[med-svn] r5960 - trunk/packages/vienna-rna/trunk/debian/patches
Alexandre Mestiashvili
malex-guest at alioth.debian.org
Sat Feb 12 16:04:31 UTC 2011
Author: malex-guest
Date: 2011-02-12 16:04:28 +0000 (Sat, 12 Feb 2011)
New Revision: 5960
Modified:
trunk/packages/vienna-rna/trunk/debian/patches/01_RNAforester_missing_header.patch
trunk/packages/vienna-rna/trunk/debian/patches/02_RNAforester_missing_libs.patch
trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch
trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch
trunk/packages/vienna-rna/trunk/debian/patches/naview_copyright.patch
trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
Log:
quilt refresh -p ab --no-timestamps --no-index
Modified: trunk/packages/vienna-rna/trunk/debian/patches/01_RNAforester_missing_header.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/01_RNAforester_missing_header.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/01_RNAforester_missing_header.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -1,7 +1,5 @@
-Index: vienna-rna-1.8.4/RNAforester/src/rnafuncs.cpp
-===================================================================
---- vienna-rna-1.8.4.orig/RNAforester/src/rnafuncs.cpp 2011-01-30 15:36:42.000000000 +0000
-+++ vienna-rna-1.8.4/RNAforester/src/rnafuncs.cpp 2011-01-30 15:37:08.000000000 +0000
+--- a/RNAforester/src/rnafuncs.cpp
++++ b/RNAforester/src/rnafuncs.cpp
@@ -6,6 +6,7 @@
#include <iostream>
#include <string>
Modified: trunk/packages/vienna-rna/trunk/debian/patches/02_RNAforester_missing_libs.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/02_RNAforester_missing_libs.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/02_RNAforester_missing_libs.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -1,7 +1,5 @@
-Index: vienna-rna-1.8.4/RNAforester/src/Makefile.in
-===================================================================
---- vienna-rna-1.8.4.orig/RNAforester/src/Makefile.in 2011-01-30 16:32:29.000000000 +0000
-+++ vienna-rna-1.8.4/RNAforester/src/Makefile.in 2011-01-30 16:33:25.000000000 +0000
+--- a/RNAforester/src/Makefile.in
++++ b/RNAforester/src/Makefile.in
@@ -102,7 +102,7 @@
INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
LDFLAGS = @LDFLAGS@
Modified: trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -1,7 +1,5 @@
-Index: viennarna-1.8.4/Perl/Makefile.PL
-===================================================================
---- viennarna-1.8.4.orig/Perl/Makefile.PL 2011-01-29 22:11:51.000000000 +0100
-+++ viennarna-1.8.4/Perl/Makefile.PL 2011-01-29 22:12:14.000000000 +0100
+--- a/Perl/Makefile.PL
++++ b/Perl/Makefile.PL
@@ -3,6 +3,7 @@
WriteMakefile(
MAKEFILE => "Makefile.perl",
Modified: trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -3,8 +3,8 @@
Description: The g2 library is just packaged for Debian and because we link
against this there is no need to even configure in this directory.
---- ViennaRNA-1.8.4.orig/RNAforester/configure
-+++ ViennaRNA-1.8.4/RNAforester/configure
+--- a/RNAforester/configure
++++ b/RNAforester/configure
@@ -748,7 +748,7 @@
CC
CFLAGS
@@ -43,11 +43,8 @@
ac_config_files="$ac_config_files Makefile src/Makefile man/Makefile"
-
-Index: ViennaRNA-1.8.4/RNAforester/Makefile.in
-===================================================================
---- ViennaRNA-1.8.4.orig/RNAforester/Makefile.in 2011-01-28 23:39:23.740182140 +0100
-+++ ViennaRNA-1.8.4/RNAforester/Makefile.in 2011-01-28 23:39:44.556182444 +0100
+--- a/RNAforester/Makefile.in
++++ b/RNAforester/Makefile.in
@@ -189,7 +189,7 @@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -2,8 +2,8 @@
Date: 2011-01-30
Description: texinfo needs "@directory Section" statement
---- ViennaRNA-1.8.4.orig/man/RNAlib.texinfo
-+++ ViennaRNA-1.8.4/man/RNAlib.texinfo
+--- a/man/RNAlib.texinfo
++++ b/man/RNAlib.texinfo
@@ -3,6 +3,10 @@
@set revision $Id: RNAlib.texinfo,v 1.25 2009/01/13 17:49:58 ivo Exp $
