BioC 3.2: CHECK report for tracktables on linux1.bioconductor.org

Package: tracktables

Version: 1.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings tracktables_1.4.0.tar.gz

StartedAt: 2015-10-27 08:48:46 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:50:27 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 101.3 seconds

RetCode: 1

Status:  ERROR

CheckDir: tracktables.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings tracktables_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/tracktables.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tracktables/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tracktables’ version ‘1.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘tracktables’ can be installed ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘tracktables-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MakeIGVSession
> ### Title: Make IGV session XML and sample information file
> ### Aliases: MakeIGVSession
> 
> ### ** Examples
> 
> fileLocations <- system.file("extdata",package="tracktables")
> 
> bigwigs <- dir(fileLocations,pattern="*.bw",full.names=TRUE)
> 
> intervals <- dir(fileLocations,pattern="*.bed",full.names=TRUE)
> 
> bigWigMat <- cbind(gsub("_Example.bw","",basename(bigwigs)),
+                    bigwigs)
> 
> intervalsMat <- cbind(gsub("_Peaks.bed","",basename(intervals)),
+                       intervals)
> 
> fileSheet <- merge(bigWigMat,intervalsMat,all=TRUE)
> 
> fileSheet <- as.matrix(cbind(fileSheet,NA))
> 
> colnames(fileSheet) <- c("SampleName","bigwig","interval","bam")
> 
> SampleSheet <- cbind(as.vector(fileSheet[,"SampleName"]),
+                      c("EBF","H3K4me3","H3K9ac","RNAPol2"),
+                      c("ProB","ProB","ProB","ProB"))
> 
> colnames(SampleSheet) <- c("SampleName","Antibody","Species")
> MakeIGVSession(SampleSheet,fileSheet,igvdirectory=getwd(),"Example","mm9")
Error in ifelse(fileName %˜% "^([A-Za-z]:)?/", fileName, file.path(base,  : 
  could not find function "%˜%"
Calls: MakeIGVSession ... relativePath -> strsplit -> expandFileName -> ifelse
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/tracktables.Rcheck/00check.log’
for details.

* installing *source* package ‘tracktables’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (tracktables)

name	user	system	elapsed
MakeIGVSampleMetadata	0.026	0.000	0.027