Attachment 13196 Details for Bug 25228 – file.diff

[patch] file.diff

file.diff (text/plain), 9.44 KB, created by johann on 2001-02-20 11:50:01 UTC

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Creator: johann

Created: 2001-02-20 11:50:01 UTC

Size: 9.44 KB

patch

obsolete

>diff -ruN emboss.bak/Makefile emboss/Makefile
>--- emboss.bak/Makefile	Tue Feb 20 13:41:58 2001
>+++ emboss/Makefile	Tue Feb 20 11:39:21 2001
>@@ -6,8 +6,7 @@
> #
> 
> PORTNAME=	emboss
>-PORTVERSION=	1.9.1
>-PORTREVISION=	1
>+PORTVERSION=	1.10.0
> CATEGORIES=	biology
> MASTER_SITES=	ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
> 		ftp://ftp.no.embnet.org/pub/EMBOSS/ \
>@@ -39,7 +38,7 @@
> 
> WRKSRC=		${WRKDIR}/${PORTNAME:U}-${PORTVERSION}
> EMBASSY_WRKDIR=	${WRKSRC}/EMBASSY
>-EMNU_VERSION=	1.0.3
>+EMNU_VERSION=	1.0.4
> MSE_VERSION=	0.0.4
> TOPO_VERSION=	0.1
> PHYLIP_VERSION=	3.573c
>@@ -105,7 +104,10 @@
> 	  ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
> 	  ${MAKE_ARGS} ${INSTALL_TARGET})
> .endfor
>-	@ ${INSTALL_DATA} ${WRKSRC}/emboss/acd/emboss.default \
>+	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
>+	  ${WRKSRC}/emboss/acd/emboss.default > \
>+	  ${PREFIX}/etc/emboss.default.sample && \
>+	  ${CHOWN} ${SHAREOWN}:${SHAREGRP} \
> 	  ${PREFIX}/etc/emboss.default.sample
> .if !defined(BATCH)
> 	@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
>diff -ruN emboss.bak/distinfo emboss/distinfo
>--- emboss.bak/distinfo	Tue Feb 20 13:41:58 2001
>+++ emboss/distinfo	Tue Feb 20 11:22:26 2001
>@@ -1,5 +1,5 @@
>-MD5 (emboss/EMBOSS-1.9.1.tar.gz) = 569ff1f9f2df08928b2dfb8ae1a331b9
>-MD5 (emboss/EMNU-1.0.3.tar.gz) = 829dedc516e72144563d3a1a77793678
>-MD5 (emboss/MSE-0.0.4.tar.gz) = 83b989776fbd59e346a2f90e7dc7f266
>-MD5 (emboss/PHYLIP-3.573c.tar.gz) = bb1d9da41c6bfdb47828a7a9e0e40b2f
>-MD5 (emboss/TOPO-0.1.tar.gz) = 039b26ed333a3ba6bed20d1caf707834
>+MD5 (emboss/EMBOSS-1.10.0.tar.gz) = cfe21d6af3683ad99546a380ac18699b
>+MD5 (emboss/EMNU-1.0.4.tar.gz) = 6ebdf128e1b531911ff97d2b8d6a59d8
>+MD5 (emboss/MSE-0.0.4.tar.gz) = ec94c169918038aa318e035cd7bd2d83
>+MD5 (emboss/PHYLIP-3.573c.tar.gz) = e1ca6cb87756836f0e1b3b6b026e826b
>+MD5 (emboss/TOPO-0.1.tar.gz) = d570fe3e41380d99646d99b5d1586da1
>diff -ruN emboss.bak/files/patch-emboss-acd-emboss.default emboss/files/patch-emboss-acd-emboss.default
>--- emboss.bak/files/patch-emboss-acd-emboss.default	Tue Feb 20 13:41:57 2001
>+++ emboss/files/patch-emboss-acd-emboss.default	Tue Feb 20 11:54:05 2001
>@@ -1,6 +1,6 @@
>---- emboss/acd/emboss.default.orig	Mon Jan 22 23:26:54 2001
>-+++ emboss/acd/emboss.default	Mon Jan 29 16:23:15 2001
>-@@ -1,9 +1,26 @@
>+--- emboss/acd/emboss.default.orig	Sun Feb 18 16:57:08 2001
>++++ emboss/acd/emboss.default	Tue Feb 20 10:45:57 2001
>+@@ -1,9 +1,31 @@
> -SET emboss_tempdata /nfs/WWW/data/EMBOSS/test
> +#####################################################
> +### Configuration options for FreeBSD EMBOSS port ###
>@@ -8,20 +8,26 @@
>  
> -# Logfile - set this to a file that any user can append to
> -# and EMBOSS applications will automatically write log information
>-+# This is the compiled-in default.  Change only if
>-+# you know what you're doing!
>++# The directory where EMBOSS expects to find run-time
>++# databases.  This is the compiled-in default - change
>++# only if you know what you're doing!
> +#
>-+#SET emboss_data /usr/local/share/EMBOSS/data
>++#SET emboss_data %%PREFIX%%/share/EMBOSS/data
>  