@setfilename RNAlib.info
Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -1,6 +1,6 @@
fixing manual pages
---- ViennaRNA-1.8.4.orig/man/RNALfold.1.in
-+++ ViennaRNA-1.8.4/man/RNALfold.1.in
+--- a/man/RNALfold.1.in
++++ b/man/RNALfold.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNALFOLD" "l" "1.5" "Ivo Hofacker" "ViennaRNA"
@@ -8,16 +8,16 @@
.SH "NAME"
RNALfold \- calculate locally stable secondary structures of RNAs
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAaliduplex.1.in
-+++ ViennaRNA-1.8.4/man/RNAaliduplex.1.in
+--- a/man/RNAaliduplex.1.in
++++ b/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
---- ViennaRNA-1.8.4.orig/man/RNAalifold.1.in
-+++ ViennaRNA-1.8.4/man/RNAalifold.1.in
+--- a/man/RNAalifold.1.in
++++ b/man/RNAalifold.1.in
@@ -1,6 +1,6 @@
.\" -*-nroff-*-
.\" .ER
@@ -26,8 +26,8 @@
.SH "NAME"
RNAalifold \- calculate secondary structures for a set of aligned RNAs
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAcofold.1.in
-+++ ViennaRNA-1.8.4/man/RNAcofold.1.in
+--- a/man/RNAcofold.1.in
++++ b/man/RNAcofold.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNACOFOLD" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
@@ -35,8 +35,8 @@
.SH "NAME"
RNAcofold \- calculate secondary structures of two RNAs with dimerization
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAdistance.1.in
-+++ ViennaRNA-1.8.4/man/RNAdistance.1.in
+--- a/man/RNAdistance.1.in
++++ b/man/RNAdistance.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNADISTANCE" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -44,16 +44,16 @@
.SH "NAME"
RNAdistance \- calculate distances between RNA secondary structures
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAduplex.1.in
-+++ ViennaRNA-1.8.4/man/RNAduplex.1.in
+--- a/man/RNAduplex.1.in
++++ b/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
---- ViennaRNA-1.8.4.orig/man/RNAeval.1.in
-+++ ViennaRNA-1.8.4/man/RNAeval.1.in
+--- a/man/RNAeval.1.in
++++ b/man/RNAeval.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAEVAL" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -61,8 +61,8 @@
.SH "NAME"
RNAEVAL \- calculate energy of RNA sequences on given secondary structure
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAfold.1.in
-+++ ViennaRNA-1.8.4/man/RNAfold.1.in
+--- a/man/RNAfold.1.in
++++ b/man/RNAfold.1.in
@@ -1,6 +1,6 @@
.\" -*-nroff-*-
.\" .ER
@@ -90,8 +90,8 @@
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
+--- a/man/RNAheat.1.in
++++ b/man/RNAheat.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAHEAT" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -99,8 +99,8 @@
.SH "NAME"
RNAheat \- calculate specific heat of RNAs
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAinverse.1.in
-+++ ViennaRNA-1.8.4/man/RNAinverse.1.in
+--- a/man/RNAinverse.1.in
++++ b/man/RNAinverse.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAINVERSE" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -108,8 +108,8 @@
.SH "NAME"
RNAINVERSE \- find RNA sequences with given secondary structure
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNApaln.1.in
-+++ ViennaRNA-1.8.4/man/RNApaln.1.in
+--- a/man/RNApaln.1.in
++++ b/man/RNApaln.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -117,8 +117,8 @@
.SH "NAME"
RNApaln \- RNA alignment based on sequence base pairing propensities
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNApdist.1.in
-+++ ViennaRNA-1.8.4/man/RNApdist.1.in
+--- a/man/RNApdist.1.in
++++ b/man/RNApdist.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPDIST" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -126,8 +126,8 @@
.SH "NAME"
RNApdist \- calculate distances between thermodynamic RNA secondary
structures ensembles
---- ViennaRNA-1.8.4.orig/man/RNAplfold.1.in
-+++ ViennaRNA-1.8.4/man/RNAplfold.1.in
+--- a/man/RNAplfold.1.in
