Package: canceR

Version: 1.14.0

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_1.14.0.tar.gz

StartedAt: 2018-10-16 20:14:20 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:22:14 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 473.5 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/canceR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.14.0’
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 
 12.351   1.423  16.990 

name	user	system	elapsed
ClinicalData	0.008	0.001	0.009
GSEA.Analyze.Sets	0.001	0.000	0.001
GSEA.ConsPlot	0.001	0.000	0.001
GSEA.EnrichmentScore	0.001	0.000	0.002
GSEA.EnrichmentScore2	0.001	0.001	0.001
GSEA.Gct2Frame	0.001	0.000	0.002
GSEA.Gct2Frame2	0.001	0.000	0.001
GSEA.GeneRanking	0.001	0.000	0.001
GSEA.HeatMapPlot	0.001	0.000	0.001
GSEA.HeatMapPlot2	0.001	0.000	0.001
GSEA.NormalizeCols	0.170	0.007	0.178
GSEA.NormalizeRows	0.001	0.000	0.001
GSEA	0.001	0.001	0.001
GSEA.ReadClsFile	0.164	0.005	0.170
GSEA.Res2Frame	0.160	0.007	0.168
GSEA.Threshold	0.161	0.005	0.166
GSEA.VarFilter	0.758	0.005	0.762
GSEA.write.gct	0.157	0.004	0.162
GeneExpMatrix	0.017	0.001	0.019
Match_GeneList_MSigDB	0.171	0.008	0.178
OLD.GSEA.EnrichmentScore	0.160	0.006	0.166
Run.GSEA	0.154	0.006	0.160
about	0.001	0.000	0.001
canceR	0.001	0.000	0.001
canceRHelp	0.001	0.001	0.001
canceR_Vignette	0.000	0.000	0.001
cbind.na	0.001	0.000	0.001
dialogGeneClassifier	0.045	0.004	0.050
dialogMetOption	0.159	0.007	0.165
dialogMut	0.154	0.006	0.161
dialogOptionCircos	0.137	0.010	0.148
dialogOptionGSEAlm	0.004	0.001	0.006
dialogOptionPhenoTest	0.187	0.008	0.195
dialogPlotOption_SkinCor	0.044	0.003	0.048
dialogSamplingGSEA	0.152	0.004	0.156
dialogSelectFiles_GSEA	0.153	0.004	0.157
dialogSpecificMut	0.155	0.004	0.159
dialogSummary_GSEA	0.155	0.004	0.159
dialoggetGeneListMSigDB	0.001	0.000	0.001
displayInTable	0.004	0.001	0.006
getCases	0.020	0.011	1.778
getCasesGenProfs	0.109	0.005	0.114
getCircos	0.132	0.006	0.139
getClinicData_MultipleCases	0.109	0.003	0.112
getClinicalDataMatrix	0.107	0.001	0.108
getCor_ExpCNAMet	0.141	0.008	0.149
getGCTCLSExample	0.157	0.005	0.161
getGCT_CLSfiles	0.154	0.002	0.155
getGSEAlm_Diseases	0.155	0.002	0.156
getGSEAlm_Variables	0.001	0.000	0.001
getGenProfs	0.017	0.008	0.899
getGeneExpMatrix	0.107	0.001	0.108
getGeneList	0.001	0.000	0.002
getGeneListExample	0.001	0.000	0.001
getGeneListFromMSigDB	0.110	0.001	0.112
getGenesClassifier	0.001	0.000	0.001
getGenesTree_MultipleCases	0.106	0.000	0.108
getGenesTree_SingleCase	0.181	0.006	0.188
getInTable	0.005	0.001	0.006
getListProfData	0.112	0.005	0.117
getMSigDB	0.001	0.000	0.001
getMSigDBExample	0.112	0.005	0.117
getMSigDBfile	0.001	0.000	0.001
getMegaProfData	0.110	0.004	0.114
getMetDataMultipleGenes	0.154	0.004	0.158
getMutData	0.155	0.004	0.159
getPhenoTest	0.197	0.010	0.207
getProfilesDataMultipleGenes	0.167	0.005	0.173
getProfilesDataSingleGene	0.110	0.004	0.115
getSpecificMut	0.173	0.004	0.178
getSummaryGSEA	0.154	0.005	0.158
getSurvival	0.001	0.000	0.001
getTextWin	0.000	0.000	0.001
geteSet	0.001	0.000	0.001
modalDialog	0.109	0.004	0.115
myGlobalEnv	0.001	0.000	0.001
plotModel	0.045	0.004	0.048
plot_1Gene_2GenProfs	0.044	0.003	0.048
plot_2Genes_1GenProf	0.152	0.003	0.157
rbind.na	0.001	0.000	0.001
setWorkspace	0.111	0.004	0.116
testCheckedCaseGenProf	0.110	0.005	0.115