>-+# This is where your local databases reside
>-+# (this will differ from site to site):
>+-#SET emboss_logfile /packages/emboss/emboss/log
>++# This is an alias which is internal to this
>++# configuration file and is set here merely as a
>++# convenience.  It points to the location where you
>++# have placed your local databases (this will differ
>++# from site to site).
> +#
>-+SET emboss_tempdata /var/db/bio
>++SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
> +
>-+# Logfile - set this to a file that any user can append to and EMBOSS
>-+# applications will automatically write log information
>++# Logfile.  If this is uncommented and set to a file
>++# that any user can append to, EMBOSS applications
>++# will automatically log usage information.
> +#
>- #SET emboss_logfile /packages/emboss/emboss/log
>++#SET emboss_logfile /var/log/emboss.log
> +
> +
> +###########################################
>diff -ruN emboss.bak/pkg-message emboss/pkg-message
>--- emboss.bak/pkg-message	Tue Feb 20 13:41:58 2001
>+++ emboss/pkg-message	Tue Feb 20 10:36:14 2001
>@@ -2,11 +2,10 @@
> 
> The EMBOSS suite has been successfully installed.
> 
>-In order to use the EMBOSS programs, you will need to set some environment
>-variables in your shell startup file.
>+In order to see graphical output from some EMBOSS programs, you will need to
>+set the following environment variable in your shell startup file:
> 
> - set PLPLOT_LIB to:     "%%PREFIX%%/share/EMBOSS"
>-- set EMBOSS_ACDROOT to: "%%PREFIX%%/share/EMBOSS/acd"
> 
> NB:  A sample configuration file has been installed to %%PREFIX%%/etc as
> emboss.default.sample.  This must be renamed to emboss.default and edited
>diff -ruN emboss.bak/pkg-plist emboss/pkg-plist
>--- emboss.bak/pkg-plist	Tue Feb 20 13:41:58 2001
>+++ emboss/pkg-plist	Tue Feb 20 11:56:19 2001
>@@ -83,6 +83,7 @@
> bin/descseq
> bin/diffseq
> bin/digest
>+bin/domainer
> bin/dotmatcher
> bin/dotpath
> bin/dottup
>@@ -109,6 +110,7 @@
> bin/infoseq
> bin/isochore
> bin/lindna
>+bin/marscan
> bin/maskfeat
> bin/maskseq
> bin/matcher
>@@ -121,6 +123,7 @@
> bin/newseq
> bin/noreturn
> bin/notseq
>+bin/nrscope
> bin/nthseq
> bin/octanol
> bin/oddcomp
>@@ -156,6 +159,7 @@
> bin/restover
> bin/restrict
> bin/revseq
>+bin/scope
> bin/seealso
> bin/seqmatchall
> bin/seqret
>@@ -238,6 +242,7 @@
> share/EMBOSS/acd/descseq.acd
> share/EMBOSS/acd/diffseq.acd
> share/EMBOSS/acd/digest.acd
>+share/EMBOSS/acd/domainer.acd
> share/EMBOSS/acd/dotmatcher.acd
> share/EMBOSS/acd/dotpath.acd
> share/EMBOSS/acd/dottup.acd
>@@ -267,6 +272,7 @@
> share/EMBOSS/acd/infoseq.acd
> share/EMBOSS/acd/isochore.acd
> share/EMBOSS/acd/lindna.acd
>+share/EMBOSS/acd/marscan.acd
> share/EMBOSS/acd/maskfeat.acd
> share/EMBOSS/acd/maskseq.acd
> share/EMBOSS/acd/matcher.acd
>@@ -279,6 +285,7 @@
> share/EMBOSS/acd/newseq.acd
> share/EMBOSS/acd/noreturn.acd
> share/EMBOSS/acd/notseq.acd
>+share/EMBOSS/acd/nrscope.acd
> share/EMBOSS/acd/nthseq.acd
> share/EMBOSS/acd/octanol.acd
> share/EMBOSS/acd/oddcomp.acd
>@@ -338,6 +345,7 @@
> share/EMBOSS/acd/silent.acd
> share/EMBOSS/acd/simplesw.acd
> share/EMBOSS/acd/splitter.acd
>+share/EMBOSS/acd/stamps.acd
> share/EMBOSS/acd/stretcher.acd
> share/EMBOSS/acd/stssearch.acd
> share/EMBOSS/acd/supermatcher.acd
>@@ -789,6 +797,7 @@
> share/doc/EMBOSS/programs/html/dnapenny.html
> share/doc/EMBOSS/programs/html/dollop.html
> share/doc/EMBOSS/programs/html/dolpenny.html
