Package: canceR

Version: 1.18.6

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_1.18.6.tar.gz

StartedAt: 2019-10-16 01:07:32 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:17:51 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 619.1 seconds

RetCode: 0

Status:  OK

CheckDir: canceR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.18.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Files named as vignettes but with no recognized vignette engine:
   ‘inst/doc/canceR.Rnw’
(Is a VignetteBuilder field missing?)
* 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 ... OK
* checking package 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘canceR.Rnw’
A ‘vignettes’ directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL canceR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘canceR’ ...
** using staged installation
** R
** 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
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘igraph::union’ by ‘GSEABase::union’ when loading ‘HTSanalyzeR’
** testing if installed package keeps a record of temporary installation path
* DONE (canceR)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.713   5.289  29.218 

name	user	system	elapsed
GSEA.Analyze.Sets	0.001	0.000	0.000
GSEA.ConsPlot	0.000	0.000	0.001
GSEA.EnrichmentScore	0.000	0.000	0.001
GSEA.EnrichmentScore2	0.001	0.001	0.001
GSEA.Gct2Frame	0.000	0.000	0.001
GSEA.Gct2Frame2	0	0	0
GSEA.GeneRanking	0.000	0.000	0.001
GSEA.HeatMapPlot	0.000	0.001	0.001
GSEA.HeatMapPlot2	0.001	0.000	0.000
GSEA.NormalizeCols	0.002	0.001	0.003
GSEA.NormalizeRows	0.000	0.000	0.001
GSEA	0.001	0.000	0.001
GSEA.ReadClsFile	0.002	0.001	0.002
GSEA.Res2Frame	0.002	0.001	0.003
GSEA.Threshold	0.002	0.001	0.004
GSEA.VarFilter	0.002	0.001	0.002
GSEA.write.gct	0.001	0.000	0.002
Match_GeneList_MSigDB	0.001	0.001	0.002
OLD.GSEA.EnrichmentScore	0.002	0.001	0.003
Run.GSEA	0.002	0.001	0.003
about	0	0	0
canceR	0	0	0
canceRHelp	0	0	0
canceR_Vignette	0	0	0
cbind.na	0.000	0.001	0.000
dialogGeneClassifier	0.001	0.000	0.001
dialogMetOption	0.001	0.000	0.002
dialogMut	0.001	0.000	0.001
dialogOptionCircos	0.001	0.001	0.002
dialogOptionGSEAlm	0.000	0.000	0.001
dialogOptionPhenoTest	0.001	0.000	0.001
dialogPlotOption_SkinCor	0.001	0.001	0.001
dialogSamplingGSEA	0.001	0.001	0.001
dialogSelectFiles_GSEA	0.002	0.001	0.002
dialogSpecificMut	0.001	0.000	0.002
dialogSummary_GSEA	0.001	0.001	0.002
dialoggetGeneListMSigDB	0.000	0.000	0.001
displayInTable	0.000	0.001	0.000
getCases	0.101	0.052	0.250
getCasesGenProfs	0.001	0.001	0.003
getCircos	0.001	0.000	0.001
getClinicData_MultipleCases	0.002	0.001	0.004
getClinicalDataMatrix	0.002	0.001	0.003
getCor_ExpCNAMet	0.001	0.001	0.002
getGCTCLSExample	0.002	0.002	0.003
getGCT_CLSfiles	0.002	0.002	0.003
getGSEAlm_Diseases	0.002	0.002	0.004
getGSEAlm_Variables	0.001	0.000	0.001
getGenProfs	0.066	0.019	0.169
getGeneList	0	0	0
getGeneListExample	0.000	0.000	0.001
getGeneListFromMSigDB	0.001	0.001	0.004
getGenesClassifier	0.001	0.001	0.000
getGenesTree_MultipleCases	0.001	0.000	0.001
getGenesTree_SingleCase	0.001	0.000	0.001
getInTable	0.001	0.000	0.001
getListProfData	0.002	0.001	0.003
getMSigDB	0.001	0.001	0.000
getMSigDBExample	0.002	0.001	0.002
getMSigDBfile	0	0	0
getMegaProfData	0.002	0.004	0.006
getMetDataMultipleGenes	0.002	0.001	0.003
getMutData	0.002	0.000	0.002
getPhenoTest	0.001	0.000	0.001
getProfilesDataMultipleGenes	0.001	0.001	0.002
getProfilesDataSingleGene	0.002	0.001	0.003
getSpecificMut	0.002	0.002	0.003
getSummaryGSEA	0.002	0.002	0.004
getSurvival	0.000	0.001	0.001
getTextWin	0	0	0
geteSet	0.001	0.000	0.000
modalDialog	0.002	0.001	0.002
myGlobalEnv	0.000	0.000	0.001
plotModel	0.000	0.001	0.001
plot_1Gene_2GenProfs	0.001	0.001	0.002
plot_2Genes_1GenProf	0.002	0.002	0.003
rbind.na	0.000	0.001	0.001
setWorkspace	0.001	0.001	0.003
testCheckedCaseGenProf	0.001	0.001	0.002