BioC 3.4: CHECK report for GenVisR on morelia

Package: GenVisR

Version: 1.4.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenVisR_1.4.1.tar.gz

StartedAt: 2017-04-15 02:50:41 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:54:39 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 237.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: GenVisR.Rcheck

Warnings: NA

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenVisR_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenVisR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.4.1’
* 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 ‘GenVisR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
* 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 ‘GenVisR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lolliplot
> ### Title: Construct a lolliplot
> ### Aliases: lolliplot
> 
> ### ** Examples
> 
> # Create input data
> data <- brcaMAF[brcaMAF$Hugo_Symbol == 'TP53',c('Hugo_Symbol', 'amino_acid_change_WU')]
> data <- as.data.frame(cbind(data, 'ENST00000269305'))
> colnames(data) <- c('gene', 'amino_acid_change', 'transcript_name')
> 
> # Call lolliplot
> lolliplot(data)
Using the following host: www.ensembl.org for biomaRt queries to change the ensembl annotation version alter this parameter!
Querying biomaRt for transcript sequence
Error in if (nchar(x)%%3 != 0) { : argument is of length zero
Calls: lolliplot -> lolliplot_DNAconv
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenVisR.Rcheck/00check.log’
for details.

* installing *source* package ‘GenVisR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenVisR)

name	user	system	elapsed
TvTi	2.928	0.090	3.021
cnFreq	0.767	0.014	0.781
cnSpec	3.638	0.013	3.653
cnView	1.322	0.182	1.506
compIdent	2.828	0.140	3.302
covBars	1.103	0.006	1.134
genCov	5.506	0.351	5.994
geneViz	3.376	0.075	3.491
ideoView	0.277	0.001	0.278
lohSpec	3.907	0.073	3.981
lohView	0.566	0.004	0.571