* using log directory '/loc/biocbuild/build-area/bioc-1.7/buildSandbox/checkOutput/maSigPro.Rcheck'
* using R version 2.2.0, 2005-10-07 
* checking for file 'maSigPro/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'maSigPro' version '1.2.0'
* checking if this is a source package ... OK
* checking whether package 'maSigPro' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking package dependencies ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking Rd files ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating maSigPro-Ex.R ... OK
* checking examples ... ERROR
Running examples in maSigPro-Ex.R failed.
The error most likely occurred in:

> ### * see.genes
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: see.genes
> ### Title: Wrapping function for visualization of gene expression values of
> ###   time course experiments
> ### Aliases: see.genes
> ### Keywords: manip aplot
> 
> ### ** Examples
> 
> 
> #### GENERATE TIME COURSE DATA
> ## generate n random gene expression profiles of a data set with 
> ## one control plus 3 treatments, 3 time points and r replicates per time point.
> 
> tc.GENE <- function(n, r,
+              var11 = 0.01, var12 = 0.01,var13 = 0.01,
+              var21 = 0.01, var22 = 0.01, var23 =0.01,
+              var31 = 0.01, var32 = 0.01, var33 = 0.01,
+              var41 = 0.01, var42 = 0.01, var43 = 0.01,
+              a1 = 0, a2 = 0, a3 = 0, a4 = 0,
+              b1 = 0, b2 = 0, b3 = 0, b4 = 0,
+              c1 = 0, c2 = 0, c3 = 0, c4 = 0)
+ {
+ 
+   tc.dat <- NULL
+   for (i in 1:n) {
+     Ctl <- c(rnorm(r, a1, var11), rnorm(r, b1, var12), rnorm(r, c1, var13))  # Ctl group
+     Tr1 <- c(rnorm(r, a2, var21), rnorm(r, b2, var22), rnorm(r, c2, var23))  # Tr1 group
+     Tr2 <- c(rnorm(r, a3, var31), rnorm(r, b3, var32), rnorm(r, c3, var33))  # Tr2 group
+     Tr3 <- c(rnorm(r, a4, var41), rnorm(r, b4, var42), rnorm(r, c4, var43))  # Tr3 group
+     gene <- c(Ctl, Tr1, Tr2, Tr3)
+     tc.dat <- rbind(tc.dat, gene)
+   }
+   tc.dat
+ }
> 
> ## Create 270 flat profiles
> flat <- tc.GENE(n = 270, r = 3)
> ## Create 10 genes with profile differences between Ctl and Tr1 groups
> twodiff <- tc.GENE (n = 10, r = 3, b2 = 0.5, c2 = 1.3)
> ## Create 10 genes with profile differences between Ctl, Tr2, and Tr3 groups
> threediff <- tc.GENE(n = 10, r = 3, b3 = 0.8, c3 = -1, a4 = -0.1, b4 = -0.8, c4 = -1.2)
> ## Create 10 genes with profile differences between Ctl and Tr2 and different variance
> vardiff <- tc.GENE(n = 10, r = 3, a3 = 0.7, b3 = 1, c3 = 1.2, var32 = 0.03, var33 = 0.03)
> ## Create dataset
> tc.DATA <- rbind(flat, twodiff, threediff, vardiff)
> rownames(tc.DATA) <- paste("feature", c(1:300), sep = "")
> colnames(tc.DATA) <- paste("Array", c(1:36), sep = "")
> tc.DATA [sample(c(1:(300*36)), 300)] <- NA  # introduce missing values
> 
> #### CREATE EXPERIMENTAL DESIGN
> Time <- rep(c(rep(c(1:3), each = 3)), 4)
> Replicates <- rep(c(1:12), each = 3)
> Control <- c(rep(1, 9), rep(0, 27))
> Treat1 <- c(rep(0, 9), rep(1, 9), rep(0, 18))
> Treat2 <- c(rep(0, 18), rep(1, 9), rep(0,9))
> Treat3 <- c(rep(0, 27), rep(1, 9))
> edesign <- cbind(Time, Replicates, Control, Treat1, Treat2, Treat3)
> rownames(edesign) <- paste("Array", c(1:36), sep = "")
> 
> see.genes(tc.DATA, edesign = edesign, k = 4, main = "Time Course")
Loading required package: limma
Warning: unable to open connection to X11 display ''
Error in X11(display, width, height, pointsize, gamma, colortype, maxcubesize,  : 
	unable to start device X11
Execution halted