[med-svn] r5766 - trunk/packages/vienna-rna/trunk/debian/patches

Alexandre Mestiashvili malex-guest at alioth.debian.org
Sat Jan 29 20:41:20 UTC 2011 

Author: malex-guest
Date: 2011-01-29 20:41:20 +0000 (Sat, 29 Jan 2011)
New Revision: 5766

Added:
   trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch
   trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch
   trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
Modified:
   trunk/packages/vienna-rna/trunk/debian/patches/series
Log:
perl


Added: trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch	                        (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch	2011-01-29 20:41:20 UTC (rev 5766)
@@ -0,0 +1,207 @@
+fixing manual pages
+Index: viennarna-1.8.4/man/RNALfold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNALfold.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNALfold.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNALFOLD" "l" "1.5" "Ivo Hofacker" "ViennaRNA"
++.TH "RNALFOLD" "1" "1.5" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNALfold \- calculate locally stable secondary structures of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAaliduplex.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAaliduplex.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAaliduplex.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,4 +1,4 @@
+-.TH "RNAaliduplex" "l" "0.0.1" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAaliduplex" "1" "0.0.1" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ .LP 
+ RNAaliduplex \- Predict conserved RNA-RNA interactions between two alignments
+Index: viennarna-1.8.4/man/RNAalifold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAalifold.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAalifold.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,6 +1,6 @@
+ .\" -*-nroff-*-
+ .\" .ER
+-.TH "RNAalifold" "l" "1.8" "Ivo Hofacker" "ViennaRNA"
++.TH "RNAalifold" "1" "1.8" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAalifold \- calculate secondary structures for a set of aligned RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAcofold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAcofold.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAcofold.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNACOFOLD" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
++.TH "RNACOFOLD" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAcofold \- calculate secondary structures of two RNAs with dimerization
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAdistance.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAdistance.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAdistance.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNADISTANCE" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNADISTANCE" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAdistance \- calculate distances between RNA secondary structures
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAduplex.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAduplex.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAduplex.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,4 +1,4 @@
+-.TH "RNAduplex" "l" "0.0.1" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAduplex" "1" "0.0.1" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ .LP 
+ RNAduplex \- Compute the structure upon hybridization of two RNA strands
+Index: viennarna-1.8.4/man/RNAeval.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAeval.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAeval.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAEVAL" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAEVAL" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAEVAL \- calculate energy of RNA sequences on given secondary structure
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAfold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAfold.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAfold.1.in	2011-01-29 18:36:40.000000000 +0100
+@@ -1,6 +1,6 @@
+ .\" -*-nroff-*-
+ .\" .ER
+-.TH "RNAFOLD" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
++.TH "RNAFOLD" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAfold \- calculate secondary structures of RNAs
+ .SH "SYNOPSIS"
+@@ -89,7 +89,7 @@
+ Calculate structures subject to constraints.
+ The program reads first the sequence, then a string containing constraints
+ on the structure encoded with the symbols:
+-. (no constraint for this base)
++\. (no constraint for this base)
+ | (the corresponding base has to be paired
+ x (the base is unpaired)
+ < (base i is paired with a base j>i)
+Index: viennarna-1.8.4/man/RNAheat.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAheat.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAheat.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAHEAT" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAHEAT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAheat \- calculate specific heat of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAinverse.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAinverse.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAinverse.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAINVERSE" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAINVERSE" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAINVERSE \- find RNA sequences with given secondary structure
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNApaln.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNApaln.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNApaln.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAPDIST" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNApaln \- RNA alignment based on sequence base pairing propensities
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNApdist.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNApdist.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNApdist.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAPDIST" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNApdist \- calculate distances between thermodynamic RNA secondary
+ structures ensembles
+Index: viennarna-1.8.4/man/RNAplfold.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAplfold.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAplfold.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPLFOLD" "l" "1.8" "Stephan Bernhart" "ViennaRNA"
++.TH "RNAPLFOLD" "1" "1.8" "Stephan Bernhart" "ViennaRNA"
+ .SH "NAME"
+ RNAplfold \- calculate locally stable secondary structure - pair probabilities 
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAplot.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAplot.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAplot.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAPLOT" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNAPLOT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAplot \- Draw RNA Secondary Structures
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAsubopt.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAsubopt.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAsubopt.1.in	2011-01-29 18:32:45.000000000 +0100
+@@ -1,6 +1,6 @@
+ \" -*-nroff-*-
+ .\" .ER
+-.TH "RNASUBOPT" "l" "" "Ivo Hofacker" "Vienna RNA"
++.TH "RNASUBOPT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .SH "NAME"
+ RNAsubopt \- calculate suboptimal secondary structures of RNAs
+ .SH "SYNOPSIS"
+Index: viennarna-1.8.4/man/RNAup.1.in
+===================================================================
+--- viennarna-1.8.4.orig/man/RNAup.1.in	2011-01-29 18:32:19.000000000 +0100
++++ viennarna-1.8.4/man/RNAup.1.in	2011-01-29 18:36:28.000000000 +0100
+@@ -1,5 +1,5 @@
+ .\" .ER
+-.TH "RNAUP" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
++.TH "RNAUP" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .SH "NAME"
+ RNAup \- calculates the thermodynamics of RNA-RNA interactions
+ .SH "SYNOPSIS"
+@@ -137,7 +137,7 @@
+ largest contribution to dG[i,j] = sum_kl dG[i,j;k,l] which is given in the
+ output file: therefore dG[i,j;k,l] <= dG[i,j].
+ 
+-'....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8'
++\'....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8'
+ .br
+ > franz
+ .br
+Index: viennarna-1.8.4/RNAforester/man/RNAforester.1
+===================================================================
+--- viennarna-1.8.4.orig/RNAforester/man/RNAforester.1	2011-01-29 18:35:07.000000000 +0100
++++ viennarna-1.8.4/RNAforester/man/RNAforester.1	2011-01-29 18:35:37.000000000 +0100
+@@ -1,4 +1,4 @@
+-.TH RNAForester 1.4 "June 2004"
++.TH "RNAForester" "1" "1.4" "June 2004"
+ .SH NAME
+ RNAforester \- compare RNA secondary structures via forest alignment
+ .SH SYNOPSIS
+

Added: trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch	                        (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch	2011-01-29 20:41:20 UTC (rev 5766)
@@ -0,0 +1,20 @@
+Index: viennarna-1.8.4/Perl/Makefile.perl
+===================================================================
+--- viennarna-1.8.4.orig/Perl/Makefile.perl	2011-01-29 21:30:44.000000000 +0100
++++ viennarna-1.8.4/Perl/Makefile.perl	2011-01-29 21:40:11.000000000 +0100
+@@ -78,13 +78,13 @@
+ PERLPREFIX = $(PREFIX)
+ SITEPREFIX = $(PREFIX)/local
+ VENDORPREFIX = $(PREFIX)
+-INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.10
++INSTALLPRIVLIB = $(PERLPREFIX)/share/perl5
+ DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
+ INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.10.0
+ DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
+ INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5
+ DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
+-INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.10
++INSTALLARCHLIB = $(PERLPREFIX)/lib/perl5
+ DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
+ INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.10.0
+ DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)

Added: trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch	                        (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch	2011-01-29 20:41:20 UTC (rev 5766)
@@ -0,0 +1,15 @@
+Readseq is a different packages which a standalone package. So we don't need to build it as a part of vienna-rna.
+Index: viennarna-1.8.4/Makefile.in
+===================================================================
+--- viennarna-1.8.4.orig/Makefile.in	2009-10-13 13:44:34.000000000 +0200
++++ viennarna-1.8.4/Makefile.in	2011-01-29 21:07:15.000000000 +0100
+@@ -234,7 +234,7 @@
+ 
+ #DIST_SUBDIRS = lib Progs man Utils AliFold H Perl Cluster
+ pkgdata_DATA = vienna13.par default.par
+-EXTRA_DIST = $(pkgdata_DATA) INSTALL.configure Readseq
++EXTRA_DIST = $(pkgdata_DATA) INSTALL.configure 
+ all: config.h
+ 	$(MAKE) $(AM_MAKEFLAGS) all-recursive
+ 
+

Modified: trunk/packages/vienna-rna/trunk/debian/patches/series
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/series	2011-01-29 20:37:09 UTC (rev 5765)
+++ trunk/packages/vienna-rna/trunk/debian/patches/series	2011-01-29 20:41:20 UTC (rev 5766)
@@ -1,2 +1,4 @@
 fix_install_relative_path.patch
-readseq-exclude.patch
+readseq_exclude.patch
+fix_manual_pages.patch
+fix_perl_path.patch

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