>+share/doc/EMBOSS/programs/html/domainer.html
> share/doc/EMBOSS/programs/html/dotmatcher.html
> share/doc/EMBOSS/programs/html/dotmatcher0.gif
> share/doc/EMBOSS/programs/html/dotpath.html
>@@ -854,6 +863,7 @@
> share/doc/EMBOSS/programs/html/isochore0.gif
> share/doc/EMBOSS/programs/html/kitsch.html
> share/doc/EMBOSS/programs/html/lindna.html
>+share/doc/EMBOSS/programs/html/marscan.html
> share/doc/EMBOSS/programs/html/maskfeat.html
> share/doc/EMBOSS/programs/html/maskseq.html
> share/doc/EMBOSS/programs/html/matcher.html
>@@ -873,6 +883,7 @@
> share/doc/EMBOSS/programs/html/newseq.html
> share/doc/EMBOSS/programs/html/noreturn.html
> share/doc/EMBOSS/programs/html/notseq.html
>+share/doc/EMBOSS/programs/html/nrscope.html
> share/doc/EMBOSS/programs/html/nthseq.html
> share/doc/EMBOSS/programs/html/octanol.html
> share/doc/EMBOSS/programs/html/octanol0.gif
>@@ -919,6 +930,7 @@
> share/doc/EMBOSS/programs/html/protein_sequence_composition_group.html
> share/doc/EMBOSS/programs/html/protein_sequence_features_group.html
> share/doc/EMBOSS/programs/html/protein_sequence_properties_group.html
>+share/doc/EMBOSS/programs/html/protein_structure_group.html
> share/doc/EMBOSS/programs/html/pscan.html
> share/doc/EMBOSS/programs/html/re_group.html
> share/doc/EMBOSS/programs/html/rebaseextract.html
>@@ -928,8 +940,11 @@
> share/doc/EMBOSS/programs/html/remap.html
> share/doc/EMBOSS/programs/html/repeats_group.html
> share/doc/EMBOSS/programs/html/restml.html
>+share/doc/EMBOSS/programs/html/restover.html
> share/doc/EMBOSS/programs/html/restrict.html
>+share/doc/EMBOSS/programs/html/restriction_enzymes_group.html
> share/doc/EMBOSS/programs/html/revseq.html
>+share/doc/EMBOSS/programs/html/scope.html
> share/doc/EMBOSS/programs/html/secondary_structure_group.html
> share/doc/EMBOSS/programs/html/seealso.html
> share/doc/EMBOSS/programs/html/seqboot.html
>@@ -1022,6 +1037,7 @@
> share/doc/EMBOSS/programs/text/dnapenny.txt
> share/doc/EMBOSS/programs/text/dollop.txt
> share/doc/EMBOSS/programs/text/dolpenny.txt
>+share/doc/EMBOSS/programs/text/domainer.txt
> share/doc/EMBOSS/programs/text/dotmatcher.txt
> share/doc/EMBOSS/programs/text/dotpath.txt
> share/doc/EMBOSS/programs/text/dottup.txt
>@@ -1077,6 +1093,7 @@
> share/doc/EMBOSS/programs/text/isochore.txt
> share/doc/EMBOSS/programs/text/kitsch.txt
> share/doc/EMBOSS/programs/text/lindna.txt
>+share/doc/EMBOSS/programs/text/marscan.txt
> share/doc/EMBOSS/programs/text/maskfeat.txt
> share/doc/EMBOSS/programs/text/maskseq.txt
> share/doc/EMBOSS/programs/text/matcher.txt
>@@ -1092,6 +1109,7 @@
> share/doc/EMBOSS/programs/text/newseq.txt
> share/doc/EMBOSS/programs/text/noreturn.txt
> share/doc/EMBOSS/programs/text/notseq.txt
>+share/doc/EMBOSS/programs/text/nrscope.txt
> share/doc/EMBOSS/programs/text/nthseq.txt
> share/doc/EMBOSS/programs/text/octanol.txt
> share/doc/EMBOSS/programs/text/oddcomp.txt
>@@ -1127,8 +1145,10 @@
> share/doc/EMBOSS/programs/text/redata.txt
> share/doc/EMBOSS/programs/text/remap.txt
> share/doc/EMBOSS/programs/text/restml.txt
>+share/doc/EMBOSS/programs/text/restover.txt
> share/doc/EMBOSS/programs/text/restrict.txt
> share/doc/EMBOSS/programs/text/revseq.txt
>+share/doc/EMBOSS/programs/text/scope.txt
> share/doc/EMBOSS/programs/text/seealso.txt
> share/doc/EMBOSS/programs/text/seqboot.txt
> share/doc/EMBOSS/programs/text/seqmatchall.txt

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Attachments on bug 25228: 13196