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BUILD report for RefNet on merida2

This page was generated on 2019-04-09 13:29:38 -0400 (Tue, 09 Apr 2019).

Package 1323/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefNet 1.19.0
Paul Shannon
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/RefNet
Branch: master
Last Commit: f384aed
Last Changed Date: 2018-10-30 11:54:32 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: RefNet
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RefNet
StartedAt: 2019-04-08 20:47:14 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:50:20 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 186.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RefNet
###
##############################################################################
##############################################################################


* checking for file ‘RefNet/DESCRIPTION’ ... OK
* preparing ‘RefNet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... 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, sd, var, xtabs

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

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

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

Warning: replacing previous import ‘IRanges::desc’ by ‘plyr::desc’ when loading ‘PSICQUIC’
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading required package: RCurl
Loading required package: bitops
Loading required package: shiny
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
snapshotDate(): 2019-04-03
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH10364 : 10364’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH10365 : 10365’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH12810 : 12810’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH12814 : 12814’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH22338 : 27766’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH22339 : 27767’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH22340 : 27768’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
downloading 1 resources
retrieving 1 resource
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
loading from cache 
    ‘AH22341 : 27769’
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
Using temporary cache /tmp/RtmpyB5Bq8/BiocFileCache
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
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



Error: processing vignette 'RefNet.Rnw' failed with diagnostics:
 chunk 12 (label = eliminateDups) 
Error in getBM(filters = biomart.filter, values = uniprots, attributes = columns,  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org
Execution halted