Package: canceR

Version: 1.16.02

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_1.16.02.tar.gz

StartedAt: 2019-04-15 22:44:56 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:52:55 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 479.5 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_1.16.02.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/canceR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.16.02’
* 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 ... 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 ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-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/3.5/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 version 3.5.3 (2019-03-11) -- "Great Truth"
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) ...  FAILED!
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 
 17.839   1.972  22.192 

name	user	system	elapsed
ClinicalData	0.009	0.001	0.011
GSEA.Analyze.Sets	0.000	0.000	0.001
GSEA.ConsPlot	0.001	0.000	0.001
GSEA.EnrichmentScore	0	0	0
GSEA.EnrichmentScore2	0.000	0.000	0.001
GSEA.Gct2Frame	0	0	0
GSEA.Gct2Frame2	0.000	0.000	0.001
GSEA.GeneRanking	0	0	0
GSEA.HeatMapPlot	0.000	0.000	0.001
GSEA.HeatMapPlot2	0	0	0
GSEA.NormalizeCols	0.184	0.007	0.192
GSEA.NormalizeRows	0	0	0
GSEA	0	0	0
GSEA.ReadClsFile	0.812	0.006	0.821
GSEA.Res2Frame	0.209	0.005	0.214
GSEA.Threshold	0.165	0.007	0.172
GSEA.VarFilter	0.213	0.007	0.220
GSEA.write.gct	0.181	0.006	0.189
GeneExpMatrix	0.027	0.002	0.029
Match_GeneList_MSigDB	0.211	0.009	0.222
OLD.GSEA.EnrichmentScore	0.213	0.008	0.222
Run.GSEA	0.186	0.008	0.196
about	0	0	0
canceR	0	0	0
canceRHelp	0.000	0.000	0.001
canceR_Vignette	0	0	0
cbind.na	0.001	0.000	0.001
dialogGeneClassifier	0.062	0.005	0.068
dialogMetOption	0.208	0.007	0.217
dialogMut	0.191	0.008	0.199
dialogOptionCircos	0.237	0.014	0.253
dialogOptionGSEAlm	0.005	0.001	0.006
dialogOptionPhenoTest	0.239	0.011	0.254
dialogPlotOption_SkinCor	0.059	0.004	0.064
dialogSamplingGSEA	0.224	0.006	0.231
dialogSelectFiles_GSEA	0.223	0.007	0.233
dialogSpecificMut	0.195	0.006	0.203
dialogSummary_GSEA	0.192	0.006	0.199
dialoggetGeneListMSigDB	0	0	0
displayInTable	0.006	0.001	0.007
getCases	0.025	0.008	0.644
getCasesGenProfs	0.142	0.006	0.148
getCircos	0.155	0.007	0.163
getClinicData_MultipleCases	0.160	0.005	0.167
getClinicalDataMatrix	0.152	0.005	0.160
getCor_ExpCNAMet	0.206	0.008	0.217
getGCTCLSExample	0.213	0.006	0.220
getGCT_CLSfiles	0.230	0.006	0.243
getGSEAlm_Diseases	0.209	0.006	0.218
getGSEAlm_Variables	0.000	0.000	0.001
getGenProfs	0.023	0.009	0.833
getGeneExpMatrix	0.175	0.007	0.182
getGeneList	0.001	0.000	0.001
getGeneListExample	0.001	0.000	0.000
getGeneListFromMSigDB	0.163	0.006	0.172
getGenesClassifier	0.000	0.001	0.000
getGenesTree_MultipleCases	0.168	0.006	0.174
getGenesTree_SingleCase	0.236	0.010	0.251
getInTable	0.006	0.001	0.007
getListProfData	0.156	0.006	0.163
getMSigDB	0	0	0
getMSigDBExample	0.160	0.007	0.169
getMSigDBfile	0.000	0.000	0.001
getMegaProfData	0.165	0.005	0.174
getMetDataMultipleGenes	0.209	0.005	0.214
getMutData	0.211	0.006	0.218
getPhenoTest	0.230	0.007	0.237
getProfilesDataMultipleGenes	0.214	0.007	0.222
getProfilesDataSingleGene	0.148	0.005	0.152
getSpecificMut	0.266	0.005	0.272
getSummaryGSEA	0.174	0.003	0.178
getSurvival	0	0	0
getTextWin	0	0	0
geteSet	0.001	0.000	0.001
modalDialog	0.162	0.002	0.167
myGlobalEnv	0	0	0
plotModel	0.060	0.004	0.065
plot_1Gene_2GenProfs	0.056	0.005	0.062
plot_2Genes_1GenProf	0.229	0.005	0.235
rbind.na	0.000	0.000	0.001
setWorkspace	0.164	0.005	0.169
testCheckedCaseGenProf	0.130	0.006	0.136