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BioC 3.4: BUILD report for htSeqTools on zin1

This page was generated on 2016-09-21 03:37:22 -0700 (Wed, 21 Sep 2016).

Package 586/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
htSeqTools 1.19.0
Oscar Reina
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/htSeqTools
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  ERROR  skipped  skipped 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: htSeqTools
Version: 1.19.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data htSeqTools
StartedAt: 2016-09-19 22:25:41 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 22:26:05 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 24.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data htSeqTools
###
##############################################################################
##############################################################################


* checking for file ‘htSeqTools/DESCRIPTION’ ... OK
* preparing ‘htSeqTools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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, which, which.max, which.min

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: 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: MASS
Loading required package: BSgenome
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer

Error: processing vignette 'htSeqTools.Rnw' failed with diagnostics:
 chunk 3 (label = getmds) 
Error : RangedDataList objects are defunct in favor of GRangesList objects (the
  GRangesList class is defined in the GenomicRanges package).
Execution halted