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CHECK report for canceR on malbec2

This page was generated on 2019-10-16 12:06:16 -0400 (Wed, 16 Oct 2019).

Package 205/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.18.6
Karim Mezhoud
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/canceR
Branch: RELEASE_3_9
Last Commit: 8557fdf
Last Changed Date: 2019-06-17 05:33:15 -0400 (Mon, 17 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.18.6
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings canceR_1.18.6.tar.gz
StartedAt: 2019-10-16 00:15:32 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:21:49 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 377.5 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings canceR_1.18.6.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL canceR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output

canceR.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 17.288   1.387  19.299 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets000
GSEA.ConsPlot0.0010.0000.000
GSEA.EnrichmentScore0.0010.0000.000
GSEA.EnrichmentScore20.0010.0000.000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.0010.0000.098
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.0010.0000.001
GSEA.Res2Frame0.0010.0000.001
GSEA.Threshold0.0010.0000.001
GSEA.VarFilter0.0010.0000.001
GSEA.write.gct0.0010.0000.008
Match_GeneList_MSigDB0.0010.0000.001
OLD.GSEA.EnrichmentScore0.0010.0000.001
Run.GSEA0.0010.0000.001
about0.0010.0000.000
canceR0.0010.0000.001
canceRHelp0.0000.0000.001
canceR_Vignette0.0000.0000.001
cbind.na0.0000.0000.001
dialogGeneClassifier0.0000.0000.001
dialogMetOption0.0010.0000.001
dialogMut0.0010.0000.001
dialogOptionCircos0.0010.0000.001
dialogOptionGSEAlm000
dialogOptionPhenoTest0.0010.0000.000
dialogPlotOption_SkinCor0.0010.0000.000
dialogSamplingGSEA0.0010.0000.001
dialogSelectFiles_GSEA0.0020.0000.001
dialogSpecificMut0.0010.0000.001
dialogSummary_GSEA0.0010.0000.001
dialoggetGeneListMSigDB000
displayInTable0.0000.0000.001
getCases0.1010.0130.208
getCasesGenProfs0.0010.0000.001
getCircos0.0010.0000.000
getClinicData_MultipleCases0.0010.0000.001
getClinicalDataMatrix0.0010.0000.001
getCor_ExpCNAMet0.0010.0000.000
getGCTCLSExample0.0010.0000.001
getGCT_CLSfiles0.0010.0000.001
getGSEAlm_Diseases0.0000.0010.001
getGSEAlm_Variables000
getGenProfs0.0660.0100.162
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.0010.0000.001
getGenesClassifier0.0000.0010.000
getGenesTree_MultipleCases0.0000.0010.000
getGenesTree_SingleCase0.0000.0000.001
getInTable0.0000.0000.001
getListProfData0.0010.0000.001
getMSigDB000
getMSigDBExample0.0000.0010.001
getMSigDBfile0.0000.0010.000
getMegaProfData0.0000.0010.000
getMetDataMultipleGenes0.0010.0000.001
getMutData0.0010.0000.001
getPhenoTest0.0000.0000.001
getProfilesDataMultipleGenes0.0000.0010.001
getProfilesDataSingleGene0.0000.0010.001
getSpecificMut0.0010.0000.001
getSummaryGSEA0.0010.0000.001
getSurvival000
getTextWin000
geteSet000
modalDialog0.0010.0000.001
myGlobalEnv0.0010.0000.000
plotModel0.0010.0000.000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf0.0010.0000.001
rbind.na000
setWorkspace0.0010.0000.001
testCheckedCaseGenProf0.0000.0000.001