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BioC experimental data: BUILD report for gskb on zin2

This page was generated on 2016-10-08 19:29:55 -0700 (Sat, 08 Oct 2016).

Package 119/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gskb 1.4.0
Valerie Bares
Snapshot Date: 2016-10-08 07:15:25 -0700 (Sat, 08 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_3/experiment/pkgs/gskb
Last Changed Rev: 3760 / Revision: 3935
Last Changed Date: 2016-05-03 14:35:06 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: gskb
Version: 1.4.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gskb
StartedAt: 2016-10-08 08:39:53 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 08:41:12 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 78.9 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gskb
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* checking for file ‘gskb/DESCRIPTION’ ... OK
* preparing ‘gskb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) ‘PGSEA’
trying URL 'https://bioconductor.org/packages/3.3/bioc/src/contrib/PGSEA_1.46.0.tar.gz'
Content type 'unknown' length 1213898 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package ‘PGSEA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PGSEA)

The downloaded source packages are in
	‘/tmp/RtmpSSIYqY/downloaded_packages’
Old packages: 'EnrichmentBrowser', 'cluster', 'reportr', 'scran', 'seqinr'
Loading required package: GO.db
Loading required package: AnnotationDbi
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:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

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

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: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums


Loading required package: KEGG.db

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

Loading required package: annaffy
Warning in file(file, "rt") :
  unable to connect to 'bioinformatics.sdstate.edu' on port 80.

Error: processing vignette 'gskb.Rnw' failed with diagnostics:
 chunk 4 
Error in file(file, "rt") : cannot open the connection
Execution halted