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Date: Fri, 29 Mar 2002 13:55:04 +0800 (CST)
From: Chen-hsiung Chan <frankch@waru.life.nthu.edu.tw>
Reply-To: Chen-hsiung Chan <frankch@waru.life.nthu.edu.tw>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: please remove biology/seaview
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         36466
>Category:       ports
>Synopsis:       please remove biology/seaview
>Confidential:   no
>Severity:       non-critical
>Priority:       high
>Responsible:    freebsd-ports
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Thu Mar 28 22:00:01 PST 2002
>Closed-Date:    Fri Nov 22 02:57:32 PST 2002
>Last-Modified:  Fri Nov 22 02:57:32 PST 2002
>Originator:     Chen-hsiung Chan
>Release:        FreeBSD 4.5-STABLE i386
>Organization:
>Environment:
System: FreeBSD feminism.life.nthu.edu.tw 4.5-STABLE FreeBSD 4.5-STABLE #0: Fri Mar 8 13:20:09 CST 2002 frankch@feminism.life.nthu.edu.tw:/usr/obj/usr/src/sys/WARU i386


	
>Description:
	The distfile for ports/biology/seaview has long gone.
	It seems there's no where we can find a site hosting the
	original distfile.
	
>How-To-Repeat:
	
>Fix:
	Anyone with commit privilege please remove the port from
	ports collection. Thanks alot.
	


>Release-Note:
>Audit-Trail:

From: jharris@widomaker.com
To: freebsd-gnats-submit@FreeBSD.org, frankch@waru.life.nthu.edu.tw
Cc: jharris@widomaker.com
Subject: Re: ports/36466: please remove biology/seaview
Date: Fri, 29 Mar 2002 01:29:49 -0500 (EST)

 >   Description
 >
 >        The distfile for ports/biology/seaview has long gone.
 >        It seems there's no where we can find a site hosting the
 >        original distfile.
 >
 >   Fix
 >
 >        Anyone with commit privilege please remove the port from
 >        ports collection. Thanks alot.
 
 Nah, try these instead:
 
 http://www.ftpfind.com/search.php?query=seaview%2Etar&method=iss
 http://www.filesearching.com/cgi-bin/s?q=seaview.tar&t=f&d=&l=en
 http://www.alltheweb.com/search?cat=ftp&cs=iso-8859-1&ftype=4&q=seaview.tar

From: Tony Maher <tonym@biolateral.com.au>
To: freebsd-gnats-submit@FreeBSD.org, frankch@waru.life.nthu.edu.tw
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Fri, 29 Mar 2002 20:01:21 +1100

 Please do *not* remove this port.
 
 The port _does_ need updating.
 
 It now relies on x11-toolkits/fltk and requires modification
 to files/patch-aa changing
 CC     ?= gcc 
 to
 CC      = c++
 
 then everything compiles.
 I am still trying to work out the linkage step and I will submit a
 complete update for this port when I have worked it out.
 
 We definitiely want this port to remain so if the current maintainer
 does not wish to continue maintaining this port then I am willing to
 take over (but am very happy if he wants to keep it ;-)
 
 thanks
 --
 tonym

From: Tony Maher <tonym@biolateral.com.au>
To: freebsd-gnats-submit@FreeBSD.org
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Fri, 29 Mar 2002 20:20:10 +1100

 Ok - I can get it to compile with following Makefile.
 (sorry its just horrible hack of original one for now).
 It appears to run ok.
 
 --
 tonym
 
 
 CC  = c++
 CFLAGS+= -I${X11BASE}/include
 #LIBS   = -L${X11BASE}/lib -lfltk -lGL -LGLU -lXext -lX11 -lm
 LIBS    = -L${X11BASE}/lib -lfltk -lGL -lGLU -lXext -lX11 -lm
 #SRCS   = align.c comlines.c load_seq.c regions.c seaview.c
 use_mase_files.c xfm
 atpt.c
 SRCS    = align.c seaview.c chooser_plus.c nexus.c \
         use_mase_files.c comlines.c regions.c xfmatpt.c load_seq.c
 resource.c
 
 #OBJS   = align.o comlines.o load_seq.o regions.o seaview.o
 use_mase_files.o xfm
 atpt.o
 
 OBJS    = ${SRCS:.c=.o}
 all: seaview
 
 seaview: $(OBJS)
     cc -o seaview $(OBJS) $(LIBS)
 
 c.o.: $(SRCS)
     $(CC) $(CFLAGS) -c $(SRCS)

From: Tony Maher <tonym@biolateral.com.au>
To: freebsd-gnats-submit@FreeBSD.org
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Fri, 29 Mar 2002 21:42:39 +1100

 This is a multi-part message in MIME format.
 --------------292820DA3D9875C171851A8A
 Content-Type: text/plain; charset=us-ascii
 Content-Transfer-Encoding: 7bit
 
 Attached is a patch to update seaview to a working state.
 
