sci-biology/repeatmasker: rename and move the patch file; drop old patch for a previous version

Package-Manager: portage-2.2.18

3 files changed, 7 insertions, 122 deletions

diff --git a/sci-biology/repeatmasker/ChangeLog b/sci-biology/repeatmasker/ChangeLog
index c7fadb62c..872aa83a0 100644
--- a/sci-biology/repeatmasker/ChangeLog
+++ b/sci-biology/repeatmasker/ChangeLog
@@ -2,6 +2,13 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+  01 Dec 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/repeatmasker-4.0.6__configure.patch,
+  -files/RepeatMasker-open-4-0-1__configure.patch,
+  -files/RepeatMasker-open-4-0-6__configure.patch:
+  sci-biology/repeatmasker: rename and move the patch file; drop old patch for a
+  previous version
+
   24 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   repeatmasker-4.0.1-r1.ebuild:
   sci-biology/repeatmasker: improve einfo message
diff --git a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch
deleted file mode 100644
index 0b8a75c67..000000000
--- a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch
+++ /dev/null
@@ -1,122 +0,0 @@
---- configure.ori	2013-02-21 02:32:30.000000000 +0100
-+++ configure	2015-11-24 19:54:50.630202150 +0100
-@@ -253,17 +253,16 @@
-   close INVERS;
- }
- else {
--  print "\nYour RepeatMasker installation is missing a library file.\n"
-+  die "\nYour RepeatMasker installation is missing a library file.\n"
-       . "RepeatMasker requires a minimal set of library sequences to run\n"
-       . "properly.  Please check that all files were extracted from the\n"
-       . "distribution before re-running the configure program.\n\n";
--  exit;
- }
- 
- print "\n  -- Building monolithic RM database...";
- system(
- "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl > $rmLocation/Libraries/RepeatMasker.lib 2>/dev/null"
--);
-+) and die "$rmLocation/util/buildRMLibFromEMBL.pl $rmLocation/Libraries/RepeatMaskerLib.embl command filed with: $!";
- 
- ##
- ## TRF location
-@@ -475,7 +474,7 @@
-     }
-     close IN;
-     close OUT;
--    system( "mv $configFile.tmp $configFile" );
-+    system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
-   }
- 
- }
-@@ -607,15 +606,15 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "Faled to mv $configFile.tmp $configFile: $!";
- 
-   # Freeze RM and RMPep libraries for RepeatModeler use among others
-   my $rmLocation = "$FindBin::Bin";
-   print "Building RMBlast frozen libraries..\n";
-   system(   "$pgLocation/makeblastdb -dbtype nucl -in "
--          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype nucl -in $rmLocation/Libraries/RepeatMasker.lib failed: $!";
-   system(   "$pgLocation/makeblastdb -dbtype prot -in "
--          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$pgLocation/makeblastdb -dbtype prot -in $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
- 
-   my $pgDefault = &promptScreen(
-     "",
-@@ -682,15 +681,15 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   # Freeze RM and RMPep libraries
-   my $rmLocation = "$FindBin::Bin";
-   print "Building WUBlast/ABBlast frozen libraries..\n";
-   system(   "$wuLocation/xdformat -n -I "
--          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatMasker.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -n -I $rmLocation/Libraries/RepeatMasker.lib failed with: $!";
-   system(   "$wuLocation/xdformat -p -I "
--          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" );
-+          . "$rmLocation/Libraries/RepeatPeps.lib > /dev/null 2>&1" ) and die "$wuLocation/xdformat -p -I $rmLocation/Libraries/RepeatPeps.lib failed with: $!";
- 
-   my $wuDefault = &promptScreen(
-     "",
-@@ -748,7 +747,7 @@
-         }
-       }
-       else {
--        print "ERROR: Could not find nhmmer program in this directory!\n";
-+        print "ERROR: Could not find nhmmer program in '$location' directory!\n";
-       }
-       if ( $goodParam == 0 ) {
-         print "<PRESS ENTER TO CONTINUE>\n";
-@@ -773,7 +772,7 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   my $default = &promptScreen(
-     "",
-@@ -827,7 +826,7 @@
-   }
-   close IN;
-   close OUT;
--  system( "mv $configFile.tmp $configFile" );
-+  system( "mv $configFile.tmp $configFile" ) and die "mv $configFile.tmp $configFile failed with: $!";
- 
-   my $deDefault = &promptScreen(
-     "",
-@@ -863,9 +862,6 @@
- 
-   my $answer = undef;
- 
--  # Clear the screen
--  system( "clear" );
--
-   print "\n\n\n";
-   print $screenText;
-   my $numLines = ( $screenText =~ s/(\n)/$1/g );
---- configure.ori	2015-11-24 20:10:58.640204679 +0100
-+++ configure	2015-11-24 20:11:00.970204685 +0100
-@@ -728,11 +728,12 @@
-         # HMMER 3.0dev (March 2010); http://hmmer.org/
-         # HMMER 3.1dev_0.33 (July 2012); http://hmmer.org
-         # HMMER hmmer3.1-snap20120830 (August 2012); http://hmmer.org/
-+	# HMMER 3.1b2 (February 2015); http://hmmer.org/
-         while ( $result =~ /([^\n\r]*)[\n\r]/ig ) {
-           my $line = $1;
- 
-           if ( $line =~ /^#\s+HMMER\s+(\d+\.\d+)((dev)?(_\d+\.\d+)?\s+\(.*\)).*/
--               || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ )
-+               || $line =~ /^#\s+HMMER\s+hmmer(\d+\.\d+)-snap.*/ || $line =~ /^#\s+HMMER\s+(\d+\.\d+).*/)
-           {
-             if ( $1 >= 3.1 ) {
-               $goodParam = 1;
diff --git a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
index e4042190f..e4042190f 100644
--- a/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
+++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch