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

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### Running command:
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###   /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.

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### Running command:
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###   /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)

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 [email protected]

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

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

//------------please report any bug to [email protected]//

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

name	user	system	elapsed
ClinicalData	0.007	0.001	0.008
GSEA.Analyze.Sets	0	0	0
GSEA.ConsPlot	0	0	0
GSEA.EnrichmentScore	0	0	0
GSEA.EnrichmentScore2	0	0	0
GSEA.Gct2Frame	0	0	0
GSEA.Gct2Frame2	0	0	0
GSEA.GeneRanking	0	0	0
GSEA.HeatMapPlot	0.000	0.001	0.001
GSEA.HeatMapPlot2	0	0	0
GSEA.NormalizeCols	0.171	0.010	0.183
GSEA.NormalizeRows	0.001	0.001	0.000
GSEA	0	0	0
GSEA.ReadClsFile	0.159	0.005	0.165
GSEA.Res2Frame	0.167	0.005	0.174
GSEA.Threshold	0.164	0.006	0.172
GSEA.VarFilter	0.159	0.005	0.165
GSEA.write.gct	0.179	0.007	0.185
GeneExpMatrix	0.017	0.001	0.018
Match_GeneList_MSigDB	0.177	0.008	0.185
OLD.GSEA.EnrichmentScore	0.158	0.004	0.162
Run.GSEA	0.166	0.005	0.173
about	0	0	0
canceR	0	0	0
canceRHelp	0	0	0
canceR_Vignette	0.000	0.000	0.001
cbind.na	0	0	0
dialogGeneClassifier	0.047	0.004	0.051
dialogMetOption	0.157	0.004	0.161
dialogMut	0.156	0.006	0.162
dialogOptionCircos	0.136	0.006	0.143
dialogOptionGSEAlm	0.004	0.002	0.005
dialogOptionPhenoTest	0.188	0.006	0.195
dialogPlotOption_SkinCor	0.047	0.003	0.051
dialogSamplingGSEA	0.160	0.004	0.164
dialogSelectFiles_GSEA	0.158	0.007	0.165
dialogSpecificMut	0.163	0.005	0.170
dialogSummary_GSEA	0.162	0.005	0.169
dialoggetGeneListMSigDB	0.000	0.000	0.001
displayInTable	0.004	0.001	0.005
getCases	0.018	0.007	0.667
getCasesGenProfs	0.110	0.005	0.116
getCircos	0.145	0.006	0.152
getClinicData_MultipleCases	0.113	0.006	0.118
getClinicalDataMatrix	0.112	0.006	0.118
getCor_ExpCNAMet	0.134	0.007	0.141
getGCTCLSExample	0.204	0.008	0.212
getGCT_CLSfiles	0.160	0.005	0.165
getGSEAlm_Diseases	0.159	0.004	0.162
getGSEAlm_Variables	0.001	0.000	0.000
getGenProfs	0.016	0.007	0.824
getGeneExpMatrix	0.112	0.005	0.118
getGeneList	0.000	0.000	0.001
getGeneListExample	0	0	0
getGeneListFromMSigDB	0.112	0.004	0.116
getGenesClassifier	0	0	0
getGenesTree_MultipleCases	0.114	0.005	0.119
getGenesTree_SingleCase	0.187	0.012	0.202
getInTable	0.004	0.001	0.005
getListProfData	0.116	0.005	0.122
getMSigDB	0	0	0
getMSigDBExample	0.111	0.005	0.117
getMSigDBfile	0	0	0
getMegaProfData	0.113	0.006	0.118
getMetDataMultipleGenes	0.161	0.004	0.166
getMutData	0.179	0.004	0.183
getPhenoTest	0.175	0.011	0.186
getProfilesDataMultipleGenes	0.176	0.014	0.189
getProfilesDataSingleGene	0.113	0.009	0.122
getSpecificMut	0.164	0.008	0.171
getSummaryGSEA	0.160	0.005	0.167
getSurvival	0	0	0
getTextWin	0	0	0
geteSet	0	0	0
modalDialog	0.109	0.004	0.113
myGlobalEnv	0	0	0
plotModel	0.046	0.004	0.050
plot_1Gene_2GenProfs	0.046	0.003	0.049
plot_2Genes_1GenProf	0.156	0.004	0.161
rbind.na	0.000	0.001	0.000
setWorkspace	0.125	0.004	0.129
testCheckedCaseGenProf	0.110	0.003	0.114