 --
 tonym
 --------------292820DA3D9875C171851A8A
 Content-Type: text/plain; charset=us-ascii;
  name="seaview.patch"
 Content-Transfer-Encoding: 7bit
 Content-Disposition: inline;
  filename="seaview.patch"
 
 diff -ruN seaview.orig/Makefile seaview/Makefile
 --- seaview.orig/Makefile	Sun Oct  8 21:19:17 2000
 +++ seaview/Makefile	Fri Mar 29 21:36:56 2002
 @@ -6,7 +6,7 @@
  #
  
  PORTNAME=	seaview
 -PORTVERSION=	1.0
 +PORTVERSION=	2002.01.16
  CATEGORIES=	biology
  MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
  DISTNAME=	${PORTNAME}
 @@ -14,7 +14,7 @@
  
  MAINTAINER=	frankch@waru.life.nthu.edu.tw
  
 -LIB_DEPENDS=	xforms.0:${PORTSDIR}/x11-toolkits/xforms
 +LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk
  
  USE_X_PREFIX=	YES
  NO_WRKSUBDIR=	YES
 @@ -22,8 +22,14 @@
  EXTRACT_BEFORE_ARGS=	-xf
  EXTRACT_AFTER_ARGS=	# empty
  
 +# The distribution does not come with its own Makefile.
 +
 +pre-build:
 +	@ ${CP} ${FILESDIR}/Makefile ${WRKSRC}
 +
  do-install:
  	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin
 +	@ ${INSTALL_SCRIPT}  ${WRKSRC}/seaview_align.sh ${PREFIX}/bin
  	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)
  	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview
  
 diff -ruN seaview.orig/distinfo seaview/distinfo
 --- seaview.orig/distinfo	Mon Apr 24 19:45:46 2000
 +++ seaview/distinfo	Fri Mar 29 21:12:52 2002
 @@ -1 +1 @@
 -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab
 +MD5 (seaview.tar) = 05ae4baeacdd00e01ce415bc5acfca13
 diff -ruN seaview.orig/files/Makefile seaview/files/Makefile
 --- seaview.orig/files/Makefile	Thu Jan  1 10:00:00 1970
 +++ seaview/files/Makefile	Fri Mar 29 21:27:08 2002
 @@ -0,0 +1,16 @@
 +CC	= c++
 +CFLAGS	+= -I${X11BASE}/include
 +LIBS	= -L${X11BASE}/lib -lfltk -lGL -lXext -lX11 -lm
 +SRCS	= align.c seaview.c chooser_plus.c nexus.c use_mase_files.c \
 +	  comlines.c regions.c xfmatpt.c load_seq.c resource.c
 +OBJS	= ${SRCS:.c=.o}
 +
 +all: seaview
 +
 +seaview: $(OBJS)
 +	$(CC) -o seaview $(OBJS) $(LIBS)
 +
 +c.o.: $(SRCS)
 +	$(CC) $(CFLAGS) -c $(SRCS)
 +
 +
 diff -ruN seaview.orig/files/patch-aa seaview/files/patch-aa
 --- seaview.orig/files/patch-aa	Tue Aug 31 13:57:56 1999
 +++ seaview/files/patch-aa	Thu Jan  1 10:00:00 1970
 @@ -1,20 +0,0 @@
 ---- Makefile.orig	Mon Aug 30 20:54:56 1999
 -+++ Makefile	Mon Aug 30 20:55:48 1999
 -@@ -0,0 +1,17 @@
 -+#matpt.h
 -+#seaview.h
 -+CC	?= gcc
 -+CFLAGS+= -I${X11BASE}/include
 -+LIBS	= -L${X11BASE}/lib -lxforms -lX11 -lm
 -+SRCS	= align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c
 -+OBJS	= align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o
 -+
 -+all: seaview
 -+
 -+seaview: $(OBJS)
 -+	$(CC) -o seaview $(OBJS) $(LIBS)
 -+
 -+c.o.: $(SRCS)
 -+	$(CC) $(CFLAGS) -c $(SRCS)
 -+
 -+
 diff -ruN seaview.orig/pkg-descr seaview/pkg-descr
 --- seaview.orig/pkg-descr	Mon May  3 07:37:59 1999
 +++ seaview/pkg-descr	Fri Mar 29 21:39:24 2002
 @@ -2,10 +2,9 @@
  You can align DNA sequences from several organisms, and find out their
  relative postions in phylogenic tree.
  
 -File test.mase can be used as an example file.
 -Open the on-line help window through button 'Help' to learn seaview usage.
 +An example file test.mase can be obtained from the ftp site.
  
 -WWW: http://acnuc.univ-lyon1.fr/phylogeny/seaview.html
 +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
  
  *****************************************************************************
  *   The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .
 diff -ruN seaview.orig/pkg-plist seaview/pkg-plist
 --- seaview.orig/pkg-plist	Mon Dec 22 09:04:39 1997
 +++ seaview/pkg-plist	Fri Mar 29 21:29:19 2002
 @@ -1,3 +1,4 @@
  bin/seaview
 +bin/seaview_align.sh
  lib/X11/seaview/seaview.help
  @dirrm lib/X11/seaview
 
 --------------292820DA3D9875C171851A8A--
 

From: Tony Maher <tonym@biolateral.com.au>
To: freebsd-gnats-submit@FreeBSD.org, frankch@waru.life.nthu.edu.tw
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Sat, 30 Mar 2002 07:16:20 +1100

 Sorry forgot to add - if you apply the above path then pease remove
 file/patch-aa which is now an empty file.
 
 --
 tonym
Responsible-Changed-From-To: freebsd-ports->cy 
Responsible-Changed-By: cy 
Responsible-Changed-When: Fri Mar 29 15:18:07 PST 2002 
Responsible-Changed-Why:  
The file fetches OK, however the checksum is invalid. 

I will work with the port's maintainer to resolve this. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=36466 
State-Changed-From-To: open->feedback 
State-Changed-By: cy 
State-Changed-When: Fri Mar 29 15:22:33 PST 2002 
State-Changed-Why:  
Sent email to maintainer about fetchability of this port.  The checksum 
appears invalid. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=36466 

From: Pete Fritchman <petef@FreeBSD.org>
To: Tony Maher <tonym@biolateral.com.au>
Cc: freebsd-gnats-submit@freebsd.org, frankch@waru.life.nthu.edu.tw
Subject: Re:  ports/36466: please remove biology/seaview
Date: Fri, 29 Mar 2002 18:20:27 -0500

 ++ 29/03/02 02:50 -0800 - Tony Maher:
 |  Attached is a patch to update seaview to a working state.
 [ patch snipped ]
 
 Does the maintainer (cc:'d) approve of this patch, and/or want to let
 Tony take over maintainership?
 
 Thanks,
 
 --pete
 
 --
 Pete Fritchman [petef@(databits.net|freebsd.org|csh.rit.edu)]
 finger petef@databits.net for PGP key

From: Cy Schubert - CITS Open Systems Group <Cy.Schubert@uumail.gov.bc.ca>
To: Chen-hsiung Chan <frankch@waru.life.nthu.edu.tw>
Cc: Pete Fritchman <petef@databits.net>,
	Tony Maher <tonym@biolateral.com.au>,
	FreeBSD-gnats-submit@FreeBSD.ORG
Subject: Re: ports/36466: please remove biology/seaview 
Date: Sat, 30 Mar 2002 05:50:44 -0800

 In message <20020330175122.B76888@waru.life.nthu.edu.tw>, Chen-hsiung =
 
 Chan writ
 es:
 > Hi,
 >         tonym@biolateral.com.au (Tony Maher) have provide a very good
 > patch in the ports list. I think it is ok. And if he like to take the
 > maintainership of this port, it is ok with me.
 
 This sounds like a plan.  I will work with Tony to resolve this PR and =
 
 will change the MAINTAINER field to him.
 
 > =
 
 > On Fri, Mar 29, 2002 at 04:07:08PM -0800, cy@FreeBSD.org wrote:
 > > I've tried sending email to you from my place of employment.  As it
 > > bounced, I'm sending this to you from the FreeBSD.org cluster.
 > > =
 
 > > The PR you submitted, ports/36466, is incorrect because I can
 > > fetch the distfile, seaview.tar.  However, the checksum fails.
 > > Would you please send me a patch to the port that fixes the
 > > checksum.
 > =
 
 > -- =
 
 > Chen-Hsiung Chan [=B8=E2=C2=ED=BA=B5](BIG5)
 > Department of Life Science      http://waru.life.nthu.edu.tw/~frankch/
 > National Tsing Hua University   email: frankch@waru.life.nthu.edu.tw
 > Taiwan
 
 Thank you for your quick response.
 
 
 
 Regards,                         Phone:  (250)387-8437
 Cy Schubert                        Fax:  (250)387-5766
 Team Leader, Sun/Alpha Team      Email:  Cy.Schubert@osg.gov.bc.ca
 Open Systems Group, CITS
 Ministry of Management Services
 Province of BC            =
 
                     FreeBSD UNIX:  cy@FreeBSD.org
 
 
 

From: Cy Schubert - CITS Open Systems Group <Cy.Schubert@uumail.gov.bc.ca>
To: Pete Fritchman <petef@FreeBSD.org>
Cc: FreeBSD GNATS <FreeBSD-gnats-submit@FreeBSD.org>
Subject: Re: ports/36466: please remove biology/seaview 
Date: Sat, 30 Mar 2002 17:48:47 -0800

 In message <200203292340.g2TNe2H59234@freefall.freebsd.org>, Pete =
 
 Fritchman wri
 tes:
 > The following reply was made to PR ports/36466; it has been noted by GN=
 ATS.
 > =
 
 > From: Pete Fritchman <petef@FreeBSD.org>
 > To: Tony Maher <tonym@biolateral.com.au>
 > Cc: freebsd-gnats-submit@freebsd.org, frankch@waru.life.nthu.edu.tw
 > Subject: Re:  ports/36466: please remove biology/seaview
 > Date: Fri, 29 Mar 2002 18:20:27 -0500
 > =
 
 >  ++ 29/03/02 02:50 -0800 - Tony Maher:
 >  |  Attached is a patch to update seaview to a working state.
 >  [ patch snipped ]
 >  =
 
 >  Does the maintainer (cc:'d) approve of this patch, and/or want to let
 >  Tony take over maintainership?
 
