BioC 3.5: CHECK report for RTCGAToolbox on oaxaca

Package: RTCGAToolbox

Version: 2.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGAToolbox_2.5.0.tar.gz

StartedAt: 2017-03-04 08:37:31 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:39:01 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 90.2 seconds

RetCode: 0

Status:  OK

CheckDir: RTCGAToolbox.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGAToolbox_2.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RTCGAToolbox.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 ‘RTCGAToolbox/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTCGAToolbox’ version ‘2.5.0’
* 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 ‘RTCGAToolbox’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
.barcodeUUID: no visible global function definition for
  ‘txtProgressBar’
.barcodeUUID: no visible global function definition for
  ‘setTxtProgressBar’
.checkFileSize: no visible global function definition for ‘read.csv’
.exportFiles: no visible global function definition for ‘download.file’
.exportFiles: no visible global function definition for ‘untar’
.makeExprMat: no visible global function definition for ‘read.delim’
getCNGECorrelation: no visible global function definition for
  ‘cor.test’
getCNGECorrelation: no visible global function definition for
  ‘p.adjust’
getDiffExpressedGenes: no visible global function definition for
  ‘model.matrix’
getDiffExpressedGenes: no visible global function definition for
  ‘colorRampPalette’
getDiffExpressedGenes: no visible global function definition for
  ‘heatmap’
getFirehoseAnalyzeDates: no visible global function definition for
  ‘read.table’
getFirehoseData: no visible global function definition for ‘read.delim’
getFirehoseData: possible error in .makeExprMat(export.file, "",
  "miRNAArray", 100, TRUE, runDate): unused argument (runDate)
getFirehoseData: no visible global function definition for
  ‘download.file’
getFirehoseData: no visible global function definition for ‘untar’
getFirehoseData : <anonymous>: no visible global function definition
  for ‘read.delim’
getFirehoseData: no visible global function definition for
  ‘write.table’
getFirehoseDatasets: no visible global function definition for
  ‘read.table’
getFirehoseRunningDates: no visible global function definition for
  ‘read.table’
getReport: no visible global function definition for ‘pdf’
getReport: no visible global function definition for ‘data’
getReport: no visible binding for global variable
  ‘UCSC.HG19.Human.CytoBandIdeogram’
getReport: no visible global function definition for ‘dev.off’
getSurvival: no visible global function definition for ‘pchisq’
getSurvival: no visible global function definition for ‘plot’
getSurvival: no visible global function definition for ‘legend’
showResults,CorResult: no visible global function definition for ‘head’
showResults,DGEResult: no visible global function definition for ‘head’
Undefined global functions or variables:
  UCSC.HG19.Human.CytoBandIdeogram colorRampPalette cor.test data
  dev.off download.file head heatmap legend model.matrix p.adjust
  pchisq pdf plot read.csv read.delim read.table setTxtProgressBar
  txtProgressBar untar write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor.test", "heatmap", "model.matrix", "p.adjust",
             "pchisq")
  importFrom("utils", "data", "download.file", "head", "read.csv",
             "read.delim", "read.table", "setTxtProgressBar",
             "txtProgressBar", "untar", "write.table")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
getReport 13.136  0.362  14.112
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/RTCGAToolbox.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
getCNGECorrelation	1.018	0.027	1.045
getData-methods	0.153	0.004	0.157
getData	0.068	0.003	0.071
getDiffExpressedGenes	0.877	0.021	0.899
getFirehoseAnalyzeDates	0.004	0.002	1.069
getFirehoseData	0.095	0.007	0.102
getFirehoseDatasets	0.002	0.001	0.546
getFirehoseRunningDates	0.003	0.001	1.013
getMutationRate	0.128	0.007	0.136
getReport	13.136	0.362	14.112
getSurvival	0.190	0.015	0.206
showResults-CorResult	1.137	0.026	1.164
showResults-DGEResult	0.304	0.014	0.318
showResults	0.238	0.015	0.255