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BioC experimental data: BUILD report for ind1KG on moscato2

This page was generated on 2016-10-08 19:30:45 -0700 (Sat, 08 Oct 2016).

Package 147/293HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ind1KG 0.10.0
VJ Carey
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/ind1KG
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: ind1KG
Version: 0.10.0
Command: chmod a+r ind1KG -R && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ind1KG
StartedAt: 2016-10-08 08:37:07 -0700 (Sat, 08 Oct 2016)
EndedAt: 2016-10-08 08:39:56 -0700 (Sat, 08 Oct 2016)
EllapsedTime: 169.6 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   chmod a+r ind1KG -R && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ind1KG
###
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* checking for file 'ind1KG/DESCRIPTION' ... OK
* preparing 'ind1KG':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...Warning: running command '"E:/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: chopsticks
Loading required package: survival
Warning: Package 'ind1KG' is deprecated and will be removed from Bioconductor
  version 3.3
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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")'.

Warning: The 'vals' argument has been renamed 'filter'. Please use the 'filter'
  argument instead.

Warning in read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
Loading required package: BSgenome
Loading required package: rtracklayer
  Please note that the SNPlocs.Hsapiens.dbSNP.20090506 package contains
  outdated dbSNP data and will be deprecated in the near future. We
  highly recommend that you use a SNPlocs package based on a more recent
  dbSNP build for your analyses instead. See available.SNPs() for the
  list of SNPlocs packages currently available and make sure to pick up
  the most recent one.
Loading required package: lumi
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Error: processing vignette 'nov09rv.Rnw' failed with diagnostics:
 chunk 8 (label = lklu) 
Error in eval(expr, envir, enclos) : 
  could not find function "dbListTables"
Execution halted