ports/67428: [PATCH] biology/fasta doesn't fetch, update to 21u1d0

[Roman Neuhauser]

>Number:         67428
>Category:       ports
>Synopsis:       [PATCH] biology/fasta doesn't fetch, update to 21u1d0
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon May 31 15:50:21 PDT 2004
>Closed-Date:
>Last-Modified:
>Originator:     Roman Neuhauser
>Release:        FreeBSD 4.9-RELEASE-p2 i386
>Organization:
>Environment:
System: FreeBSD isis.wad.cz 4.9-RELEASE-p2 FreeBSD 4.9-RELEASE-p2 #3: Sun Mar 7 02:11:16 CET 2004 root at isis.wad.cz:/usr/obj/usr/src/sys/FREEPUPPY2_6 i386


	
>Description:
has been unfetchable since Feb 2002!

I only confirmed it builds and the plist is correct, also ran one of
the programs (ok, asked form input), so it seems to be ok but really
needs testing. there's also a "sindex" program that doesn't get built
by default, is that an omission in the upstream Makefile? maintainer
might want to add it to $(PROGS) (and pkg-plist etc)

nb: portlint complains:

FATAL: PORTVERSION looks illegal. should modify "21.u1d0".

I'm not sure what to do about it, the info given in Porter's Handbook
is insufficient.

maintainer cc'd

>How-To-Repeat:
	
>Fix:

	

--- biology::fasta-21u1d0.patch begins here ---
Index: biology/fasta/Makefile
===================================================================
RCS file: /home/ncvs/ports/biology/fasta/Makefile,v
retrieving revision 1.4
diff -u -r1.4 Makefile
--- biology/fasta/Makefile	7 Mar 2003 05:56:41 -0000	1.4
+++ biology/fasta/Makefile	31 May 2004 21:59:07 -0000
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	fasta
-PORTVERSION=	20.u66
+PORTVERSION=	21.u1d0
 CATEGORIES=	biology
 MASTER_SITES=	http://ftp.virginia.edu/pub/fasta/
 DISTNAME=	fasta${PORTVERSION:S/.//g}
@@ -18,7 +18,6 @@
 NO_CDROM=	May not be sold or incorporated into a commercial product
 WRKSRC=		${WRKDIR}/fasta
 PKGMESSAGE=	${WRKDIR}/pkg-message
-FASTA_DOCDIR=	${PREFIX}/share/doc/fasta
 FASTA_DOCS=	COPYRIGHT README.versions fasta20.doc fasta20.me format.doc \
 		readme.*
 
@@ -39,9 +38,9 @@
 	@ ${INSTALL_MAN} ${WRKSRC}/${manpage} ${MAN1PREFIX}/man/man1/
 .endfor
 .if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${FASTA_DOCDIR}
+	@ ${MKDIR} ${DOCSDIR}
 .for docfile in ${FASTA_DOCS}
-	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${FASTA_DOCDIR}
+	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
 .endfor
 .endif
 
Index: biology/fasta/distinfo
===================================================================
RCS file: /home/ncvs/ports/biology/fasta/distinfo,v
retrieving revision 1.2
diff -u -r1.2 distinfo
--- biology/fasta/distinfo	31 Mar 2004 03:06:18 -0000	1.2
+++ biology/fasta/distinfo	31 May 2004 21:51:05 -0000
@@ -1,2 +1,2 @@
-MD5 (fasta20u66.shar.Z) = 3960df040e5006969cf02568544751e9
-SIZE (fasta20u66.shar.Z) = 425608
+MD5 (fasta21u1d0.shar.Z) = df423465929b2f8ceaf508dceffa3403
+SIZE (fasta21u1d0.shar.Z) = 463293
Index: biology/fasta/pkg-plist
===================================================================
RCS file: /home/ncvs/ports/biology/fasta/pkg-plist,v
retrieving revision 1.2
diff -u -r1.2 pkg-plist
--- biology/fasta/pkg-plist	22 Oct 2003 09:29:54 -0000	1.2
+++ biology/fasta/pkg-plist	31 May 2004 22:12:19 -0000
@@ -10,6 +10,7 @@
 %%PORTDOCS%%%%DOCSDIR%%/readme.v20u4
 %%PORTDOCS%%%%DOCSDIR%%/readme.v20u5
 %%PORTDOCS%%%%DOCSDIR%%/readme.v20u6
+%%PORTDOCS%%%%DOCSDIR%%/readme.v21u0
 bin/aacomp
 bin/align
 bin/align0
@@ -30,6 +31,7 @@
 bin/psgrease
 bin/randseq
 bin/relate
+bin/revcomp
 bin/ssearch
 bin/tfasta
 bin/tfastx
Index: biology/fasta/files/patch-Makefile
===================================================================
RCS file: /home/ncvs/ports/biology/fasta/files/patch-Makefile,v
retrieving revision 1.1
diff -u -r1.1 patch-Makefile
--- biology/fasta/files/patch-Makefile	11 Feb 2001 16:24:18 -0000	1.1
+++ biology/fasta/files/patch-Makefile	31 May 2004 22:03:46 -0000
@@ -1,15 +1,16 @@
 --- Makefile.orig	Mon Jan 29 15:10:42 2001
 +++ Makefile	Mon Jan 29 15:15:08 2001
-@@ -3,13 +3,13 @@
+@@ -3,14 +3,14 @@
  # for mips, also use: -mips2 -O2
  #
  
 -CC= cc -O
 +#CC= cc -O
  #CC=cc -g
+ #CC=insure -g
  
--CFLAGS= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS
-+CFLAGS+= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS
+-CFLAGS= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN
++CFLAGS+= -DUNIX -DBIGMEM -DSFCHAR="':'" -DEXPM1 -DPROGRESS -DGAP_OPEN
  LFLAGS= -lm -o
  
 -BIN = /seqprg/slib/bin
--- biology::fasta-21u1d0.patch ends here ---


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