[med-svn] r5869 - trunk/packages/vienna-rna/trunk/debian/patches
Alexandre Mestiashvili
malex-guest at alioth.debian.org
Thu Feb 3 12:19:57 UTC 2011
Author: malex-guest
Date: 2011-02-03 12:19:48 +0000 (Thu, 03 Feb 2011)
New Revision: 5869
Added:
trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch
Removed:
trunk/packages/vienna-rna/trunk/debian/patches/fix_cluster_manpages.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_install_relative_path.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_missing_header.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_modules_path.patch
trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch
trunk/packages/vienna-rna/trunk/debian/patches/lintian_messages01.patch
trunk/packages/vienna-rna/trunk/debian/patches/missing_x11.patch
Modified:
trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
trunk/packages/vienna-rna/trunk/debian/patches/series
Log:
some cleanup in patches , some are merged , others renamed.
Copied: trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch (from rev 5868, trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_modules_path.patch)
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -0,0 +1,12 @@
+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
+@@ -3,6 +3,7 @@
+ WriteMakefile(
+ MAKEFILE => "Makefile.perl",
+ NAME => "RNA",
++ INSTALLDIRS => "vendor",
+ LIBS => ["-lm"],
+ MYEXTLIB => "../lib/libRNA.a",
+ PM => {"RNA.pm", '$(INST_LIBDIR)/RNA.pm'},
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/fix_cluster_manpages.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_cluster_manpages.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_cluster_manpages.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,20 +0,0 @@
-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
-@@ -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
-@@ -1,4 +1,4 @@
--.TH ANALYSESEQS l
-+.TH "ANALYSESEQS" "1"
- .ER
- .SH NAME
- AnalyseSeqs \- Analyse a set of sequences of common length
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/fix_install_relative_path.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_install_relative_path.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_install_relative_path.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,13 +0,0 @@
-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
-@@ -189,7 +189,7 @@
- top_build_prefix = @top_build_prefix@
- top_builddir = @top_builddir@
- top_srcdir = @top_srcdir@
--SUBDIRS = g2-0.70 src man
-+SUBDIRS = src man
- all: config.h
- $(MAKE) $(AM_MAKEFLAGS) all-recursive
-
Copied: trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch (from rev 5868, trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch)
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -0,0 +1,202 @@
+fixing manual pages
+--- 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"
++.TH "RNALFOLD" "1" "1.5" "Ivo Hofacker" "ViennaRNA"
+ .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
+@@ -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
+@@ -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"
+--- 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"
++.TH "RNACOFOLD" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
+ .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
+@@ -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"
+--- 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
+--- 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"
++.TH "RNAEVAL" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .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
+@@ -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"
+@@ -89,12 +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)
+-| (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"
++.TH "RNAHEAT" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .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
+@@ -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"
+--- 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"
++.TH "RNAPDIST" "1" "" "Ivo Hofacker" "Vienna RNA"
+ .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
+@@ -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
+--- 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"
++.TH "RNAPLFOLD" "1" "1.8" "Stephan Bernhart" "ViennaRNA"
+ .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
+@@ -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"
+--- ViennaRNA-1.8.4.orig/man/RNAsubopt.1.in
++++ ViennaRNA-1.8.4/man/RNAsubopt.1.in
+@@ -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"
+--- 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"
++.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
+--- 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
+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
+@@ -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
+@@ -1,4 +1,4 @@
+-.TH ANALYSESEQS l
++.TH "ANALYSESEQS" "1"
+ .ER
+ .SH NAME
+ AnalyseSeqs \- Analyse a set of sequences of common length
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_manual_pages.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,182 +0,0 @@
-fixing manual pages
---- 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"
-+.TH "RNALFOLD" "1" "1.5" "Ivo Hofacker" "ViennaRNA"
- .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
-@@ -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
-@@ -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"
---- 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"
-+.TH "RNACOFOLD" "1" "1.6" "Ivo Hofacker" "ViennaRNA"
- .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
-@@ -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"
---- 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
---- 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"
-+.TH "RNAEVAL" "1" "" "Ivo Hofacker" "Vienna RNA"
- .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
-@@ -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"
-@@ -89,12 +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)
--| (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"
-+.TH "RNAHEAT" "1" "" "Ivo Hofacker" "Vienna RNA"
- .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
-@@ -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"
---- 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"
-+.TH "RNAPDIST" "1" "" "Ivo Hofacker" "Vienna RNA"
- .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
-@@ -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
---- 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"
-+.TH "RNAPLFOLD" "1" "1.8" "Stephan Bernhart" "ViennaRNA"
- .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
-@@ -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"
---- ViennaRNA-1.8.4.orig/man/RNAsubopt.1.in
-+++ ViennaRNA-1.8.4/man/RNAsubopt.1.in
-@@ -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"
---- 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"
-+.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
---- 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
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/fix_missing_header.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_missing_header.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_missing_header.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,12 +0,0 @@
-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
-@@ -6,6 +6,7 @@
- #include <iostream>
- #include <string>
- #include <sstream>
-+#include <cstdio>
-
- #ifndef WIN32
- #include "config.h"
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_modules_path.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_modules_path.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_modules_path.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,12 +0,0 @@
-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
-@@ -3,6 +3,7 @@
- WriteMakefile(
- MAKEFILE => "Makefile.perl",
- NAME => "RNA",
-+ INSTALLDIRS => "vendor",
- LIBS => ["-lm"],
- MYEXTLIB => "../lib/libRNA.a",
- PM => {"RNA.pm", '$(INST_LIBDIR)/RNA.pm'},
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_perl_path.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,20 +0,0 @@
-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)
Copied: trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch (from rev 5868, trunk/packages/vienna-rna/trunk/debian/patches/lintian_messages01.patch)
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch (rev 0)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -0,0 +1,17 @@
+scripts shuould be stripped off .pl extensions and are copied to /usr/bin via debian/rules
+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
+@@ -468,7 +468,7 @@
+
+ info-am:
+
+-install-data-am: install-pkgbinPROGRAMS install-pkgbinSCRIPTS
++#install-data-am: install-pkgbinPROGRAMS install-pkgbinSCRIPTS
+
+ install-dvi: install-dvi-am
+
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/lintian_messages01.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/lintian_messages01.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/lintian_messages01.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,13 +0,0 @@
-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
-@@ -468,7 +468,7 @@
-
- info-am:
-
--install-data-am: install-pkgbinPROGRAMS install-pkgbinSCRIPTS
-+#install-data-am: install-pkgbinPROGRAMS install-pkgbinSCRIPTS
-
- install-dvi: install-dvi-am
-
Deleted: trunk/packages/vienna-rna/trunk/debian/patches/missing_x11.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/missing_x11.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/missing_x11.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,13 +0,0 @@
-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
-@@ -102,7 +102,7 @@
- INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
- LDFLAGS = @LDFLAGS@
- LIBOBJS = @LIBOBJS@
--LIBS = @LIBS@
-+LIBS = @LIBS@ -lm -lX11 -lgd
- LTLIBOBJS = @LTLIBOBJS@
- MAKEINFO = @MAKEINFO@
- MKDIR_P = @MKDIR_P@
Modified: trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,4 +1,4 @@
-Readseq is a different packages which a standalone package. So we don't need to build it as a part of vienna-rna.
+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
Modified: trunk/packages/vienna-rna/trunk/debian/patches/series
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/series 2011-02-03 09:22:28 UTC (rev 5868)
+++ trunk/packages/vienna-rna/trunk/debian/patches/series 2011-02-03 12:19:48 UTC (rev 5869)
@@ -1,8 +1,7 @@
-fix_cluster_manpages.patch
-lintian_messages01.patch
+fix_utils_make_install.patch
readseq_exclude.patch
-fix_manual_pages.patch
-fix_perl_modules_path.patch
+fix_manpages.patch
+debian_perl_modules_path.patch
02_RNAforester_missing_libs.patch
01_RNAforester_missing_header.patch
do_not_configure_g2-0.70.patch
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