[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/files/, sci-biology/repeatmasker/

[Martin Mokrejs]

commit:     f7e2b8faced793d6f723a7da224fca410ae3c9ca
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec  1 00:09:23 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec  1 00:09:23 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7e2b8fa

sci-biology/repeatmasker: added file checksum; add missing quotes

Package-Manager: portage-2.2.18

 ...ch => RepeatMasker-open-4-0-1__configure.patch} |  0
 ...ch => RepeatMasker-open-4-0-6__configure.patch} | 42 +++++++---------------
 ...r-4.0.1-r1.ebuild => repeatmasker-4.0.6.ebuild} |  6 ++--
 3 files changed, 16 insertions(+), 32 deletions(-)

diff --git a/sci-biology/repeatmasker/files/configure.patch b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch
similarity index 100%
copy from sci-biology/repeatmasker/files/configure.patch
copy to sci-biology/repeatmasker/files/RepeatMasker-open-4-0-1__configure.patch

diff --git a/sci-biology/repeatmasker/files/configure.patch b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
similarity index 74%
rename from sci-biology/repeatmasker/files/configure.patch
rename to sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
index 0b8a75c..e404219 100644
--- a/sci-biology/repeatmasker/files/configure.patch
+++ b/sci-biology/repeatmasker/files/RepeatMasker-open-4-0-6__configure.patch
@@ -1,5 +1,5 @@
---- configure.ori	2013-02-21 02:32:30.000000000 +0100
-+++ configure	2015-11-24 19:54:50.630202150 +0100
+--- configure.ori	2015-11-24 20:56:46.000000000 +0100
++++ configure	2015-11-24 20:59:58.000000000 +0100
 @@ -253,17 +253,16 @@
    close INVERS;
  }
@@ -67,16 +67,16 @@
  
    my $wuDefault = &promptScreen(
      "",
-@@ -748,7 +747,7 @@
-         }
+@@ -756,7 +755,7 @@
        }
-       else {
--        print "ERROR: Could not find nhmmer program in this directory!\n";
-+        print "ERROR: Could not find nhmmer program in '$location' directory!\n";
-       }
-       if ( $goodParam == 0 ) {
-         print "<PRESS ENTER TO CONTINUE>\n";
-@@ -773,7 +772,7 @@
+     }
+     else {
+-      print "ERROR: Could not find nhmmer program in this directory!\n";
++      print "ERROR: Could not find nhmmer program in '$location' directory!\n";
+     }
+   }
+ 
+@@ -776,7 +775,7 @@
    }
    close IN;
    close OUT;
@@ -85,7 +85,7 @@
  
    my $default = &promptScreen(
      "",
-@@ -827,7 +826,7 @@
+@@ -830,7 +829,7 @@
    }
    close IN;
    close OUT;
@@ -94,7 +94,7 @@
  
    my $deDefault = &promptScreen(
      "",
-@@ -863,9 +862,6 @@
+@@ -866,9 +865,6 @@
  
    my $answer = undef;
  
@@ -104,19 +104,3 @@
    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/repeatmasker-4.0.1-r1.ebuild b/sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
similarity index 94%
rename from sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
rename to sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
index 0899978..89b7c7f 100644
--- a/sci-biology/repeatmasker/repeatmasker-4.0.1-r1.ebuild
+++ b/sci-biology/repeatmasker/repeatmasker-4.0.6.ebuild
@@ -28,7 +28,7 @@ RDEPEND="
 S="${WORKDIR}/RepeatMasker"
 
 src_prepare(){
-	epatch "${FILESDIR}"/configure.patch
+	epatch "${FILESDIR}"/"${P}"__configure.patch
 }
 
 src_configure() {
@@ -37,11 +37,11 @@ src_configure() {
 	#  -- Building monolithic RM database...sh: /var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib: No such file or directory
 	# -e 's|> \($rmLocation/Libraries/RepeatMasker.lib\)|> '${D}'/\1|'
 	sed -i -e 's/system( "clear" );//' "${S}/configure" || die
-	mkdir -p ${D}//usr/share/repeatmasker/Libraries/ || die
+	mkdir -p "${D}"/usr/share/repeatmasker/Libraries/ || die
 	#
 	# the below files is actually overwritten by buildRMLibFromEMBL.pl so the 'blah'
 	# item does not get installed
-	echo ">blah\natgc" > ${D}//usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
+	echo ">blah\natgc" > "${D}"/usr/share/repeatmasker/Libraries/RepeatMasker.lib || die
 	# below try to define paths to trf, cross_match, rmblast and nhmmer as search tools
 	echo "
 env