++++ b/man/RNAplfold.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPLFOLD" "l" "1.8" "Stephan Bernhart" "ViennaRNA"
@@ -135,8 +135,8 @@
.SH "NAME"
RNAplfold \- calculate locally stable secondary structure - pair probabilities
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAplot.1.in
-+++ ViennaRNA-1.8.4/man/RNAplot.1.in
+--- a/man/RNAplot.1.in
++++ b/man/RNAplot.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAPLOT" "l" "" "Ivo Hofacker" "Vienna RNA"
@@ -144,8 +144,8 @@
.SH "NAME"
RNAplot \- Draw RNA Secondary Structures
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAsubopt.1.in
-+++ ViennaRNA-1.8.4/man/RNAsubopt.1.in
+--- a/man/RNAsubopt.1.in
++++ b/man/RNAsubopt.1.in
@@ -1,6 +1,6 @@
\" -*-nroff-*-
.\" .ER
@@ -154,8 +154,8 @@
.SH "NAME"
RNAsubopt \- calculate suboptimal secondary structures of RNAs
.SH "SYNOPSIS"
---- ViennaRNA-1.8.4.orig/man/RNAup.1.in
-+++ ViennaRNA-1.8.4/man/RNAup.1.in
+--- a/man/RNAup.1.in
++++ b/man/RNAup.1.in
@@ -1,5 +1,5 @@
.\" .ER
-.TH "RNAUP" "l" "1.6" "Ivo Hofacker" "ViennaRNA"
@@ -172,28 +172,24 @@
.br
> franz
.br
---- ViennaRNA-1.8.4.orig/RNAforester/man/RNAforester.1
-+++ ViennaRNA-1.8.4/RNAforester/man/RNAforester.1
+--- a/RNAforester/man/RNAforester.1
++++ b/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
-Index: vienna-rna-1.8.4/Cluster/AnalyseDists.1
-===================================================================
---- vienna-rna-1.8.4.orig/Cluster/AnalyseDists.1 2011-02-02 20:19:51.000000000 +0100
-+++ vienna-rna-1.8.4/Cluster/AnalyseDists.1 2011-02-02 20:21:22.000000000 +0100
+--- a/Cluster/AnalyseDists.1
++++ b/Cluster/AnalyseDists.1
@@ -1,4 +1,4 @@
-.TH ANALYSEDISTS l
+.TH "ANALYSEDISTS" "1"
.ER
.SH NAME
AnalyseDists \- Analyse a distance matrix
-Index: vienna-rna-1.8.4/Cluster/AnalyseSeqs.1
-===================================================================
---- vienna-rna-1.8.4.orig/Cluster/AnalyseSeqs.1 2011-02-02 20:21:35.000000000 +0100
-+++ vienna-rna-1.8.4/Cluster/AnalyseSeqs.1 2011-02-02 20:21:51.000000000 +0100
+--- a/Cluster/AnalyseSeqs.1
++++ b/Cluster/AnalyseSeqs.1
@@ -1,4 +1,4 @@
-.TH ANALYSESEQS l
+.TH "ANALYSESEQS" "1"
Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -2,10 +2,8 @@
binaries are copied by dh_install
so I commented out this target to avoid installation by Makefile processing.
-Index: viennarna-1.8.4/Utils/Makefile.in
-===================================================================
---- viennarna-1.8.4.orig/Utils/Makefile.in 2011-01-29 23:09:24.000000000 +0100
-+++ viennarna-1.8.4/Utils/Makefile.in 2011-01-29 23:09:37.000000000 +0100
+--- a/Utils/Makefile.in
++++ b/Utils/Makefile.in
@@ -468,7 +468,7 @@
info-am:
Modified: trunk/packages/vienna-rna/trunk/debian/patches/naview_copyright.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/naview_copyright.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/naview_copyright.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -1,8 +1,6 @@
Copyright change to GPL2 for lib/naview.c Kindly granted by auhtor Robert E Bruccoleri.
-Index: ViennaRNA-1.8.4/lib/naview.c
-===================================================================
---- ViennaRNA-1.8.4.orig/lib/naview.c 2011-02-08 10:04:31.000000000 +0100
-+++ ViennaRNA-1.8.4/lib/naview.c 2011-02-08 10:09:11.000000000 +0100
+--- a/lib/naview.c
++++ b/lib/naview.c
@@ -3,12 +3,26 @@
* secondary structure.
*
Modified: trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch 2011-02-12 15:52:48 UTC (rev 5959)
+++ trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch 2011-02-12 16:04:28 UTC (rev 5960)
@@ -1,8 +1,6 @@
Readseq is a different 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
+--- a/Makefile.in
++++ b/Makefile.in
@@ -234,7 +234,7 @@
#DIST_SUBDIRS = lib Progs man Utils AliFold H Perl Cluster
@@ -12,4 +10,3 @@
all: config.h
$(MAKE) $(AM_MAKEFLAGS) all-recursive
-
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