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CHECK report for canceR on nebbiolo1

This page was generated on 2021-02-22 12:33:20 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the canceR package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 227/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.24.0
Karim Mezhoud
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/canceR
Branch: RELEASE_3_12
Last Commit: 84f757f
Last Changed Date: 2020-10-27 11:03:04 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.24.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings canceR_1.24.0.tar.gz
StartedAt: 2021-02-21 20:30:18 -0500 (Sun, 21 Feb 2021)
EndedAt: 2021-02-21 20:36:07 -0500 (Sun, 21 Feb 2021)
EllapsedTime: 349.3 seconds
RetCode: 0
Status:   OK  
CheckDir: canceR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings canceR_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/canceR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.24.0’
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL canceR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘canceR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (canceR)

Tests output

canceR.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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

> 
> 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
══ Skipped tests ═══════════════════════════════════════════════════════════════
● empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  8.464   0.960  12.400 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame20.0000.0000.001
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.0000.0010.001
GSEA.NormalizeRows000
GSEA0.0000.0010.000
GSEA.ReadClsFile0.0000.0010.001
GSEA.Res2Frame0.0000.0010.001
GSEA.Threshold0.0000.0010.001
GSEA.VarFilter0.0000.0010.001
GSEA.write.gct0.0010.0000.001
Match_GeneList_MSigDB0.0000.0000.001
OLD.GSEA.EnrichmentScore0.0000.0010.001
Run.GSEA0.0000.0010.001
about0.0000.0000.001
canceR000
canceRHelp0.0010.0000.000
canceR_Vignette0.0000.0000.001
cbind.na000
dialogGeneClassifier0.0000.0000.001
dialogMetOption0.0000.0010.001
dialogMut0.0000.0010.001
dialogOptionCircos0.0000.0010.001
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor000
dialogSamplingGSEA0.0000.0010.001
dialogSelectFiles_GSEA0.0000.0010.001
dialogSpecificMut0.0000.0010.001
dialogSummary_GSEA0.0000.0010.001
dialoggetGeneListMSigDB0.0000.0010.000
displayInTable000
getCases0.0630.0100.192
getCasesGenProfs0.0000.0020.004
getCircos0.0010.0000.002
getClinicData_MultipleCases0.0010.0000.002
getClinicalDataMatrix0.0010.0000.001
getCor_ExpCNAMet0.0010.0000.001
getGCTCLSExample0.0010.0000.002
getGCT_CLSfiles0.0010.0000.002
getGSEAlm_Diseases0.0010.0000.001
getGSEAlm_Variables0.0010.0000.000
getGenProfs0.0660.0030.181
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.0010.0000.002
getGenesClassifier0.0000.0000.001
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData0.0000.0010.001
getMSigDB0.0000.0000.001
getMSigDBExample0.0000.0010.001
getMSigDBfile0.0000.0010.000
getMegaProfData0.0000.0010.002
getMetDataMultipleGenes0.0000.0010.001
getMutData0.0000.0010.001
getPhenoTest0.0000.0000.001
getProfilesDataMultipleGenes0.0000.0010.001
getProfilesDataSingleGene0.0000.0020.001
getSpecificMut0.0000.0020.002
getSummaryGSEA0.0000.0020.002
getSurvival0.0000.0010.001
getTextWin0.0000.0000.001
geteSet0.0000.0000.001
modalDialog0.0000.0010.001
myGlobalEnv000
plotModel000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf0.0000.0010.001
rbind.na000
setWorkspace0.0000.0010.001
testCheckedCaseGenProf0.0000.0010.001