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BioC 3.3: CHECK report for RTCGAToolbox on oaxaca

This page was generated on 2016-10-13 13:01:47 -0700 (Thu, 13 Oct 2016).

Package 1018/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RTCGAToolbox 2.2.2
Mehmet Kemal Samur
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/RTCGAToolbox
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RTCGAToolbox
Version: 2.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGAToolbox_2.2.2.tar.gz
StartedAt: 2016-10-13 06:00:45 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 06:02:03 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 77.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RTCGAToolbox.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RTCGAToolbox_2.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RTCGAToolbox.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.2.2’
* 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 9.59  0.281  10.598
* 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-3.3-bioc/meat/RTCGAToolbox.Rcheck/00check.log’
for details.


RTCGAToolbox.Rcheck/00install.out:

* 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)

RTCGAToolbox.Rcheck/RTCGAToolbox-Ex.timings:

nameusersystemelapsed
getCNGECorrelation1.3240.0291.354
getData-methods0.0750.0040.080
getData0.1040.0050.110
getDiffExpressedGenes0.3900.0140.405
getFirehoseAnalyzeDates0.0050.0011.081
getFirehoseData0.0990.0050.104
getFirehoseDatasets0.0020.0010.542
getFirehoseRunningDates0.0030.0011.006
getMutationRate0.1300.0080.138
getReport 9.590 0.28110.598
getSurvival0.5460.0130.560
showResults-CorResult1.3090.0381.349
showResults-DGEResult0.2970.0140.317
showResults0.2740.0180.294