Back to Workflows build report for BioC 3.7

BUILD WEB VIG report for recountWorkflow on malbec2

This page was generated on 2018-05-18 12:48:06 -0400 (Fri, 18 May 2018).

Package 14/21HostnameOS / ArchINSTALLBUILDBUILD WEB VIG
recountWorkflow 1.2.0
Leonardo Collado-Torres
Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/recountWorkflow
Branch: RELEASE_3_7
Last Commit: 8623ed5
Last Changed Date: 2018-04-30 10:07:09 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: recountWorkflow
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/recountWorkflow/recount-workflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/recountWorkflow/recount-workflow.Rmd", ".buildwebvig/recountWorkflow/recount-workflow.R")'
StartedAt: 2018-05-18 08:48:19 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 09:02:26 -0400 (Fri, 18 May 2018)
EllapsedTime: 846.6 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/recountWorkflow/recount-workflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/recountWorkflow/recount-workflow.Rmd", ".buildwebvig/recountWorkflow/recount-workflow.R")'
###
##############################################################################
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> rmarkdown::render(".buildwebvig/recountWorkflow/recount-workflow.Rmd", output_format="BiocStyle:::html_fragment")


processing file: recount-workflow.Rmd

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label: Figure1 (with options) 
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label: load libraries (with options) 
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 $ message: logi FALSE
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Loading required package: SummarizedExperiment
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':

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    clusterExport, clusterMap, parApply, parCapply, parLapply,
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    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
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Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'

Attaching package: 'limma'

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clusterProfiler v3.8.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

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Loading required package: AnnotationDbi


Attaching package: 'gplots'

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Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22

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label: Figure3 (with options) 
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label: Figure4 (with options) 
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label: Figure5 (with options) 
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label: Figure8 (with options) 
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 $ out.width: language ifelse(on.bioc, "100%", "70%")
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label: coverage

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label: Figure10 (with options) 
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label: download gene
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
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trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
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label: limmaplots1 (with options) 
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label: limmaplots2 (with options) 
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label: exondeanalysis1 (with options) 
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trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_exon.Rdata'
Content type 'application/octet-stream' length 110177449 bytes (105.1 MB)
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 $ fig.cap  : chr "voom mean-variance plot of the expressed regions level data."


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trying URL 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'
Content type 'unknown' length 38817086 bytes (37.0 MB)
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label: regionplots (with options) 
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output file: recount-workflow.knit.md

/usr/bin/pandoc +RTS -K512m -RTS recount-workflow.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output recount-workflow.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.7-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --filter /usr/bin/pandoc-citeproc 

Output created: recount-workflow.html
> 
> 
> knitr::purl(".buildwebvig/recountWorkflow/recount-workflow.Rmd", ".buildwebvig/recountWorkflow/recount-workflow.R")


processing file: .buildwebvig/recountWorkflow/recount-workflow.Rmd

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  |                                                                       
  |..........................................                       |  64%Error in eval(x, envir = envir) : object 'on.bioc' not found

  |                                                                       
  |..........................................                       |  65%
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  |.................................................................| 100%
output file: .buildwebvig/recountWorkflow/recount-workflow.R

[1] ".buildwebvig/recountWorkflow/recount-workflow.R"
> 
>