 It is OK to let Tony take over maintainership.  I received the =
 
 following email from the maintainer:
 
     Subject: Re: ports/36466: please remove biology/seaview
     From: Chen-hsiung Chan <frankch@waru.life.nthu.edu.tw>
     Date: Sat, 30 Mar 2002 17:51:22 +0800
     To: cy@FreeBSD.org
 
     (Unknown charset: <big5>)
 
     Hi,
             tonym@biolateral.com.au (Tony Maher) have provide a very =
 
 good
     patch in the ports list. I think it is ok. And if he like to take =
 
 the
     maintainership of this port, it is ok with me.
 
     On Fri, Mar 29, 2002 at 04:07:08PM -0800, cy@FreeBSD.org wrote:
     > I've tried sending email to you from my place of employment.  As =
 
 it
     > bounced, I'm sending this to you from the FreeBSD.org cluster.
     > =
 
     > The PR you submitted, ports/36466, is incorrect because I can
     > fetch the distfile, seaview.tar.  However, the checksum fails.
     > Would you please send me a patch to the port that fixes the
     > checksum.
 
     -- =
 
     Chen-Hsiung Chan [=B8=E2=C2=ED=BA=B5](BIG5)
     Department of Life Science      http://waru.life.nthu.edu.tw/~frankc
 h/
     National Tsing Hua University   email: frankch@waru.life.nthu.edu.tw
     Taiwan
 
 
 Regards,                         Phone:  (250)387-8437
 Cy Schubert                        Fax:  (250)387-5766
 Team Leader, Sun/Alpha Team      Email:  Cy.Schubert@osg.gov.bc.ca
 Open Systems Group, CITS
 Ministry of Management Services
 Province of BC            =
 
                     FreeBSD UNIX:  cy@FreeBSD.org
 
 

From: Cy Schubert - CITS Open Systems Group <Cy.Schubert@uumail.gov.bc.ca>
To: Tony Maher <tonym@biolateral.com.au>
Cc: FreeBSD GNATS <FreeBSD-gnats-submit@FreeBSD.org>,
	Pete Fritchman <petef@databits.net>
Subject: Re: ports/36466: please remove biology/seaview 
Date: Sat, 30 Mar 2002 19:01:44 -0800

 In message <200203302330.g2UNUm4h012177@dt.home>, Tony Maher writes:
 > Hello Cy,
 
 Hi Tom,
 
 > 
 > > This sounds like a plan.  I will work with Tony to resolve this PR and 
 > > will change the MAINTAINER field to him.
 > 
 > Fine by me. Are there any problems with the patch that need resolving?
 > (well there is the warning about tmpname() - following patch silences that)
 
 Thanks for the patch.
 
 I'd prefer to not delete patch-aa and replace it with your Makefile 
 patch.  I'd rather replace the contents of patch-aa with a new Makefile 
 patch.
 
 I had a problem linking seaview.  Adding -pthread fixed the problem.
 
 Your email address is now in the MAINTAINER field.  Do you maintain any 
 other ports?  If not, I will have to add you to the FreeBSD 
 contributors web page.
 
 Here is the the patch I will commit.  Please have a look at it and give 
 it a test drive.
 
 Index: Makefile
 ===================================================================
 RCS file: /home/ncvs/ports/biology/seaview/Makefile,v
 retrieving revision 1.17
 diff -u -r1.17 Makefile
 --- Makefile	8 Oct 2000 10:19:17 -0000	1.17
 +++ Makefile	31 Mar 2002 02:56:58 -0000
 @@ -6,15 +6,15 @@
  #
  
  PORTNAME=	seaview
 -PORTVERSION=	1.0
 +PORTVERSION=	2002.01.16
  CATEGORIES=	biology
  MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
  DISTNAME=	${PORTNAME}
  EXTRACT_SUFX=	.tar
  
 -MAINTAINER=	frankch@waru.life.nthu.edu.tw
 +MAINTAINER=	tonym@biolateral.com.au
  
 -LIB_DEPENDS=	xforms.0:${PORTSDIR}/x11-toolkits/xforms
 +LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk
  
  USE_X_PREFIX=	YES
  NO_WRKSUBDIR=	YES
 @@ -24,6 +24,7 @@
  
  do-install:
  	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin
 +	@ ${INSTALL_SCRIPT}  ${WRKSRC}/seaview_align.sh ${PREFIX}/bin
  	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)
  	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview
  
 Index: distinfo
 ===================================================================
 RCS file: /home/ncvs/ports/biology/seaview/distinfo,v
 retrieving revision 1.10
 diff -u -r1.10 distinfo
 --- distinfo	24 Apr 2000 09:45:46 -0000	1.10
 +++ distinfo	31 Mar 2002 02:56:58 -0000
 @@ -1 +1 @@
 -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab
 +MD5 (seaview.tar) = 05ae4baeacdd00e01ce415bc5acfca13
 Index: pkg-descr
 ===================================================================
 RCS file: /home/ncvs/ports/biology/seaview/pkg-descr,v
 retrieving revision 1.2
 diff -u -r1.2 pkg-descr
 --- pkg-descr	2 May 1999 21:37:59 -0000	1.2
 +++ pkg-descr	31 Mar 2002 02:56:58 -0000
 @@ -2,10 +2,9 @@
  You can align DNA sequences from several organisms, and find out their
  relative postions in phylogenic tree.
  
