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
