[med-svn] r5962 - trunk/packages/vienna-rna/trunk/debian/patches

Alexandre Mestiashvili malex-guest at alioth.debian.org
Sat Feb 12 18:33:39 UTC 2011 

Author: malex-guest
Date: 2011-02-12 18:33:37 +0000 (Sat, 12 Feb 2011)
New Revision: 5962

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/readseq_exclude.patch
Log:
removed index&timestamps ,added DEP3 header .


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 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/01_RNAforester_missing_header.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,5 +1,10 @@
---- a/RNAforester/src/rnafuncs.cpp
-+++ b/RNAforester/src/rnafuncs.cpp
+Description: Add missing header.
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Applied-Upstream: version 1.8.5 .
+Last-Update: 2011-02-12
+ 
+--- ViennaRNA-1.8.4.orig/RNAforester/src/rnafuncs.cpp
++++ ViennaRNA-1.8.4/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 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/02_RNAforester_missing_libs.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,5 +1,10 @@
---- a/RNAforester/src/Makefile.in
-+++ b/RNAforester/src/Makefile.in
+Description: Fix Makefile - missing libraries .
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Applied-Upstream: version 1.8.5
+Last-Update: 2011-02-12
+
+--- ViennaRNA-1.8.4.orig/RNAforester/src/Makefile.in
++++ ViennaRNA-1.8.4/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 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/debian_perl_modules_path.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,5 +1,8 @@
---- a/Perl/Makefile.PL
-+++ b/Perl/Makefile.PL
+Description: Place perl modules to vendor location .
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2011-02-12
+--- ViennaRNA-1.8.4.orig/Perl/Makefile.PL
++++ ViennaRNA-1.8.4/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 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/do_not_configure_g2-0.70.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,10 +1,11 @@
-Author: Andreas Tille <tille at debian.org>
-Date: 2011-01-31
 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.
+Author: Andreas Tille <tille at debian.org>
+Applied-Upstream: 1.8.5 .
+Last-Update: 2011-01-31
 
---- a/RNAforester/configure
-+++ b/RNAforester/configure
+--- ViennaRNA-1.8.4.orig/RNAforester/configure
++++ ViennaRNA-1.8.4/RNAforester/configure
 @@ -748,7 +748,7 @@
  CC
  CFLAGS
@@ -43,8 +44,8 @@
  
  ac_config_files="$ac_config_files Makefile src/Makefile man/Makefile"
  
---- a/RNAforester/Makefile.in
-+++ b/RNAforester/Makefile.in
+--- ViennaRNA-1.8.4.orig/RNAforester/Makefile.in
++++ ViennaRNA-1.8.4/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 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_RNAlib_info.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,6 +1,6 @@
+Description: texinfo needs "@directory Section" statement
 Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
-Date: 2011-01-30
-Description: texinfo needs "@directory Section" statement
+Last-Update: 2011-01-30
 
