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This page was generated on 2022-01-28 11:11:41 -0500 (Fri, 28 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4167
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4062
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4004
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4121
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

BUILD results for ELMER on merida1


To the developers/maintainers of the ELMER package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ELMER.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 573/2077HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELMER 2.19.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2022-01-27 13:55:17 -0500 (Thu, 27 Jan 2022)
git_url: https://git.bioconductor.org/packages/ELMER
git_branch: master
git_last_commit: cc0e36c
git_last_commit_date: 2021-11-09 11:00:18 -0500 (Tue, 09 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: ELMER
Version: 2.19.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
StartedAt: 2022-01-27 17:48:24 -0500 (Thu, 27 Jan 2022)
EndedAt: 2022-01-27 17:52:49 -0500 (Thu, 27 Jan 2022)
EllapsedTime: 265.4 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 ELMER
###
##############################################################################
##############################################################################


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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Returning distal probes: 15561
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: 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

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

    cache

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

    cache

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Checking if samples have both DNA methylation and Gene expression and if they are in the same order...
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
lusc subtype information from:doi:10.1038/nature11404
Creating MultiAssayExperiment
MAE saved as: mae.rda
--- finished re-building ‘analysis_data_input.Rmd’

--- re-building ‘analysis_diff_meth.Rmd’ using rmarkdown
ELMER will search for probes hypomethylated in group Primary solid Tumor (n:226) compared to Solid Tissue Normal (n:8)
ooo Arguments ooo
o Number of probes: 1642
o Beta value difference cut-off: 0.3
o FDR cut-off: 0.01
o Mode: unsupervised
o % of samples per group in each comparison: 0.2
o Min number of samples per group in each comparison: 5
o Nb of samples group1 in each comparison: 45
o Nb of samples group2 in each comparison: 5
Output direction: result
ooooooooooooooooo
Saving results
Quitting from lines 69-80 (analysis_diff_meth.Rmd) 
Error: processing vignette 'analysis_diff_meth.Rmd' failed with diagnostics:
Graphics API version mismatch
--- failed re-building ‘analysis_diff_meth.Rmd’

--- re-building ‘analysis_get_pair.Rmd’ using rmarkdown
Warning in file(file, "rt") :
  cannot open file 'result/getMethdiff.hypo.probes.significant.csv': No such file or directory
Quitting from lines 109-133 (analysis_get_pair.Rmd) 
Error: processing vignette 'analysis_get_pair.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis_get_pair.Rmd’

--- re-building ‘analysis_gui.Rmd’ using rmarkdown
--- finished re-building ‘analysis_gui.Rmd’

--- re-building ‘analysis_motif_enrichment.Rmd’ using rmarkdown
Warning in file(file, "rt") :
  cannot open file 'result/getMethdiff.hypo.probes.significant.csv': No such file or directory
Quitting from lines 68-82 (analysis_motif_enrichment.Rmd) 
Error: processing vignette 'analysis_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis_motif_enrichment.Rmd’

--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'result/getMotif.hypo.enriched.motifs.rda', probable reason 'No such file or directory'
Quitting from lines 87-90 (analysis_regulatory_tf.Rmd) 
Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis_regulatory_tf.Rmd’

--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’

--- re-building ‘input.Rmd’ using rmarkdown
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Checking if samples have both DNA methylation and Gene expression and if they are in the same order...
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
lusc subtype information from:doi:10.1038/nature11404
Creating MultiAssayExperiment
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Removing samples not found in both DNA methylation and gene expression (we are considering the names of the gene expression and DNA methylation columns to be the same) 
MAE saved as: mae_hg19_450K.rda
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Removing samples not found in both DNA methylation and gene expression (we are considering the names of the gene expression and DNA methylation columns to be the same) 
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
Checking if samples have both DNA methylation and Gene expression and if they are in the same order...
Starting to add information to samples
 => Add clinical information to samples
 => Adding TCGA molecular information from marker papers
 => Information will have prefix 'paper_' 
lusc subtype information from:doi:10.1038/nature11404
Creating MultiAssayExperiment
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
MAE saved as: mae_hg38_450K.rda
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
MAE saved as: mae_hg38_450K.rda
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from gene expression input
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Creating a SummarizedExperiment from DNA methylation input
MAE saved as: mae_hg38_450K.rda
--- finished re-building ‘input.Rmd’

--- re-building ‘pipe.Rmd’ using rmarkdown
--- finished re-building ‘pipe.Rmd’

--- re-building ‘plots_TF.Rmd’ using rmarkdown
Quitting from lines 41-46 (plots_TF.Rmd) 
Error: processing vignette 'plots_TF.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_TF.Rmd’

--- re-building ‘plots_heatmap.Rmd’ using rmarkdown
--- finished re-building ‘plots_heatmap.Rmd’

--- re-building ‘plots_motif_enrichment.Rmd’ using rmarkdown
Quitting from lines 36-40 (plots_motif_enrichment.Rmd) 
Error: processing vignette 'plots_motif_enrichment.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_motif_enrichment.Rmd’

--- re-building ‘plots_scatter.Rmd’ using rmarkdown
Searching for the 20 near genes
Identifying gene position for each probe
Warning in readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file 'result/getMotif.hypo.enriched.motifs.rda', probable reason 'No such file or directory'
Quitting from lines 69-77 (plots_scatter.Rmd) 
Error: processing vignette 'plots_scatter.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_scatter.Rmd’

--- re-building ‘plots_schematic.Rmd’ using rmarkdown
Warning in file(file, "rt") :
  cannot open file 'result/getPair.hypo.pairs.significant.csv': No such file or directory
Quitting from lines 32-35 (plots_schematic.Rmd) 
Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots_schematic.Rmd’

--- re-building ‘usecase.Rmd’ using rmarkdown
--- finished re-building ‘usecase.Rmd’

SUMMARY: processing the following files failed:
  ‘analysis_diff_meth.Rmd’ ‘analysis_get_pair.Rmd’
  ‘analysis_motif_enrichment.Rmd’ ‘analysis_regulatory_tf.Rmd’
  ‘plots_TF.Rmd’ ‘plots_motif_enrichment.Rmd’ ‘plots_scatter.Rmd’
  ‘plots_schematic.Rmd’

Error: Vignette re-building failed.
Execution halted