Date: Wed, 18 Sep 2002 09:48:14 +1000 (EST) From: Tony Maher <tonym@biolateral.com.au> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/42915: Maintainer update: biology/primer3 Message-ID: <200209172348.g8HNmEoS091869@dt.home>
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>Number: 42915
>Category: ports
>Synopsis: Maintainer update: biology/primer3
>Confidential: no
>Severity: non-critical
>Priority: high
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Tue Sep 17 16:50:01 PDT 2002
>Closed-Date:
>Last-Modified:
>Originator: Tony Maher
>Release: FreeBSD 4.7-PRERELEASE i386
>Organization:
Biolateral
>Environment:
System: FreeBSD dt.home 4.7-PRERELEASE FreeBSD 4.7-PRERELEASE #0: Wed Sep 4 12:22:57 EST 2002 root@dt.home:/usr/obj/usr/src/sys/DT i386
>Description:
Primer3 has just been commited so I tested it and found a couple of
problems when making packages:
1) The copyright message is not displayed (so added a pkg-message)
2) packages use mtree to generate directories and it seems empty
directories do not get created (or added to the mtree list).
The port uses cpio to install the examples directory so the
empty directories get created. Therefore have a mismatch in pkg-plist
depending on whether it was added as a package or from the port.
Fix by removing the empty directories before using cpio to install
and adjust the pkg-plist to match.
It would be good if this went in before 4.7 freeze due to point 1
(though I do not think the biology ports are packaged onto the CD's
but I assume the DVD's??)
Sorry I should have tested this more thoroughly when I initially
submitted the port.
>How-To-Repeat:
cd /usr/ports/biology/primer3
make package
make deinstall
pkg_add /usr/ports/package/All/primer3-0.9.tbz <-- no message here
pkg_delete primer3-0.9 <-- warnings here
>Fix:
diff -ruN primer3.orig/Makefile primer3/Makefile
--- primer3.orig/Makefile Wed Sep 18 01:31:09 2002
+++ primer3/Makefile Wed Sep 18 09:26:18 2002
@@ -40,6 +40,7 @@
.for file in ${DOCUMENTS}
@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR}
.endfor
+ @${RMDIR} ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp
@${MKDIR} ${EXAMPLESDIR}
@cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | \
${CPIO} ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
diff -ruN primer3.orig/pkg-message primer3/pkg-message
--- primer3.orig/pkg-message Thu Jan 1 10:00:00 1970
+++ primer3/pkg-message Wed Sep 18 09:13:31 2002
@@ -0,0 +1,41 @@
+ Copyright (c) 1996,1997,1998
+ Whitehead Institute for Biomedical Research. All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions must reproduce the above copyright notice, this
+list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution. Redistributions of
+source code must also reproduce this information in the source code itself.
+
+2. If the program is modified, redistributions must include a notice
+(in the same places as above) indicating that the redistributed program is
+not identical to the version distributed by Whitehead Institute.
+
+3. All advertising materials mentioning features or use of this
+software must display the following acknowledgment:
+ This product includes software developed by the
+ Whitehead Institute for Biomedical Research.
+
+4. The name of the Whitehead Institute may not be used to endorse or
+promote products derived from this software without specific prior written
+permission.
+
+We also request that use of this software be cited in publications as
+
+Steve Rozen, Helen J. Skaletsky (1996,1997,1998)
+ Primer3. Code available at
+ http://www-genome.wi.mit.edu/genome_software/other/primer3.html
+
+THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ``AS IS'' AND ANY
+EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGE.
diff -ruN primer3.orig/pkg-plist primer3/pkg-plist
--- primer3.orig/pkg-plist Wed Sep 18 01:31:09 2002
+++ primer3/pkg-plist Wed Sep 18 09:24:12 2002
@@ -353,8 +353,6 @@
@dirrm share/primer3
%%PORTDOCS%%@dirrm share/doc/primer3/
%%PORTDOCS%%@dirrm share/examples/primer3/primer1_list_last
-%%PORTDOCS%%@dirrm share/examples/primer3/primer1_list_tmp
%%PORTDOCS%%@dirrm share/examples/primer3/primer_global_err
%%PORTDOCS%%@dirrm share/examples/primer3/primer_list_last
-%%PORTDOCS%%@dirrm share/examples/primer3/primer_list_tmp
%%PORTDOCS%%@dirrm share/examples/primer3/
>Release-Note:
>Audit-Trail:
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