Back to Workflows build report for BioC 3.7

BUILD WEB VIG report for EGSEA123 on malbec2

This page was generated on 2018-05-18 12:48:04 -0400 (Fri, 18 May 2018).

Package 6/21HostnameOS / ArchINSTALLBUILDBUILD WEB VIG
EGSEA123 1.2.0
Matthew Ritchie
Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/EGSEA123
Branch: RELEASE_3_7
Last Commit: 824254d
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: EGSEA123
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/EGSEA123/EGSEAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/EGSEA123/EGSEAWorkflow.Rmd", ".buildwebvig/EGSEA123/EGSEAWorkflow.R")'
StartedAt: 2018-05-18 08:42:35 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 08:54:18 -0400 (Fri, 18 May 2018)
EllapsedTime: 702.2 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/EGSEA123/EGSEAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/EGSEA123/EGSEAWorkflow.Rmd", ".buildwebvig/EGSEA123/EGSEAWorkflow.R")'
###
##############################################################################
##############################################################################


> rmarkdown::render(".buildwebvig/EGSEA123/EGSEAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")


processing file: EGSEAWorkflow.Rmd

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label: setup (with options) 
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 $ message: logi FALSE
 $ echo   : logi FALSE

trying URL 'http://bioinf.wehi.edu.au/EGSEA/mam.rnaseq.rdata'
Content type 'text/plain; charset=UTF-8' length 1786017 bytes (1.7 MB)
==================================================
downloaded 1.7 MB


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label: collections

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label: collectionlist

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label: loadegsea (with options) 
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 $ message: logi FALSE
 $ warning: logi FALSE

Loading required package: Biobase
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 object is masked from 'package:limma':

    plotMA

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

    IQR, mad, sd, var, xtabs

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

    anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
    colnames, colSums, dirname, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
    rowSums, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: gage
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

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

    geneData

Loading required package: pathview
Loading required package: org.Hs.eg.db

##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages






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trying URL 'http://bioinf.wehi.edu.au/EGSEA/arraydata.zip'
Content type 'application/zip' length 37406670 bytes (35.7 MB)
==================================================
downloaded 35.7 MB


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output file: EGSEAWorkflow.knit.md

/usr/bin/pandoc +RTS -K512m -RTS EGSEAWorkflow.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output EGSEAWorkflow.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: EGSEAWorkflow.html
> 
> 
> knitr::purl(".buildwebvig/EGSEA123/EGSEAWorkflow.Rmd", ".buildwebvig/EGSEA123/EGSEAWorkflow.R")


processing file: .buildwebvig/EGSEA123/EGSEAWorkflow.Rmd

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output file: .buildwebvig/EGSEA123/EGSEAWorkflow.R

[1] ".buildwebvig/EGSEA123/EGSEAWorkflow.R"
> 
>