Package: canceR

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings canceR_1.10.0.tar.gz

StartedAt: 2018-04-12 01:15:10 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:21:21 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 370.5 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 --no-vignettes --timings canceR_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/canceR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 35.8Mb
  sub-directories of 1Mb or more:
    data      7.1Mb
    doc      25.3Mb
    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 loading without being on the library search path ... 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.HeatMapPlot2: possible error in rainbow(100, s = 1, v = 0.75,
  start = 0, end = 0.75, gamma = 1.5): unused argument (gamma = 1.5)
* 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 installed files from ‘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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/canceR.Rcheck/00check.log’
for details.

* installing *source* package ‘canceR’ ...
** R
** data
** inst
** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
 13.204   1.206  17.242 

name	user	system	elapsed
ClinicalData	0.008	0.002	0.010
GSEA.Analyze.Sets	0.001	0.000	0.001
GSEA.ConsPlot	0.000	0.000	0.001
GSEA.EnrichmentScore	0.001	0.001	0.001
GSEA.EnrichmentScore2	0	0	0
GSEA.Gct2Frame	0	0	0
GSEA.Gct2Frame2	0.000	0.000	0.001
GSEA.GeneRanking	0.001	0.000	0.001
GSEA.HeatMapPlot	0.001	0.000	0.001
GSEA.HeatMapPlot2	0.000	0.000	0.001
GSEA.NormalizeCols	0.177	0.013	0.191
GSEA.NormalizeRows	0.000	0.000	0.001
GSEA	0.001	0.000	0.001
GSEA.ReadClsFile	0.183	0.011	0.194
GSEA.Res2Frame	0.188	0.016	0.205
GSEA.Threshold	0.168	0.016	0.187
GSEA.VarFilter	0.182	0.015	0.199
GSEA.write.gct	0.183	0.016	0.201
GeneExpMatrix	0.026	0.001	0.028
Match_GeneList_MSigDB	0.182	0.016	0.204
OLD.GSEA.EnrichmentScore	0.170	0.016	0.188
Run.GSEA	0.196	0.013	0.210
about	0.074	0.004	0.081
canceR	0.001	0.000	0.001
canceRHelp	0.002	0.000	0.002
canceR_Vignette	0.004	0.002	0.006
cbind.na	0.003	0.000	0.003
dialogGeneClassifier	0.063	0.015	0.078
dialogMetOption	0.206	0.014	0.225
dialogMut	0.260	0.017	0.284
dialogOptionCircos	0.166	0.005	0.172
dialogOptionGSEAlm	0.008	0.001	0.009
dialogOptionPhenoTest	0.222	0.015	0.239
dialogPlotOption_SkinCor	0.051	0.015	0.069
dialogSamplingGSEA	0.205	0.016	0.230
dialogSelectFiles_GSEA	0.198	0.018	0.216
dialogSpecificMut	0.210	0.013	0.225
dialogSummary_GSEA	0.162	0.011	0.178
dialoggetGeneListMSigDB	0	0	0
displayInTable	0.008	0.001	0.008
getCases	0.196	0.021	0.865
getCasesGenProfs	0.132	0.014	0.146
getCircos	0.149	0.006	0.157
getClinicData_MultipleCases	0.125	0.014	0.142
getClinicalDataMatrix	0.135	0.015	0.154
getCor_ExpCNAMet	0.130	0.004	0.134
getGCTCLSExample	0.197	0.011	0.211
getGCT_CLSfiles	0.175	0.014	0.191
getGSEAlm_Diseases	0.185	0.012	0.199
getGSEAlm_Variables	0	0	0
getGenProfs	0.018	0.009	0.867
getGeneExpMatrix	0.115	0.014	0.135
getGeneList	0	0	0
getGeneListExample	0.001	0.000	0.000
getGeneListFromMSigDB	0.122	0.014	0.140
getGenesClassifier	0.000	0.000	0.001
getGenesTree_MultipleCases	0.121	0.016	0.139
getGenesTree_SingleCase	0.171	0.017	0.190
getInTable	0.008	0.001	0.010
getListProfData	0.136	0.015	0.160
getMSigDB	0.001	0.000	0.001
getMSigDBExample	0.130	0.016	0.147
getMSigDBfile	0.001	0.000	0.001
getMegaProfData	0.129	0.013	0.142
getMetDataMultipleGenes	0.176	0.013	0.193
getMutData	0.180	0.015	0.195
getPhenoTest	0.195	0.014	0.213
getProfilesDataMultipleGenes	0.211	0.013	0.227
getProfilesDataSingleGene	0.118	0.015	0.138
getSpecificMut	0.185	0.016	0.205
getSummaryGSEA	0.170	0.015	0.187
getSurvival	0.000	0.000	0.001
getTextWin	0.000	0.000	0.001
geteSet	0.000	0.000	0.001
modalDialog	0.138	0.017	0.162
myGlobalEnv	0.000	0.000	0.001
plotModel	0.059	0.013	0.072
plot_1Gene_2GenProfs	0.058	0.012	0.071
plot_2Genes_1GenProf	0.191	0.013	0.228
rbind.na	0.003	0.000	0.002
setWorkspace	0.123	0.012	0.135
testCheckedCaseGenProf	0.129	0.010	0.141