BioC 3.5: CHECK report for RareVariantVis on oaxaca

Package: RareVariantVis

Version: 2.0.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RareVariantVis_2.0.9.tar.gz

StartedAt: 2017-03-04 07:42:14 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:47:48 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 334.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: RareVariantVis.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RareVariantVis_2.0.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RareVariantVis.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RareVariantVis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RareVariantVis’ version ‘2.0.9’
* 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 ‘RareVariantVis’ can be installed ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘RareVariantVis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: callHomozygous
> ### Title: Call homozygous regions from sequencing data
> ### Aliases: callHomozygous
> ### Keywords: ˜call homozygous regions
> 
> ### ** Examples
> 
> sample = system.file("extdata", "CoriellIndex_S1.vcf.gz",
+                      package = "DataRareVariantVis")
> callHomozygous(sample=sample, chromosomes=c("19"))
Warning in file(file, "rt") :
  file("") only supports open = "w+" and open = "w+b": using the former
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
Calls: callHomozygous -> read.delim -> read.table
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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RareVariantVis.Rcheck/00check.log’
for details.

* installing *source* package ‘RareVariantVis’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘toJSON’ from package ‘jsonlite’ in package ‘googleVis’
* DONE (RareVariantVis)

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