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This page was generated on 2024-04-18 11:32:07 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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

Package 264/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.36.8  (landing page)
Karim Mezhoud
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/canceR
git_branch: RELEASE_3_18
git_last_commit: 696261f
git_last_commit_date: 2024-04-12 08:21:55 -0400 (Fri, 12 Apr 2024)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for canceR on kjohnson1


To the developers/maintainers of the canceR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: canceR
Version: 1.36.8
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings canceR_1.36.8.tar.gz
StartedAt: 2024-04-17 08:02:20 -0400 (Wed, 17 Apr 2024)
EndedAt: 2024-04-17 08:10:26 -0400 (Wed, 17 Apr 2024)
EllapsedTime: 486.4 seconds
RetCode: 0
Status:   OK  
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:canceR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings canceR_1.36.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/canceR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘canceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘canceR’ version ‘1.36.8’
* 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 for sufficient/correct file permissions ... 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 ... 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 ... NOTE
S3 methods shown with full name in documentation object 'cbind.na':
  ‘cbind.na’

S3 methods shown with full name in documentation object 'rbind.na':
  ‘rbind.na’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/canceR.Rcheck/00check.log’
for details.



Installation output

canceR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
** 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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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: cBioPortalData
Loading required package: AnVIL
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following object is masked from 'package:dplyr':

    count


Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:dplyr':

    combine, intersect, setdiff, union

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:dplyr':

    first, rename

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following objects are masked from 'package:dplyr':

    collapse, desc, slice

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


> 
> test_check("canceR")
getCancerStudies...  OK
getCaseLists (1/1) ...  OK
getClinicalData (1/1) ...  OK
getGeneticProfiles (1/1) ...  OK
getProfileData (1/1) ...  OK
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_funs.R:8:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 23.364   2.146  28.162 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets0.0000.0000.001
GSEA.ConsPlot000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore2000
GSEA.Gct2Frame000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot0.0000.0010.001
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.0010.0010.002
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile000
GSEA.Res2Frame000
GSEA.Threshold0.0000.0010.001
GSEA.VarFilter0.0010.0000.001
GSEA.write.gct000
Match_GeneList_MSigDB0.0000.0010.000
OLD.GSEA.EnrichmentScore0.0010.0000.001
Run.GSEA0.0000.0000.001
UnifyRowNames0.0670.0080.422
about000
canceR000
canceR_Issue000
canceR_Vignette0.0000.0000.001
cbind.na000
dialogGeneClassifier0.0000.0000.001
dialogMetOption0.0000.0000.001
dialogMut0.0010.0010.002
dialogOptionCircos0.0000.0010.001
dialogOptionGSEAlm000
dialogOptionPhenoTest000
dialogPlotOption_SkinCor0.0000.0010.000
dialogSamplingGSEA0.0000.0000.001
dialogSelectFiles_GSEA0.0010.0000.000
dialogSpecificMut0.0000.0010.001
dialogSummary_GSEA0.0010.0000.001
dialoggetGeneListMSigDB000
displayInTable0.0000.0000.001
getCases0.0550.0030.156
getCasesGenProfs0.0630.0040.164
getCircos0.0010.0000.001
getClinicData_MultipleCases0.0010.0010.001
getClinicalDataMatrix0.0000.0010.001
getCor_ExpCNAMet0.0000.0000.001
getFreqMutData0.0630.0030.164
getGCTCLSExample0.0010.0000.001
getGCT_CLSfiles0.0010.0000.002
getGSEAlm_Diseases0.0010.0000.002
getGSEAlm_Variables000
getGenProfs0.0650.0040.166
getGeneExpMatrix0.0000.0010.001
getGeneList000
getGeneListExample000
getGeneListFromMSigDB0.0000.0010.001
getGenesClassifier0.0000.0000.001
getGenesTree_MultipleCases0.0000.0010.001
getGenesTree_SingleCase0.0000.0000.001
getInTable0.0010.0000.000
getListProfData0.0010.0010.001
getMSigDB000
getMSigDBExample0.0010.0000.001
getMSigDBfile000
getMegaProfData0.0000.0000.001
getMetDataMultipleGenes0.0000.0010.002
getMutData0.0000.0010.002
getPhenoTest0.0000.0000.001
getProfData0.0610.0040.184
getProfilesDataMultipleGenes0.0010.0010.001
getProfilesDataSingleGene0.0000.0010.002
getSpecificMut0.0000.0010.001
getSummaryGSEA0.0010.0010.002
getSurvival000
getTextWin0.0010.0000.000
geteSet0.0000.0010.001
modalDialog0.0010.0010.001
myGlobalEnv0.0010.0000.000
plotModel0.0000.0000.001
plot_1Gene_2GenProfs0.0010.0000.013
plot_2Genes_1GenProf0.0010.0010.003
rbind.na0.0000.0010.000
setWorkspace0.0000.0010.001
testCheckedCaseGenProf0.0000.0010.001