Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-18 17:57 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 268/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
canceR 1.38.0  (landing page)
Karim Mezhoud
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/canceR
git_branch: RELEASE_3_19
git_last_commit: 281311f
git_last_commit_date: 2024-04-30 10:42:04 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for canceR on nebbiolo1

To the developers/maintainers of the canceR package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.38.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings canceR_1.38.0.tar.gz
StartedAt: 2024-06-16 21:19:11 -0400 (Sun, 16 Jun 2024)
EndedAt: 2024-06-16 21:26:29 -0400 (Sun, 16 Jun 2024)
EllapsedTime: 437.7 seconds
RetCode: 0
Status:   OK  
CheckDir: canceR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:canceR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings canceR_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/canceR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘canceR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘canceR’ version ‘1.38.0’
* 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 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 code 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 loading without being on the library search path ... 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 Rd file 'cbind.na.Rd':
  ‘cbind.na’

S3 methods shown with full name in Rd file 'rbind.na.Rd':
  ‘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 ... NOTE
Argument items with no description in Rd file 'GSEA.EnrichmentScore.Rd':
  ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’
Argument items with no description in Rd file 'GSEA.EnrichmentScore2.Rd':
  ‘gene.list’ ‘gene.set’ ‘weighted.score.type’ ‘correl.vector’
Argument items with no description in Rd file 'GSEA.Gct2Frame.Rd':
  ‘filename’
Argument items with no description in Rd file 'GSEA.Gct2Frame2.Rd':
  ‘filename’
Argument items with no description in Rd file 'GSEA.GeneRanking.Rd':
  ‘A’ ‘class.labels’ ‘gene.labels’ ‘nperm’ ‘permutation.type’
  ‘sigma.correction’ ‘fraction’ ‘replace’ ‘reverse.sign’
Argument items with no description in Rd file 'GSEA.NormalizeCols.Rd':
  ‘V’
Argument items with no description in Rd file 'GSEA.NormalizeRows.Rd':
  ‘V’
Argument items with no description in Rd file 'GSEA.ReadClsFile.Rd':
  ‘file’
Argument items with no description in Rd file 'GSEA.Res2Frame.Rd':
  ‘filename’
Argument items with no description in Rd file 'GSEA.Threshold.Rd':
  ‘V’ ‘thres’ ‘ceil’
Argument items with no description in Rd file 'GSEA.VarFilter.Rd':
  ‘V’ ‘fold’ ‘delta’ ‘gene.names’
Argument items with no description in Rd file 'GSEA.write.gct.Rd':
  ‘gct’ ‘filename’
Argument items with no description in Rd file 'OLD.GSEA.EnrichmentScore.Rd':
  ‘gene.list’ ‘gene.set’
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/canceR.Rcheck/00check.log’
for details.


Installation output

canceR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL canceR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, 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 
 18.953   3.433  22.749 

Example timings

canceR.Rcheck/canceR-Ex.timings

nameusersystemelapsed
GSEA.Analyze.Sets000
GSEA.ConsPlot0.0010.0000.000
GSEA.EnrichmentScore000
GSEA.EnrichmentScore20.0000.0000.001
GSEA.Gct2Frame0.0010.0000.000
GSEA.Gct2Frame2000
GSEA.GeneRanking000
GSEA.HeatMapPlot000
GSEA.HeatMapPlot2000
GSEA.NormalizeCols0.0000.0020.002
GSEA.NormalizeRows000
GSEA000
GSEA.ReadClsFile0.0010.0000.002
GSEA.Res2Frame0.0010.0000.001
GSEA.Threshold0.0000.0010.001
GSEA.VarFilter0.0000.0010.001
GSEA.write.gct0.0000.0010.001
Match_GeneList_MSigDB0.0000.0010.001
OLD.GSEA.EnrichmentScore0.0000.0010.001
Run.GSEA0.0010.0000.002
UnifyRowNames0.1440.0160.239
about000
canceR000
canceR_Issue000
canceR_Vignette0.0010.0000.000
cbind.na0.0000.0000.001
dialogGeneClassifier0.0010.0000.001
dialogMetOption0.0020.0000.001
dialogMut0.0000.0010.001
dialogOptionCircos0.0000.0010.001
dialogOptionGSEAlm000
dialogOptionPhenoTest0.0010.0000.000
dialogPlotOption_SkinCor0.0000.0000.001
dialogSamplingGSEA0.0010.0000.001
dialogSelectFiles_GSEA0.0020.0000.001
dialogSpecificMut0.0010.0000.001
dialogSummary_GSEA0.0010.0000.002
dialoggetGeneListMSigDB000
displayInTable000
getCases0.0600.0080.084
getCasesGenProfs0.0610.0070.084
getCircos0.0010.0000.001
getClinicData_MultipleCases0.0020.0000.002
getClinicalDataMatrix0.0010.0000.001
getCor_ExpCNAMet0.0010.0010.001
getFreqMutData0.0700.0070.093
getGCTCLSExample0.0010.0010.002
getGCT_CLSfiles0.0010.0000.001
getGSEAlm_Diseases0.0010.0000.001
getGSEAlm_Variables000
getGenProfs0.0590.0140.089
getGeneExpMatrix0.0010.0000.001
getGeneList0.0010.0000.000
getGeneListExample000
getGeneListFromMSigDB0.0000.0010.002
getGenesClassifier0.0000.0010.001
getGenesTree_MultipleCases0.0000.0010.001
getGenesTree_SingleCase0.0000.0010.001
getInTable000
getListProfData0.0000.0010.001
getMSigDB000
getMSigDBExample0.0000.0010.001
getMSigDBfile000
getMegaProfData0.0000.0010.001
getMetDataMultipleGenes0.0000.0010.001
getMutData0.0020.0000.001
getPhenoTest0.0010.0000.001
getProfData0.0550.0160.086
getProfilesDataMultipleGenes0.0010.0000.001
getProfilesDataSingleGene0.0000.0010.001
getSpecificMut0.0000.0010.001
getSummaryGSEA0.0000.0010.001
getSurvival000
getTextWin000
geteSet0.0000.0010.000
modalDialog0.0000.0010.001
myGlobalEnv000
plotModel0.0000.0010.001
plot_1Gene_2GenProfs0.0000.0000.001
plot_2Genes_1GenProf0.0010.0000.002
rbind.na000
setWorkspace0.0010.0000.001
testCheckedCaseGenProf0.0000.0010.001