[Patchwork-commits] r173 - in pkg: TAPS patchwork patchwork/inst/perl

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2013-06-12 15:31:03 +0200 (Wed, 12 Jun 2013)
New Revision: 173

Modified:
   pkg/TAPS/DESCRIPTION
   pkg/patchwork/DESCRIPTION
   pkg/patchwork/NAMESPACE
   pkg/patchwork/inst/perl/mpile2alleles.pl
Log:
Removed dependencies from description because Rforge cant handle them at the moment

Modified: pkg/TAPS/DESCRIPTION
===================================================================
--- pkg/TAPS/DESCRIPTION	2013-06-05 14:12:24 UTC (rev 172)
+++ pkg/TAPS/DESCRIPTION	2013-06-12 13:31:03 UTC (rev 173)
@@ -7,5 +7,5 @@
 Maintainer: Sebastian DiLorenzo <Sebastian.DiLorenzo at medsci.uu.se> #Markus Mayrhofer <Markus.Mayrhofer at medsci.uu.se>
 Description: Performs a allele-specific copy number analysis of array data.
 License: GPL-2
-Depends:R (>= 2.10), DNAcopy, fields, affxparser
+Depends:R (>= 2.10)
 #Imports: DNAcopy, fields, affxparser
\ No newline at end of file

Modified: pkg/patchwork/DESCRIPTION
===================================================================
--- pkg/patchwork/DESCRIPTION	2013-06-05 14:12:24 UTC (rev 172)
+++ pkg/patchwork/DESCRIPTION	2013-06-12 13:31:03 UTC (rev 173)
@@ -7,5 +7,5 @@
 Maintainer: Markus Mayrhofer <Markus.Mayrhofer at medsci.uu.se>
 Description: Performs a allele-specific copy number analysis of whole genome data.
 License: GPL-2
-Imports: patchworkData
-Depends: DNAcopy
+#Imports: patchworkData
+#Depends: DNAcopy

Modified: pkg/patchwork/NAMESPACE
===================================================================
--- pkg/patchwork/NAMESPACE	2013-06-05 14:12:24 UTC (rev 172)
+++ pkg/patchwork/NAMESPACE	2013-06-12 13:31:03 UTC (rev 173)
@@ -1,4 +1,4 @@
-import(patchworkData)
+#import(patchworkData)
 
 export(karyotype_check,
 		karyotype_chroms,

Modified: pkg/patchwork/inst/perl/mpile2alleles.pl
===================================================================
--- pkg/patchwork/inst/perl/mpile2alleles.pl	2013-06-05 14:12:24 UTC (rev 172)
+++ pkg/patchwork/inst/perl/mpile2alleles.pl	2013-06-12 13:31:03 UTC (rev 173)
@@ -54,7 +54,6 @@
 		my ($chr, $pos, $ref, $depth, $baseString) = (split /\t/, $_)[0,1,2,3,4];
 
 		#If the position and chromosome match between pileup and vcf
-
 		# add if smaller than
 		if ($vchr eq $chr && $vpos == $pos)
 			{