[med-svn] r5845 - trunk/packages/vienna-rna/trunk/debian/patches
Andreas Tille
tille at alioth.debian.org
Tue Feb 1 19:39:35 UTC 2011
Author: tille
Date: 2011-02-01 19:39:33 +0000 (Tue, 01 Feb 2011)
New Revision: 5845
Modified:
trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch
Log:
Fix texinfo properly
Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch 2011-02-01 19:31:39 UTC (rev 5844)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch 2011-02-01 19:39:33 UTC (rev 5845)
@@ -4,11 +4,14 @@
--- ViennaRNA-1.8.4.orig/man/RNAlib.texinfo
+++ ViennaRNA-1.8.4/man/RNAlib.texinfo
-@@ -3,6 +3,7 @@
+@@ -3,6 +3,10 @@
@set revision $Id: RNAlib.texinfo,v 1.25 2009/01/13 17:49:58 ivo Exp $
@setfilename RNAlib.info
@settitle Vienna RNA Package
+ at dircategory Science
++ at direntry
++* RNAlib: (RNAlib). Library for folding and comparing RNA secondary structures
++ at end direntry
@ifclear Version
@set Version 1.6
@end ifclear
Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch 2011-02-01 19:31:39 UTC (rev 5844)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch 2011-02-01 19:39:33 UTC (rev 5845)
@@ -1,8 +1,6 @@
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
+--- ViennaRNA-1.8.4.orig/man/RNALfold.1.in
++++ ViennaRNA-1.8.4/man/RNALfold.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNALFOLD" "l" "1.5" "Ivo Hofacker" "ViennaRNA"
@@ -10,20 +8,16 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAaliduplex.1.in
++++ ViennaRNA-1.8.4/man/RNAaliduplex.1.in
@@ -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
+--- ViennaRNA-1.8.4.orig/man/RNAalifold.1.in
++++ ViennaRNA-1.8.4/man/RNAalifold.1.in
@@ -1,6 +1,6 @@
.\" -*-nroff-*-
.\" .ER
@@ -32,10 +26,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAcofold.1.in
++++ ViennaRNA-1.8.4/man/RNAcofold.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNACOFOLD" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
@@ -43,10 +35,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAdistance.1.in
++++ ViennaRNA-1.8.4/man/RNAdistance.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNADISTANCE" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -54,20 +44,16 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAduplex.1.in
++++ ViennaRNA-1.8.4/man/RNAduplex.1.in
@@ -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
+--- ViennaRNA-1.8.4.orig/man/RNAeval.1.in
++++ ViennaRNA-1.8.4/man/RNAeval.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAEVAL" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -75,10 +61,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAfold.1.in
++++ ViennaRNA-1.8.4/man/RNAfold.1.in
@@ -1,6 +1,6 @@
.\" -*-nroff-*-
.\" .ER
@@ -87,19 +71,27 @@
.SH "NAME"
RNAfold \- calculate secondary structures of RNAs
.SH "SYNOPSIS"
-@@ -89,7 +89,7 @@
+@@ -89,12 +89,12 @@
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
+-| (the corresponding base has to be paired
+-x (the base is unpaired)
+-< (base i is paired with a base j>i)
+-> (base i is paired with a base j<i)
+-and matching brackets ( ) (base i pairs base j)
++ . (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)
++ > (base i is paired with a base j<i)
++ and matching brackets ( ) (base i pairs base j)
+ With the exception of "|", constraints will disallow all pairs conflicting
+ with the constraint. This is usually sufficient to enforce the constraint,
+ but occasionally a base may stay unpaired in spite of constraints. PF
+--- ViennaRNA-1.8.4.orig/man/RNAheat.1.in
++++ ViennaRNA-1.8.4/man/RNAheat.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAHEAT" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -107,10 +99,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAinverse.1.in
++++ ViennaRNA-1.8.4/man/RNAinverse.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAINVERSE" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -118,10 +108,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNApaln.1.in
++++ ViennaRNA-1.8.4/man/RNApaln.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -129,10 +117,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNApdist.1.in
++++ ViennaRNA-1.8.4/man/RNApdist.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -140,10 +126,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAplfold.1.in
++++ ViennaRNA-1.8.4/man/RNAplfold.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPLFOLD" "l" "1.8" "Stephan Bernhart" "ViennaRNA"
@@ -151,10 +135,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAplot.1.in
++++ ViennaRNA-1.8.4/man/RNAplot.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPLOT" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -162,10 +144,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAsubopt.1.in
++++ ViennaRNA-1.8.4/man/RNAsubopt.1.in
@@ -1,6 +1,6 @@
\" -*-nroff-*-
.\" .ER
@@ -174,10 +154,8 @@
.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
+--- ViennaRNA-1.8.4.orig/man/RNAup.1.in
++++ ViennaRNA-1.8.4/man/RNAup.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAUP" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
@@ -194,14 +172,11 @@
.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
+--- ViennaRNA-1.8.4.orig/RNAforester/man/RNAforester.1
++++ ViennaRNA-1.8.4/RNAforester/man/RNAforester.1
@@ -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
-
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