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CHECK report for canceR on merida2

This page was generated on 2019-04-09 13:31:09 -0400 (Tue, 09 Apr 2019).

Package 202/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.17.1
Karim Mezhoud
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/canceR
Branch: master
Last Commit: d0e4002
Last Changed Date: 2019-02-21 17:03:40 -0400 (Thu, 21 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: canceR
Version: 1.17.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.17.1.tar.gz
StartedAt: 2019-04-08 23:39:16 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 23:46:57 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 460.0 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings canceR_1.17.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘canceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘canceR’ version ‘1.17.1’
* package encoding: UTF-8
* 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 ‘canceR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    extdata   2.9Mb
* 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 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
GSEA: no visible global function definition for ‘savePlot’
GSEA: no visible global function definition for ‘dev.new’
GSEA.Analyze.Sets: no visible global function definition for ‘savePlot’
Undefined global functions or variables:
  dev.new savePlot
Consider adding
  importFrom("grDevices", "dev.new", "savePlot")
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 ... NOTE
S3 methods shown with full name in documentation object 'cbind.na':
  ‘cbind.na’

S3 methods shown with full name in documentation object 'rbind.na':
  ‘rbind.na’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL canceR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘canceR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
* DONE (canceR)

Tests output

canceR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(canceR)
Loading required package: tcltk
Loading required package: tcltk2
Loading required package: cgdsr
Please send questions to cbioportal@googlegroups.com

/////////////////////////////////////////////////////////////////////////////

//------------------    Thanks for using HTSanalyzeR    -------------------//
 
//------------please use function changes() to see new changes-------------//

//------------please report any bug to xinwang2hms@gmail.com---------------//

/////////////////////////////////////////////////////////////////////////////
Warning message:
replacing previous import 'igraph::union' by 'GSEABase::union' when loading 'HTSanalyzeR' 
> 
> test_check("canceR")
getCancerStudies...  OK
getCaseLists (1/2) ...  OK
getCaseLists (2/2) ...  OK
getGeneticProfiles (1/2) ...  OK
getGeneticProfiles (2/2) ...  OK
getClinicalData (1/1) ...  OK
getProfileData (1/6) ...  OK
getProfileData (2/6) ...  OK
getProfileData (3/6) ...  OK
getProfileData (4/6) ...  OK
getProfileData (5/6) ...  OK
getProfileData (6/6) ...  OK
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.959   1.693  18.060 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
ClinicalData0.0070.0010.008
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot0.0000.0010.001
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.1710.0100.183
GSEA.NormalizeRows0.0010.0010.000
GSEA000
GSEA.ReadClsFile0.1590.0050.165
GSEA.Res2Frame0.1670.0050.174
GSEA.Threshold0.1640.0060.172
GSEA.VarFilter0.1590.0050.165
GSEA.write.gct0.1790.0070.185
GeneExpMatrix0.0170.0010.018
Match_GeneList_MSigDB0.1770.0080.185
OLD.GSEA.EnrichmentScore0.1580.0040.162
Run.GSEA0.1660.0050.173
about000
canceR000
canceRHelp000
canceR_Vignette0.0000.0000.001
cbind.na000
dialogGeneClassifier0.0470.0040.051
dialogMetOption0.1570.0040.161
dialogMut0.1560.0060.162
dialogOptionCircos0.1360.0060.143
dialogOptionGSEAlm0.0040.0020.005
dialogOptionPhenoTest0.1880.0060.195
dialogPlotOption_SkinCor0.0470.0030.051
dialogSamplingGSEA0.1600.0040.164
dialogSelectFiles_GSEA0.1580.0070.165
dialogSpecificMut0.1630.0050.170
dialogSummary_GSEA0.1620.0050.169
dialoggetGeneListMSigDB0.0000.0000.001
displayInTable0.0040.0010.005
getCases0.0180.0070.667
getCasesGenProfs0.1100.0050.116
getCircos0.1450.0060.152
getClinicData_MultipleCases0.1130.0060.118
getClinicalDataMatrix0.1120.0060.118
getCor_ExpCNAMet0.1340.0070.141
getGCTCLSExample0.2040.0080.212
getGCT_CLSfiles0.1600.0050.165
getGSEAlm_Diseases0.1590.0040.162
getGSEAlm_Variables0.0010.0000.000
getGenProfs0.0160.0070.824
getGeneExpMatrix0.1120.0050.118
getGeneList0.0000.0000.001
getGeneListExample000
getGeneListFromMSigDB0.1120.0040.116
getGenesClassifier000
getGenesTree_MultipleCases0.1140.0050.119
getGenesTree_SingleCase0.1870.0120.202
getInTable0.0040.0010.005
getListProfData0.1160.0050.122
getMSigDB000
getMSigDBExample0.1110.0050.117
getMSigDBfile000
getMegaProfData0.1130.0060.118
getMetDataMultipleGenes0.1610.0040.166
getMutData0.1790.0040.183
getPhenoTest0.1750.0110.186
getProfilesDataMultipleGenes0.1760.0140.189
getProfilesDataSingleGene0.1130.0090.122
getSpecificMut0.1640.0080.171
getSummaryGSEA0.1600.0050.167
getSurvival000
getTextWin000
geteSet000
modalDialog0.1090.0040.113
myGlobalEnv000
plotModel0.0460.0040.050
plot_1Gene_2GenProfs0.0460.0030.049
plot_2Genes_1GenProf0.1560.0040.161
rbind.na0.0000.0010.000
setWorkspace0.1250.0040.129
testCheckedCaseGenProf0.1100.0030.114