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) |
| Back to Workflows build report for BioC 3.7 |
This page was generated on 2018-05-18 12:48:04 -0400 (Fri, 18 May 2018).
| Package 6/21 | Hostname | OS / Arch | INSTALL | BUILD | BUILD WEB VIG | ||||||
| EGSEA123 1.2.0 Matthew Ritchie
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | |
| 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 |
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### Running command:
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### /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")'
###
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> 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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$ 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"
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