 -File test.mase can be used as an example file.
 -Open the on-line help window through button 'Help' to learn seaview 
 usage.
 +An example file test.mase can be obtained from the ftp site.
  
 -WWW: http://acnuc.univ-lyon1.fr/phylogeny/seaview.html
 +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
  
  ***********************************************************************
 ******
  *   The help file (seaview.help) is located in /usr/X11R6/lib/X11/seavi
 ew/ .
 Index: pkg-plist
 ===================================================================
 RCS file: /home/ncvs/ports/biology/seaview/pkg-plist,v
 retrieving revision 1.1.1.1
 diff -u -r1.1.1.1 pkg-plist
 --- pkg-plist	21 Dec 1997 22:04:39 -0000	1.1.1.1
 +++ pkg-plist	31 Mar 2002 02:56:58 -0000
 @@ -1,3 +1,4 @@
  bin/seaview
 +bin/seaview_align.sh
  lib/X11/seaview/seaview.help
  @dirrm lib/X11/seaview
 Index: files/patch-aa
 ===================================================================
 RCS file: /home/ncvs/ports/biology/seaview/files/patch-aa,v
 retrieving revision 1.3
 diff -u -r1.3 patch-aa
 --- files/patch-aa	31 Aug 1999 03:57:56 -0000	1.3
 +++ files/patch-aa	31 Mar 2002 02:56:58 -0000
 @@ -1,20 +1,18 @@
 ---- Makefile.orig	Mon Aug 30 20:54:56 1999
 -+++ Makefile	Mon Aug 30 20:55:48 1999
 -@@ -0,0 +1,17 @@
 -+#matpt.h
 -+#seaview.h
 -+CC	?= gcc
 -+CFLAGS+= -I${X11BASE}/include
 -+LIBS	= -L${X11BASE}/lib -lxforms -lX11 -lm
 -+SRCS	= align.c comlines.c load_seq.c regions.c seaview.c 
 use_mase_files.c xfmatpt.c
 -+OBJS	= align.o comlines.o load_seq.o regions.o seaview.o 
 use_mase_files.o xfmatpt.o
 +--- Makefile.orig	Sat Mar 30 18:22:08 2002
 ++++ Makefile	Sat Mar 30 18:29:44 2002
 +@@ -0,0 +1,15 @@
 ++CC	= c++
 ++CFLAGS	+= -I${X11BASE}/include
 ++LIBS	= -L${X11BASE}/lib -lfltk -lGL -lXext -lX11 -lm
 ++SRCS	= align.c seaview.c chooser_plus.c nexus.c use_mase_files.c \
 ++	  comlines.c regions.c xfmatpt.c load_seq.c resource.c
 ++OBJS	= ${SRCS:.c=.o}
  +
  +all: seaview
  +
  +seaview: $(OBJS)
 -+	$(CC) -o seaview $(OBJS) $(LIBS)
 ++	$(CC) -pthread -o seaview $(OBJS) $(LIBS)
  +
  +c.o.: $(SRCS)
  +	$(CC) $(CFLAGS) -c $(SRCS)
 -+
  +
 
 
 Regards,                         Phone:  250-387-8437
 Cy Schubert                        Fax:  250-387-5766
 Team Leader, Sun/Alpha Team      Email:  Cy.Schubert@osg.gov.bc.ca
 Open Systems Group, CITS
 Ministry of Management Services
 Province of BC            
                     FreeBSD UNIX:  cy@FreeBSD.org
 
 

From: Cy Schubert - CITS Open Systems Group <Cy.Schubert@uumail.gov.bc.ca>
To: freebsd-gnats-submit@FreeBSD.org
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Sat, 13 Apr 2002 19:39:09 -0700

 Sent ping to new MAINTAINER, Tony Maher <tonym@biolateral.com.au> about 
 status.
 
 
 Cheers,                          Phone:  250-387-8437
 Cy Schubert                        Fax:  250-387-5766
 Team Leader, Sun/Alpha Team      Email:  Cy.Schubert@osg.gov.bc.ca
 Open Systems Group, CITS
 Ministry of Management Services
 Province of BC            
                     FreeBSD UNIX:  cy@FreeBSD.org
 
 

From: Tony Maher <tonym@biolateral.com.au>
To: freebsd-gnats-submit@FreeBSD.org
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Mon, 17 Jun 2002 09:42:25 +1000 (EST)

 Hello,
 
 finally found some time to work on this again.  During this time a
 new release has come out.  This time they provide a makefile
 so files/patch-aa can be deleted. Also using REINPLACE command so no longer
 need patch for align.cxx.
 
 So when the following patch is applied I think you will need to manually
 remove the files subdir completely.
 
 Re the utah-glx vs Mesa3 detection, I tried to use ${PKG_INFO} to see
 if utah-glx was installed (and this worked fine) but I could not get
 the info back into the Makefile easily/cleanly (the difference between
 running shell commands vs defining things in Makefile).
 I know it can be done (see emboss port for one way) but it did not seem
 worth the effort (I did spend a couple of hours trying).
 
