[Patchwork-commits] r46 - pkg/patchwork/R

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

Author: sebastian_d
Date: 2011-12-09 14:35:41 +0100 (Fri, 09 Dec 2011)
New Revision: 46

Modified:
   pkg/patchwork/R/patchwork.CNA.r
   pkg/patchwork/R/patchwork.readChroms.r
Log:
coulden't inhibit pysam build/install output easily (tried several things) so now theres just a waiting period so people have time to read that all the commands dumped on your screen are pysam building atleast =)

Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r	2011-12-09 11:24:30 UTC (rev 45)
+++ pkg/patchwork/R/patchwork.CNA.r	2011-12-09 13:35:41 UTC (rev 46)
@@ -138,6 +138,8 @@
 	cat("Plotting Complete \n")
 	cat("Shutting down..... \n")
 	
+	options(show.error.messages=FALSE)
+	
 	}
 	
 	
\ No newline at end of file

Modified: pkg/patchwork/R/patchwork.readChroms.r
===================================================================
--- pkg/patchwork/R/patchwork.readChroms.r	2011-12-09 11:24:30 UTC (rev 45)
+++ pkg/patchwork/R/patchwork.readChroms.r	2011-12-09 13:35:41 UTC (rev 46)
@@ -33,13 +33,14 @@
 			{
 			setwd(".python")
 			cat("Pysam has not yet been installed on your system. \n Attempting to Build \n")
+			system("sleep 5")
 			# build pysam
-			system("python setup.py build > pysam_build_output.txt",invisible=F)
+			system("python setup.py build > pysam_build_output.txt")
 			system("cp pysam_build_output.txt ..")
 			cat("Build complete. Output of build can be viewed in file pysam_build_output.txt.
 				\n Attempting to Install \n")
 			# install pysam to site.USER_BASE
-			system("python setup.py install --user > pysam_install_output.txt",invisible=F)
+			system("python setup.py install --user > pysam_install_output.txt")
 			system("cp pysam_install_output.txt ..")
 			cat("Install complete. Output of install can be viewed in file pysam_install_output.txt. \n")
 			setwd("..")