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This page was generated on 2022-10-19 13:23:50 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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BUILD results for TCGAutils on merida1


To the developers/maintainers of the TCGAutils package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TCGAutils.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
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raw results

Package 1989/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TCGAutils 1.16.1  (landing page)
Marcel Ramos
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/TCGAutils
git_branch: RELEASE_3_15
git_last_commit: c707a87
git_last_commit_date: 2022-10-11 13:11:53 -0400 (Tue, 11 Oct 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: TCGAutils
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data TCGAutils
StartedAt: 2022-10-18 22:14:10 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 22:17:32 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 201.4 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 TCGAutils
###
##############################################################################
##############################################################################


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


Attaching package: 'MultiAssayExperiment'

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

    splitAssays


Attaching package: 'RTCGAToolbox'

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

    makeSummarizedExperimentFromGISTIC

Loading required package: dbplyr
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.25.0 (2022-06-12 02:20:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

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

    trim

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

    trim

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

    trim

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

    getClasses, getMethods

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

    attach, detach, load, save

R.utils v2.12.0 (2022-06-28 03:20:05 UTC) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    timestamp

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

    cat, commandArgs, getOption, isOpen, nullfile, parse, warnings

snapshotDate(): 2022-04-26
Working on: COAD_CNASeq-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
require("RaggedExperiment")
Working on: COAD_miRNASeqGene-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_mRNAArray-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_Mutation-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_RNASeq2GeneNorm-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_Methylation_methyl27-20160128,
 COAD_Methylation_methyl450-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
require("rhdf5")
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Loading required package: HDF5Array
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep


Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls

Working on: COAD_Methylation_methyl27-20160128,
 COAD_Methylation_methyl450-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_colData-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_metadata-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
Working on: COAD_sampleMap-20160128
see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
loading from cache
harmonizing input:
  removing 3545 sampleMap rows not in names(experiments)

Attaching package: 'AnnotationHub'

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

    hubUrl

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

    cache

snapshotDate(): 2022-04-25
Quitting from lines 374-382 (TCGAutils.Rmd) 
Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics:
failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/"

--- failed re-building ‘TCGAutils.Rmd’

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

Error: Vignette re-building failed.
Execution halted