 --- a/man/RNAlib.texinfo
 +++ b/man/RNAlib.texinfo

Modified: trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch	2011-02-12 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_manpages.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,6 +1,10 @@
-fixing manual pages
---- a/man/RNALfold.1.in
-+++ b/man/RNALfold.1.in
+Description: fixing manual pages typo - replacing l->1 .
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Applied-Upstream: expected to be applied in version 1.8.5.
+Last-Update: 2011-02-12
+
+--- 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"
@@ -8,16 +12,16 @@
  .SH "NAME"
  RNALfold \- calculate locally stable secondary structures of RNAs
  .SH "SYNOPSIS"
---- a/man/RNAaliduplex.1.in
-+++ b/man/RNAaliduplex.1.in
+--- 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
---- a/man/RNAalifold.1.in
-+++ b/man/RNAalifold.1.in
+--- ViennaRNA-1.8.4.orig/man/RNAalifold.1.in
++++ ViennaRNA-1.8.4/man/RNAalifold.1.in
 @@ -1,6 +1,6 @@
  .\" -*-nroff-*-
  .\" .ER
@@ -26,8 +30,8 @@
  .SH "NAME"
  RNAalifold \- calculate secondary structures for a set of aligned RNAs
  .SH "SYNOPSIS"
---- a/man/RNAcofold.1.in
-+++ b/man/RNAcofold.1.in
+--- 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"
@@ -35,8 +39,8 @@
  .SH "NAME"
  RNAcofold \- calculate secondary structures of two RNAs with dimerization
  .SH "SYNOPSIS"
---- a/man/RNAdistance.1.in
-+++ b/man/RNAdistance.1.in
+--- 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"
@@ -44,16 +48,16 @@
  .SH "NAME"
  RNAdistance \- calculate distances between RNA secondary structures
  .SH "SYNOPSIS"
---- a/man/RNAduplex.1.in
-+++ b/man/RNAduplex.1.in
+--- 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
---- a/man/RNAeval.1.in
-+++ b/man/RNAeval.1.in
+--- 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"
@@ -61,8 +65,8 @@
  .SH "NAME"
  RNAEVAL \- calculate energy of RNA sequences on given secondary structure
  .SH "SYNOPSIS"
---- a/man/RNAfold.1.in
-+++ b/man/RNAfold.1.in
+--- ViennaRNA-1.8.4.orig/man/RNAfold.1.in
++++ ViennaRNA-1.8.4/man/RNAfold.1.in
 @@ -1,6 +1,6 @@
  .\" -*-nroff-*-
  .\" .ER
@@ -90,8 +94,8 @@
  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
---- a/man/RNAheat.1.in
-+++ b/man/RNAheat.1.in
+--- 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"
@@ -99,8 +103,8 @@
  .SH "NAME"
  RNAheat \- calculate specific heat of RNAs
  .SH "SYNOPSIS"
---- a/man/RNAinverse.1.in
-+++ b/man/RNAinverse.1.in
+--- 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"
@@ -108,8 +112,8 @@
  .SH "NAME"
  RNAINVERSE \- find RNA sequences with given secondary structure
  .SH "SYNOPSIS"
---- a/man/RNApaln.1.in
-+++ b/man/RNApaln.1.in
+--- 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"
@@ -117,8 +121,8 @@
  .SH "NAME"
  RNApaln \- RNA alignment based on sequence base pairing propensities
  .SH "SYNOPSIS"
---- a/man/RNApdist.1.in
-+++ b/man/RNApdist.1.in
+--- 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"
@@ -126,8 +130,8 @@
  .SH "NAME"
  RNApdist \- calculate distances between thermodynamic RNA secondary
  structures ensembles
---- a/man/RNAplfold.1.in
-+++ b/man/RNAplfold.1.in
+--- 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"
@@ -135,8 +139,8 @@
  .SH "NAME"
  RNAplfold \- calculate locally stable secondary structure - pair probabilities 
  .SH "SYNOPSIS"
---- a/man/RNAplot.1.in
-+++ b/man/RNAplot.1.in
+--- 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"
@@ -144,8 +148,8 @@
  .SH "NAME"
  RNAplot \- Draw RNA Secondary Structures
  .SH "SYNOPSIS"
---- a/man/RNAsubopt.1.in
-+++ b/man/RNAsubopt.1.in
+--- ViennaRNA-1.8.4.orig/man/RNAsubopt.1.in
++++ ViennaRNA-1.8.4/man/RNAsubopt.1.in
 @@ -1,6 +1,6 @@
  \" -*-nroff-*-
  .\" .ER
@@ -154,8 +158,8 @@
  .SH "NAME"
  RNAsubopt \- calculate suboptimal secondary structures of RNAs
  .SH "SYNOPSIS"
---- a/man/RNAup.1.in
-+++ b/man/RNAup.1.in
+--- 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"
@@ -172,24 +176,24 @@
  .br
  > franz
  .br
---- a/RNAforester/man/RNAforester.1
-+++ b/RNAforester/man/RNAforester.1
+--- 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
---- a/Cluster/AnalyseDists.1
-+++ b/Cluster/AnalyseDists.1
+--- ViennaRNA-1.8.4.orig/Cluster/AnalyseDists.1
++++ ViennaRNA-1.8.4/Cluster/AnalyseDists.1
 @@ -1,4 +1,4 @@
 -.TH ANALYSEDISTS l
 +.TH "ANALYSEDISTS" "1"
  .ER
  .SH NAME
  AnalyseDists \- Analyse a distance matrix 
---- a/Cluster/AnalyseSeqs.1
-+++ b/Cluster/AnalyseSeqs.1
+--- ViennaRNA-1.8.4.orig/Cluster/AnalyseSeqs.1
++++ ViennaRNA-1.8.4/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 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/fix_utils_make_install.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,7 +1,9 @@
-scripts shuould be stripped off .pl extensions and are copied to /usr/bin via debian/rules
-binaries are copied by dh_install 
+Description: Remove .pl extensions from scripts and place 
+ them to /usr/bin via debian/rules file
+ binaries are copied by dh_install 
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2011-02-12
 
-so I commented out this target to avoid installation by Makefile processing.
 --- a/Utils/Makefile.in
 +++ b/Utils/Makefile.in
 @@ -468,7 +468,7 @@

Modified: trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch
===================================================================
--- trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch	2011-02-12 17:06:39 UTC (rev 5961)
+++ trunk/packages/vienna-rna/trunk/debian/patches/readseq_exclude.patch	2011-02-12 18:33:37 UTC (rev 5962)
@@ -1,6 +1,10 @@
-Readseq is a different standalone package. So we don't need to build it as a part of vienna-rna.
---- a/Makefile.in
-+++ b/Makefile.in
+Description: Readseq is a different standalone package. 
+ So we don't need to build it as a part of vienna-rna.
+Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Last-Update: 2011-02-12
+
+--- ViennaRNA-1.8.4.orig/Makefile.in
++++ ViennaRNA-1.8.4/Makefile.in
 @@ -234,7 +234,7 @@
  
  #DIST_SUBDIRS = lib Progs man Utils AliFold H Perl Cluster

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