Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:22 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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 palomino5


To the developers/maintainers of the canceR package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 244/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.33.0  (landing page)
Karim Mezhoud
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/canceR
git_branch: master
git_last_commit: 60e88c6
git_last_commit_date: 2022-11-01 11:11:13 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: canceR
Version: 1.33.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:canceR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings canceR_1.33.0.tar.gz
StartedAt: 2022-12-28 22:13:16 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 22:16:24 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 188.0 seconds
RetCode: 0
Status:   OK  
CheckDir: canceR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:canceR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings canceR_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/canceR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'canceR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'canceR' version '1.33.0'
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'canceR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... NOTE
Namespace in Imports field not imported from: 'R.methodsS3'
  All declared Imports should be used.
* 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 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/canceR.Rcheck/00check.log'
for details.



Installation output

canceR.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL canceR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-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
** installing vignettes
** 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 Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

> 
> 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 
   8.96    0.73    9.95 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets000
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot0.000.020.01
GSEA.HeatMapPlot2000
GSEA.NormalizeCols000
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile000
GSEA.Res2Frame000
GSEA.Threshold000
GSEA.VarFilter000
GSEA.write.gct000
Match_GeneList_MSigDB000
OLD.GSEA.EnrichmentScore000
Run.GSEA000
about000
canceR000
canceR_Issue000
canceR_Vignette000
cbind.na000
dialogGeneClassifier000
dialogMetOption000
dialogMut000
dialogOptionCircos0.000.020.02
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor000
dialogSamplingGSEA000
dialogSelectFiles_GSEA000
dialogSpecificMut000
dialogSummary_GSEA000
dialoggetGeneListMSigDB000
displayInTable000
getCases000
getCasesGenProfs000
getCircos000
getClinicData_MultipleCases000
getClinicalDataMatrix000
getCor_ExpCNAMet0.000.020.01
getGCTCLSExample000
getGCT_CLSfiles000
getGSEAlm_Diseases000
getGSEAlm_Variables000
getGenProfs000
getGeneList000
getGeneListExample000
getGeneListFromMSigDB000
getGenesClassifier000
getGenesTree_MultipleCases000
getGenesTree_SingleCase000
getInTable000
getListProfData000
getMSigDB000
getMSigDBExample000
getMSigDBfile000
getMegaProfData000
getMetDataMultipleGenes000
getMutData000
getPhenoTest000
getProfilesDataMultipleGenes000
getProfilesDataSingleGene000
getSpecificMut000
getSummaryGSEA0.020.000.02
getSurvival000
getTextWin000
geteSet000
modalDialog000
myGlobalEnv000
plotModel000
plot_1Gene_2GenProfs000
plot_2Genes_1GenProf000
rbind.na000
setWorkspace000
testCheckedCaseGenProf000