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CHECK report for canceR on merida1

This page was generated on 2020-08-11 11:57:10 -0400 (Tue, 11 Aug 2020).

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 217/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.23.0
Karim Mezhoud
Snapshot Date: 2020-08-10 14:50:56 -0400 (Mon, 10 Aug 2020)
URL: https://git.bioconductor.org/packages/canceR
Branch: master
Last Commit: eaa1ca4
Last Changed Date: 2020-04-27 14:47:07 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: canceR
Version: 1.23.0
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_1.23.0.tar.gz
StartedAt: 2020-08-11 01:18:53 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-11 01:24:21 -0400 (Tue, 11 Aug 2020)
EllapsedTime: 327.5 seconds
RetCode: 0
Status:  OK 
CheckDir: canceR.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/canceR.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.23.0’
* 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 ... 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL canceR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

> 
> 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 
 14.819   1.923  17.050 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets0.0000.0010.000
GSEA.ConsPlot0.0000.0000.001
GSEA.EnrichmentScore0.0000.0010.000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame20.0000.0000.001
GSEA.GeneRanking000
GSEA.HeatMapPlot0.0000.0010.000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.0010.0000.003
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.0020.0010.003
GSEA.Res2Frame0.0010.0010.003
GSEA.Threshold0.0010.0010.002
GSEA.VarFilter0.0010.0010.002
GSEA.write.gct0.0020.0020.003
Match_GeneList_MSigDB0.0000.0010.002
OLD.GSEA.EnrichmentScore0.0020.0010.002
Run.GSEA0.0010.0010.002
about0.0000.0000.001
canceR000
canceRHelp0.0000.0010.000
canceR_Vignette000
cbind.na0.0000.0010.001
dialogGeneClassifier0.0010.0010.001
dialogMetOption0.0010.0010.003
dialogMut0.0020.0010.002
dialogOptionCircos0.0000.0000.001
dialogOptionGSEAlm0.0000.0000.001
dialogOptionPhenoTest0.0000.0000.001
dialogPlotOption_SkinCor0.0010.0010.002
dialogSamplingGSEA0.0020.0010.003
dialogSelectFiles_GSEA0.0010.0010.002
dialogSpecificMut0.0020.0010.003
dialogSummary_GSEA0.0010.0010.002
dialoggetGeneListMSigDB0.0010.0000.000
displayInTable0.0000.0000.001
getCases0.0820.0280.206
getCasesGenProfs0.0010.0010.001
getCircos0.0000.0000.001
getClinicData_MultipleCases0.0010.0010.002
getClinicalDataMatrix0.0010.0000.001
getCor_ExpCNAMet0.0000.0000.001
getGCTCLSExample0.0020.0010.002
getGCT_CLSfiles0.0010.0010.003
getGSEAlm_Diseases0.0020.0020.004
getGSEAlm_Variables0.0010.0000.000
getGenProfs0.0610.0090.159
getGeneList000
getGeneListExample0.0000.0000.001
getGeneListFromMSigDB0.0010.0020.002
getGenesClassifier0.0000.0000.001
getGenesTree_MultipleCases0.0010.0010.000
getGenesTree_SingleCase0.0000.0010.001
getInTable000
getListProfData0.0010.0000.001
getMSigDB0.0010.0000.000
getMSigDBExample0.0010.0010.002
getMSigDBfile000
getMegaProfData0.0010.0000.002
getMetDataMultipleGenes0.0010.0010.001
getMutData0.0010.0010.002
getPhenoTest0.0010.0000.001
getProfilesDataMultipleGenes0.0000.0000.001
getProfilesDataSingleGene0.0010.0000.002
getSpecificMut0.0000.0010.002
getSummaryGSEA0.0010.0010.001
getSurvival000
getTextWin000
geteSet0.0000.0000.001
modalDialog0.0010.0010.001
myGlobalEnv0.0010.0000.001
plotModel0.0010.0010.001
plot_1Gene_2GenProfs0.0010.0010.001
plot_2Genes_1GenProf0.0010.0010.002
rbind.na000
setWorkspace0.0000.0010.001
testCheckedCaseGenProf0.0010.0010.002