RefNet 1.7.0 Paul Shannon
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RefNet | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | [ ERROR ] | skipped | skipped | |
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### Running command:
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### chmod a+r RefNet -R && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RefNet
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* checking for file 'RefNet/DESCRIPTION' ... OK
* preparing 'RefNet':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"c:/biocbld/bbs-3.3-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
ERROR
Loading required package: IRanges
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,
as.vector, 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, unlist, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: PSICQUIC
Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: AnnotationHub
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
Warning in .loadRegistry() :
failed to get response from PSICQUIC registry at http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=ACTIVE&format=txt
snapshotDate(): 2015-08-26
loading from cache 'C:/Users/biocbuild/Documents/AppData/.AnnotationHub/27766'
loading from cache 'C:/Users/biocbuild/Documents/AppData/.AnnotationHub/27767'
loading from cache 'C:/Users/biocbuild/Documents/AppData/.AnnotationHub/27768'
loading from cache 'C:/Users/biocbuild/Documents/AppData/.AnnotationHub/27769'
Loading required package: AnnotationDbi
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:AnnotationHub':
cache
The following object is masked from 'package:httr':
content
Loading required package: DBI
Error: processing vignette 'RefNet.Rnw' failed with diagnostics:
chunk 12 (label = eliminateDups)
Error in addStandardNames(idMapper, tbl.8) :
error in evaluating the argument 'object' in selecting a method for function 'addStandardNames': Error: object 'idMapper' not found
Execution halted