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×tamps ,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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 <[email protected]> -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 <[email protected]> +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 <[email protected]> -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 <[email protected]> +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 <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
