=> fasta-36.3.6d.tar.gz doesn't seem to exist in 
/usr/ports/distfiles/fasta3/20140126.  => Attempting to fetch 
http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.6d.tar.gz 
fetch: 
http://faculty.virginia.edu/wrpearson/fasta/fasta36/fasta-36.3.6d.tar.gz: 
size mismatch: expected 970941, actual 969973 => Attempting to fetch 
ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/fasta3/20140126/fasta-36.3.6d.tar.gz 


http://www.freebsd.org/cgi/query-pr.cgi?pr=185698 
>Unformatted:
