Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:10 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for canceR on nebbiolo2


To the developers/maintainers of the canceR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/canceR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 240/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.28.0  (landing page)
Karim Mezhoud
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/canceR
git_branch: RELEASE_3_14
git_last_commit: 2fbf44c
git_last_commit_date: 2021-10-26 12:19:05 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: canceR
Version: 1.28.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings canceR_1.28.0.tar.gz
StartedAt: 2022-01-25 06:43:03 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 06:46:48 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 225.0 seconds
RetCode: 0
Status:   OK  
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings canceR_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/canceR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.28.0’
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL canceR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 10.685   1.264  12.271 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets0.0010.0000.000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore20.0010.0000.000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking0.0000.0000.001
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.0010.0000.001
GSEA.NormalizeRows000
GSEA0.0000.0000.001
GSEA.ReadClsFile0.0010.0000.000
GSEA.Res2Frame0.0010.0000.000
GSEA.Threshold000
GSEA.VarFilter000
GSEA.write.gct000
Match_GeneList_MSigDB0.0000.0000.001
OLD.GSEA.EnrichmentScore0.0010.0000.001
Run.GSEA0.0010.0000.001
about000
canceR0.0010.0000.000
canceRHelp000
canceR_Vignette000
cbind.na000
dialogGeneClassifier0.0010.0000.001
dialogMetOption000
dialogMut000
dialogOptionCircos000
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor0.0010.0000.001
dialogSamplingGSEA0.0010.0000.001
dialogSelectFiles_GSEA000
dialogSpecificMut000
dialogSummary_GSEA000
dialoggetGeneListMSigDB0.0010.0000.001
displayInTable000
getCases0.0740.0010.247
getCasesGenProfs0.0000.0000.001
getCircos0.0000.0000.001
getClinicData_MultipleCases000
getClinicalDataMatrix000
getCor_ExpCNAMet0.0010.0000.000
getGCTCLSExample0.0010.0000.001
getGCT_CLSfiles0.0010.0000.001
getGSEAlm_Diseases0.0000.0000.001
getGSEAlm_Variables000
getGenProfs0.0660.0000.334
getGeneList0.0010.0000.000
getGeneListExample000
getGeneListFromMSigDB0.0010.0000.001
getGenesClassifier0.0010.0000.001
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData000
getMSigDB000
getMSigDBExample000
getMSigDBfile000
getMegaProfData0.0010.0000.001
getMetDataMultipleGenes0.0010.0000.001
getMutData000
getPhenoTest000
getProfilesDataMultipleGenes0.0010.0000.001
getProfilesDataSingleGene0.0000.0010.001
getSpecificMut0.0000.0010.000
getSummaryGSEA000
getSurvival000
getTextWin000
geteSet000
modalDialog000
myGlobalEnv000
plotModel0.0010.0000.001
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf000
rbind.na000
setWorkspace000
testCheckedCaseGenProf000