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This page was generated on 2021-09-24 15:06:39 -0400 (Fri, 24 Sep 2021).

BUILD results for ELMER on machv2

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raw results

Package 565/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELMER 2.16.0  (landing page)
Tiago Chedraoui Silva
Snapshot Date: 2021-09-23 04:50:12 -0400 (Thu, 23 Sep 2021)
git_url: https://git.bioconductor.org/packages/ELMER
git_branch: RELEASE_3_13
git_last_commit: 31e996d
git_last_commit_date: 2021-05-19 12:13:57 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: ELMER
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ELMER
StartedAt: 2021-09-23 11:51:23 -0400 (Thu, 23 Sep 2021)
EndedAt: 2021-09-23 11:57:46 -0400 (Thu, 23 Sep 2021)
EllapsedTime: 383.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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 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

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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
Warning: The `path` argument of `write_csv()` is deprecated as of readr 1.4.0.
Please use the `file` argument instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Number of relevant probes found: 710
Rows: 1642 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (1): probe
dbl (3): pvalue, Primary.solid.Tumor_Minus_Solid.Tissue.Normal, adjust.p

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
--- finished re-building ‘analysis_diff_meth.Rmd’

--- re-building ‘analysis_get_pair.Rmd’ using rmarkdown
Searching for the 20 near genes
Identifying gene position for each probe
Selecting U (unmethylated) and M (methylated) groups. Each groups has 20% of samples
-------------------
* Filtering probes
-------------------
For more information see function preAssociationProbeFiltering
Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3.
Removing 592 probes out of 1642
Calculating Pp (probe - gene) for all nearby genes
File created: result/getPair.hypo.all.pairs.statistic.csv
Calculating Pr (random probe - gene). Permutating  100 probes for 747 genes
Calculate empirical P value.

--- finished 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
Loading object: Probes.motif.hg19.450K
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
------------------------------------
** Filtering motifs based on quality
------------------------------------
Number of enriched motifs with quality:
-----------
 => A: 4
 => B: 1
 => C: 1
 => D: 0
 => S: 0
-----------
Considering only motifs with quality from A up to DS: 6 motifs are enriched.
---------------------------------------------------
* Adding enriched motifs to significant pairs file
---------------------------------------------------
Adding coordinates for probes and genes from the provided data
Joining, by = "GeneID"
Joining, by = "Probe"
Saving file: result/getPair.hypo.pairs.significant.withmotif.csv
--- finished re-building ‘analysis_motif_enrichment.Rmd’

--- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown
Selecting U (unmethylated) and M (methylated) groups. Each groups has 20% of samples
-------------------------------------------------------------------------------------------------------------------
** Downloading TF list from Lambert, Samuel A., et al. The human transcription factors. Cell 172.4 (2018): 650-665.
-------------------------------------------------------------------------------------------------------------------
Accessing TF families from TFClass database to indentify known potential TF
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Calculating the average methylation at all motif-adjacent probes 
Performing Mann-Whitney U test
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Finding potential TF and known potential TF
--- finished 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
Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished 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
--- finished 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
--- finished re-building ‘plots_scatter.Rmd’

--- re-building ‘plots_schematic.Rmd’ using rmarkdown
Searching for the 20 near genes
Identifying gene position for each probe
Quitting from lines 44-49 (plots_schematic.Rmd) 
Error: processing vignette 'plots_schematic.Rmd' failed with diagnostics:
Could not resolve host: api.genome.ucsc.edu
--- failed re-building ‘plots_schematic.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted