[Patchwork-commits] r45 - pkg/patchwork/R

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

Author: sebastian_d
Date: 2011-12-09 12:24:30 +0100 (Fri, 09 Dec 2011)
New Revision: 45

Modified:
   pkg/patchwork/R/patchwork.readChroms.r
Log:
Added output to file, instead of showing it on screen, for pysam package installation, should it be necessary.

Modified: pkg/patchwork/R/patchwork.readChroms.r
===================================================================
--- pkg/patchwork/R/patchwork.readChroms.r	2011-12-09 10:30:19 UTC (rev 44)
+++ pkg/patchwork/R/patchwork.readChroms.r	2011-12-09 11:24:30 UTC (rev 45)
@@ -32,10 +32,16 @@
 	if (system(paste("python ",getwd(),"/.python/Check.py",sep=""),intern=T) == "Pysam Not Available")
 			{
 			setwd(".python")
+			cat("Pysam has not yet been installed on your system. \n Attempting to Build \n")
 			# build pysam
-			system("python setup.py build",invisible=F)
+			system("python setup.py build > pysam_build_output.txt",invisible=F)
+			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",invisible=F)
+			system("python setup.py install --user > pysam_install_output.txt",invisible=F)
+			system("cp pysam_install_output.txt ..")
+			cat("Install complete. Output of install can be viewed in file pysam_install_output.txt. \n")
 			setwd("..")
 			}