BioC 3.5: CHECK report for ssviz on oaxaca

Package: ssviz

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ssviz_1.9.0.tar.gz

StartedAt: 2017-03-04 09:41:12 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:43:09 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 117.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: ssviz.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 ssviz_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ssviz.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 ‘ssviz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ssviz’ version ‘1.9.0’
* 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 ‘ssviz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
ntfreq,DataFrame-numeric : fun: no visible global function definition
  for ‘aggregate’
plotDistro,list: no visible global function definition for ‘aggregate’
plotRegion,list-character: no visible global function definition for
  ‘txtProgressBar’
plotRegion,list-character: no visible global function definition for
  ‘setTxtProgressBar’
plotRegion,list-character: no visible global function definition for
  ‘hist’
plotRegion,list-character: no visible global function definition for
  ‘density’
Undefined global functions or variables:
  aggregate density hist setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "aggregate", "density")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
* 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 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 ‘ssviz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pingpong
> ### Title: pingpong
> ### Aliases: pingpong
> 
> ### ** Examples
> 
> data(ssviz)
> pp<-pingpong(pctrlbam)
No counts column provided in bam file. Running unique counts.
Otherwise provide a count matrix or run getCountMatrix.
Error in `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels,  : 
  factor level [2] is duplicated
Calls: pingpong -> pingpong
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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ssviz.Rcheck/00check.log’
for details.

* installing *source* package ‘ssviz’ ...
** 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 (ssviz)

name	user	system	elapsed
getCountMatrix	0.621	0.012	0.634
logicalORmissing-class	0.001	0.000	0.001
ntfreq	0.574	0.023	0.598