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This page was generated on 2021-11-30 13:55:36 -0500 (Tue, 30 Nov 2021).

BUILD results for PDATK on merida1

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raw results

Package 1377/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PDATK 1.3.0  (landing page)
Benjamin Haibe-Kains
Snapshot Date: 2021-11-29 14:50:17 -0500 (Mon, 29 Nov 2021)
git_url: https://git.bioconductor.org/packages/PDATK
git_branch: master
git_last_commit: acec60e
git_last_commit_date: 2021-10-26 13:07:20 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    ERROR  skipped
riesling1Windows Server 2019 Standard / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: PDATK
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PDATK
StartedAt: 2021-11-29 22:03:58 -0500 (Mon, 29 Nov 2021)
EndedAt: 2021-11-29 22:07:28 -0500 (Mon, 29 Nov 2021)
EllapsedTime: 209.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PDATK
###
##############################################################################
##############################################################################


* checking for file ‘PDATK/DESCRIPTION’ ... OK
* preparing ‘PDATK’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘PCOSP_model_analysis.Rmd’ using rmarkdown
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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:stats':

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, 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:base':

    I, expand.grid, unname

Loading required package: IRanges
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

Registered S3 method overwritten by 'verification':
  method    from
  lines.roc pROC
Registered S3 method overwritten by 'sets':
  method        from   
  print.element ggplot2

Attaching package: 'data.table'

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

    shift

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

    shift

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

    shift

The following objects are masked from 'package:S4Vectors':

    first, second


[PDATK::SurvivalModel] Merging trainCohorts `CohortList` into a `SurvivalExperiment` with shared genes and samples...
Warning in FUN(X[[i]], ...) :
  
[PDATK::predictClasses] Dropped samples with NA survival data!
Warning in FUN(X[[i]], ...) :
  
[PDATK::predictClasses] Dropped samples with NA survival data!
Warning in FUN(X[[i]], ...) :
  
[PDATK::predictClasses] Dropped samples with NA survival data!
Setting levels: control = 0, case = 1
Warning in wilcox.test.default(predictor[table.gold == 1], predictor[table.gold ==  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") :
  cannot compute exact p-value with ties
Setting levels: control = 0, case = 1

Setting levels: control = 0, case = 1
Warning in wilcox.test.default(predictor[table.gold == 1], predictor[table.gold ==  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") :
  cannot compute exact p-value with ties
Setting levels: control = 0, case = 1
Warning in wilcox.test.default(predictor[table.gold == 1], predictor[table.gold ==  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") :
  cannot compute exact p-value with ties

Setting levels: control = 0, case = 1
Warning in wilcox.test.default(predictor[table.gold == 1], predictor[table.gold ==  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") :
  cannot compute exact p-value with ties
Setting levels: control = 0, case = 1
Warning in wilcox.test.default(predictor[table.gold == 1], predictor[table.gold ==  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") :
  cannot compute exact p-value with ties
Setting levels: control = 0, case = 1
Warning in wilcox.test.default(predictor[table.gold == 1], predictor[table.gold ==  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") :
  cannot compute exact p-value with ties

Setting levels: control = 0, case = 1
Setting levels: control = 0, case = 1
Setting levels: control = 0, case = 1

Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls > cases
Setting levels: control = 0, case = 1
Setting direction: controls > cases
Quitting from lines 490-491 (PCOSP_model_analysis.Rmd) 
Error: processing vignette 'PCOSP_model_analysis.Rmd' failed with diagnostics:
'initialize' method returned an object of class "DFrame" instead of the required class "ModelComparison"
--- failed re-building ‘PCOSP_model_analysis.Rmd’

--- re-building ‘PDATK_introduction.rmd’ using rmarkdown
--- finished re-building ‘PDATK_introduction.rmd’

SUMMARY: processing the following file failed:
  ‘PCOSP_model_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted