Date: Tue, 1 Jun 2004 00:41:00 +0200 (CEST) From: Roman Neuhauser <neuhauser@chello.cz> To: FreeBSD-gnats-submit@FreeBSD.org Cc: wjv@FreeBSD.org Subject: ports/67428: [PATCH] biology/fasta doesn't fetch, update to 21u1d0 Message-ID: <20040531224100.51E292FDA01@isis.wad.cz> Resent-Message-ID: <200405312250.i4VMoMW4066127@freefall.freebsd.org>
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>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@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 --- >Release-Note: >Audit-Trail: >Unformatted:
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