 Instead I have allowed for defining HAVE_UTAH which will then link
 against the threaded library directly.
 
 --
 thanks
 tony maher
 
 
 
 
 diff -u seaview.orig/Makefile seaview/Makefile
 --- seaview.orig/Makefile	Sat May 18 12:36:56 2002
 +++ seaview/Makefile	Mon Jun 17 09:34:11 2002
 @@ -2,34 +2,61 @@
  # Date created:         Dec 5 1997
  # Whom:                 frankch@waru.life.nthu.edu.tw
  #
 -# $FreeBSD: ports/biology/seaview/Makefile,v 1.18 2002/05/18 02:36:56 kris Exp $
 +# $FreeBSD: ports/biology/seaview/Makefile,v 1.17 2000/10/08 10:19:17 asami Exp $
  #
  
  PORTNAME=	seaview
 -PORTVERSION=	1.0
 +PORTVERSION=	2002.04.09
  CATEGORIES=	biology
  MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
  DISTNAME=	${PORTNAME}
  EXTRACT_SUFX=	.tar
  
 -MAINTAINER=	frankch@waru.life.nthu.edu.tw
 +MAINTAINER=	tonym@biolateral.com.au
  
 -BROKEN=		"Checksum is incorrect"
 -
 -LIB_DEPENDS=	xforms.0:${PORTSDIR}/x11-toolkits/xforms
 +LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk
  
  USE_X_PREFIX=	YES
 +USE_MESA=	YES
  NO_WRKSUBDIR=	YES
 -EXTRACT_CMD=		${TAR}
 +MAKEFILE=	makefile
 +ALL_TARGET=	seaview
 +EXTRACT_CMD=	${TAR}
  EXTRACT_BEFORE_ARGS=	-xf
  EXTRACT_AFTER_ARGS=	# empty
 +DOCDIR=		${PREFIX}/share/doc/${PORTNAME}
 +
 +pre-extract:
 +.if !defined(BATCH) && !defined(PACKAGE_BUILDING) && !defined(HAVE_UTAH)
 +	@(/usr/bin/dialog --textbox ${MASTERDIR}/pkg-warning 8 70 || ${TRUE})
 +.endif
 +
 +pre-patch:
 +.if defined(HAVE_UTAH)
 +P_CFLAGS=	${PTHREAD_CFLAGS}
 +P_LIBS=		${PTHREAD_LIBS}
 +.endif
 +
 +post-patch:
 +	@ ${REINPLACE_CMD} -e 's|../fltk|${X11BASE}|;' \
 +			   -e "s|I(.*)$$|I\\1/include|;" \
 +			   -e 's|-lfltk|-lfltk -lGL -lXext|;' \
 +			   -e 's|^CFLAGS  =|CFLAGS += ${P_CFLAGS} |;' \
 +			   -e 's|-lm|-lm ${P_LIBS}|;' \
 +			   ${WRKSRC}/${MAKEFILE}
 +	@ ${REINPLACE_CMD} -e "s|tmpnam|mkstemp|;" \
 +			   -e "s|(<stdlib.h>)|\1\n#include <unistd.h>|;" \
 +			   ${WRKSRC}/align.cxx
  
  do-install:
  	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin
 -	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)
 -	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview
 +	@ ${INSTALL_SCRIPT}  ${WRKSRC}/seaview_align.sh ${PREFIX}/bin
 +.if !defined(NOPORTDOCS)
 +	@ ${MKDIR} ${DOCDIR}
 +	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${DOCDIR}
 +.endif
  
  post-install:
 -	@ ${CAT} ${DESCR}
 +	@ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE}
  
  .include <bsd.port.mk>
 diff -u seaview.orig/distinfo seaview/distinfo
 --- seaview.orig/distinfo	Mon Apr 24 19:45:46 2000
 +++ seaview/distinfo	Mon Jun 17 09:22:43 2002
 @@ -1 +1 @@
 -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab
 +MD5 (seaview.tar) = 28b96855e50986b7e6ff6a0249b062b7
 Only in seaview.orig/: files
 diff -u seaview.orig/pkg-descr seaview/pkg-descr
 --- seaview.orig/pkg-descr	Mon May  3 07:37:59 1999
 +++ seaview/pkg-descr	Mon Jun 17 09:22:43 2002
 @@ -2,14 +2,6 @@
  You can align DNA sequences from several organisms, and find out their
  relative postions in phylogenic tree.
  
 -File test.mase can be used as an example file.
 -Open the on-line help window through button 'Help' to learn seaview usage.
 +An example file test.mase can be obtained from the ftp site.
  
 -WWW: http://acnuc.univ-lyon1.fr/phylogeny/seaview.html
 -
 -*****************************************************************************
 -*   The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .
 -*   Add an entry in your Xresources or Xdefaults file with:
 -*
 -*   seaview*helpfile:	/usr/X11R6/lib/X11/seaview/seaview.help
 -*****************************************************************************
 +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
 Only in seaview: pkg-message
 diff -u seaview.orig/pkg-plist seaview/pkg-plist
 --- seaview.orig/pkg-plist	Mon Dec 22 09:04:39 1997
 +++ seaview/pkg-plist	Mon Jun 17 09:22:43 2002
 @@ -1,3 +1,4 @@
  bin/seaview
 -lib/X11/seaview/seaview.help
 -@dirrm lib/X11/seaview
 +bin/seaview_align.sh
 +%%PORTDOCS%%share/doc/seaview/seaview.help
 +%%PORTDOCS%%@dirrm share/doc/seaview/
 Only in seaview: pkg-warning

From: Tony Maher <tonym@biolateral.com.au>
To: freebsd-gnats-submit@FreeBSD.org, tonym@biolateral.com.au
Cc:  
Subject: Re: ports/36466: please remove biology/seaview
Date: Mon, 17 Jun 2002 10:53:28 +1000 (EST)

 Sorry last patch set was incomplete as I used diff -u instead of
 diff -ruN
 
 --
 tonym
 
 
 
 diff -ruN seaview.orig/Makefile seaview/Makefile
 --- seaview.orig/Makefile	Sat May 18 12:36:56 2002
 +++ seaview/Makefile	Mon Jun 17 10:05:18 2002
 @@ -2,34 +2,61 @@
  # Date created:         Dec 5 1997
  # Whom:                 frankch@waru.life.nthu.edu.tw
  #
 -# $FreeBSD: ports/biology/seaview/Makefile,v 1.18 2002/05/18 02:36:56 kris Exp $
 +# $FreeBSD: ports/biology/seaview/Makefile,v 1.17 2000/10/08 10:19:17 asami Exp $
  #
  
  PORTNAME=	seaview
 -PORTVERSION=	1.0
 +PORTVERSION=	2002.04.09
  CATEGORIES=	biology
  MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
  DISTNAME=	${PORTNAME}
  EXTRACT_SUFX=	.tar
  
 -MAINTAINER=	frankch@waru.life.nthu.edu.tw
 +MAINTAINER=	tonym@biolateral.com.au
  
 -BROKEN=		"Checksum is incorrect"
 -
 -LIB_DEPENDS=	xforms.0:${PORTSDIR}/x11-toolkits/xforms
 +LIB_DEPENDS=	fltk.1:${PORTSDIR}/x11-toolkits/fltk
  
  USE_X_PREFIX=	YES
 +USE_MESA=	YES
  NO_WRKSUBDIR=	YES
 -EXTRACT_CMD=		${TAR}
 +MAKEFILE=	makefile
 +ALL_TARGET=	seaview
 +EXTRACT_CMD=	${TAR}
  EXTRACT_BEFORE_ARGS=	-xf
  EXTRACT_AFTER_ARGS=	# empty
 +DOCDIR=		${PREFIX}/share/doc/${PORTNAME}
 +
 +pre-extract:
 +.if !defined(BATCH) && !defined(PACKAGE_BUILDING) && !defined(HAVE_UTAH)
 +	@(/usr/bin/dialog --textbox ${MASTERDIR}/pkg-warning 8 70 || ${TRUE})
 +.endif
 +
 +pre-patch:
 +.if defined(HAVE_UTAH)
 +P_CFLAGS=	${PTHREAD_CFLAGS}
 +P_LIBS=		${PTHREAD_LIBS}
 +.endif
 +
 +post-patch:
 +	@ ${REINPLACE_CMD} -e 's|../fltk|${X11BASE}|;' \
 +			   -e "s|I(.*)$$|I\\1/include|;" \
 +			   -e 's|-lfltk|-lfltk -lGL -lXext|;' \
 +			   -e 's|^CFLAGS  =|CFLAGS += ${P_CFLAGS} |;' \
 +			   -e 's|-lm|-lm ${P_LIBS}|;' \
 +			   ${WRKSRC}/${MAKEFILE}
 +	@ ${REINPLACE_CMD} -e "s|tmpnam|mkstemp|;" \
 +			   -e "s|(<stdlib.h>)|\1\n#include <unistd.h>|;" \
 +			   ${WRKSRC}/align.cxx
  
  do-install:
  	@ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME} ${PREFIX}/bin
 -	@ (${MKDIR} ${PREFIX}/lib/X11/seaview)
 -	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${PREFIX}/lib/X11/seaview
 +	@ ${INSTALL_SCRIPT}  ${WRKSRC}/seaview_align.sh ${PREFIX}/bin
 +.if !defined(NOPORTDOCS)
 +	@ ${MKDIR} ${DOCDIR}
 +	@ ${INSTALL_DATA} ${WRKSRC}/seaview.help ${DOCDIR}
 +.endif
  
  post-install:
 -	@ ${CAT} ${DESCR}
 +	@ ${SED} -e "s#%%PREFIX%%#${PREFIX}#" ${PKGMESSAGE}
  
  .include <bsd.port.mk>
 diff -ruN seaview.orig/distinfo seaview/distinfo
 --- seaview.orig/distinfo	Mon Apr 24 19:45:46 2000
 +++ seaview/distinfo	Sun Jun 16 16:12:24 2002
 @@ -1 +1 @@
 -MD5 (seaview.tar) = 2e0b15423aae80a91709b253fc7c5cab
 +MD5 (seaview.tar) = 28b96855e50986b7e6ff6a0249b062b7
 diff -ruN seaview.orig/files/patch-aa seaview/files/patch-aa
 --- seaview.orig/files/patch-aa	Tue Aug 31 13:57:56 1999
 +++ seaview/files/patch-aa	Thu Jan  1 10:00:00 1970
 @@ -1,20 +0,0 @@
 ---- Makefile.orig	Mon Aug 30 20:54:56 1999
 -+++ Makefile	Mon Aug 30 20:55:48 1999
 -@@ -0,0 +1,17 @@
 -+#matpt.h
 -+#seaview.h
 -+CC	?= gcc
 -+CFLAGS+= -I${X11BASE}/include
 -+LIBS	= -L${X11BASE}/lib -lxforms -lX11 -lm
 -+SRCS	= align.c comlines.c load_seq.c regions.c seaview.c use_mase_files.c xfmatpt.c
 -+OBJS	= align.o comlines.o load_seq.o regions.o seaview.o use_mase_files.o xfmatpt.o
 -+
 -+all: seaview
 -+
 -+seaview: $(OBJS)
 -+	$(CC) -o seaview $(OBJS) $(LIBS)
 -+
 -+c.o.: $(SRCS)
 -+	$(CC) $(CFLAGS) -c $(SRCS)
 -+
 -+
 diff -ruN seaview.orig/pkg-descr seaview/pkg-descr
 --- seaview.orig/pkg-descr	Mon May  3 07:37:59 1999
 +++ seaview/pkg-descr	Sun Jun 16 18:27:38 2002
 @@ -2,14 +2,6 @@
  You can align DNA sequences from several organisms, and find out their
  relative postions in phylogenic tree.
  
 -File test.mase can be used as an example file.
 -Open the on-line help window through button 'Help' to learn seaview usage.
 +An example file test.mase can be obtained from the ftp site.
  
 -WWW: http://acnuc.univ-lyon1.fr/phylogeny/seaview.html
 -
 -*****************************************************************************
 -*   The help file (seaview.help) is located in /usr/X11R6/lib/X11/seaview/ .
 -*   Add an entry in your Xresources or Xdefaults file with:
 -*
 -*   seaview*helpfile:	/usr/X11R6/lib/X11/seaview/seaview.help
 -*****************************************************************************
 +WWW: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
 diff -ruN seaview.orig/pkg-message seaview/pkg-message
 --- seaview.orig/pkg-message	Thu Jan  1 10:00:00 1970
 +++ seaview/pkg-message	Sun Jun 16 18:31:49 2002
 @@ -0,0 +1,6 @@
 +*****************************************************************************
 +* The help file (seaview.help) is located in %%PREFIX%%/share/doc/seaview/  *
 +* Add an entry in your Xresources or Xdefaults file with:                   *
 +*                                                                           *
 +* seaview*helpfile:   %%PREFIX%%/share/doc/seaview/seaview.help             *
 +*****************************************************************************
 diff -ruN seaview.orig/pkg-plist seaview/pkg-plist
 --- seaview.orig/pkg-plist	Mon Dec 22 09:04:39 1997
 +++ seaview/pkg-plist	Sun Jun 16 18:26:13 2002
 @@ -1,3 +1,4 @@
  bin/seaview
 -lib/X11/seaview/seaview.help
 -@dirrm lib/X11/seaview
 +bin/seaview_align.sh
 +%%PORTDOCS%%share/doc/seaview/seaview.help
 +%%PORTDOCS%%@dirrm share/doc/seaview/
 diff -ruN seaview.orig/pkg-warning seaview/pkg-warning
 --- seaview.orig/pkg-warning	Thu Jan  1 10:00:00 1970
 +++ seaview/pkg-warning	Mon Jun 17 08:53:42 2002
 @@ -0,0 +1,3 @@
 +If you are using XFree86 version 3 with utah-glx hit Ctrl-C now
 +and use 'make -DHAVE_UTAH'
 +Otherwise hit OK and continue.
State-Changed-From-To: feedback->open 
State-Changed-By: dinoex 
State-Changed-When: Mon Sep 16 21:09:46 PDT 2002 
State-Changed-Why:  
Feedback was given, can the last patch be applied? 

http://www.freebsd.org/cgi/query-pr.cgi?pr=36466 
State-Changed-From-To: open->analyzed 
State-Changed-By: arved 
State-Changed-When: Tue Nov 12 23:21:46 PST 2002 
State-Changed-Why:  
The new version of seaview requires an update of the fltk port. 
The submitter has send a patch to the fltk maintainer (demon) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=36466 
Responsible-Changed-From-To: cy->freebsd-ports 
Responsible-Changed-By: cy 
Responsible-Changed-When: Mon Nov 18 07:47:14 PST 2002 
Responsible-Changed-Why:  
As per my note to developers, my time is limited at the current time. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=36466 
State-Changed-From-To: analyzed->closed 
State-Changed-By: arved 
State-Changed-When: Fri Nov 22 02:56:48 PST 2002 
State-Changed-Why:  
The old Maintainer has submitted an update, which was committed two days ago. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=36466 
>Unformatted:
