Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

BUILD report for rMAT on malbec2

This page was generated on 2019-10-16 11:57:21 -0400 (Wed, 16 Oct 2019).

Package 1389/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rMAT 3.34.0
Arnaud Droit and Raphael Gottardo
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/rMAT
Branch: RELEASE_3_9
Last Commit: 71c1a2e
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: rMAT
Version: 3.34.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rMAT
StartedAt: 2019-10-15 19:51:07 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 19:51:28 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 21.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rMAT
###
##############################################################################
##############################################################################


* checking for file ‘rMAT/DESCRIPTION’ ... OK
* preparing ‘rMAT’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘rMAT.Rnw’ using Sweave
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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

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: affxparser
Warning: Package 'rMAT' is deprecated and will be removed from Bioconductor
  version 3.10
Reading Sequence Information from /tmp/RtmpAzAXo0/Rinst2e0d78147581/rMAT/extdata/Sc03b_MR_v04_10000.bpmap
Reading Sequence Information from /tmp/RtmpAzAXo0/Rinst2e0d78147581/rMAT/extdata/Sc03b_MR_v04_10000.bpmap
Warning:   RangedData objects are deprecated. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData

Error: processing vignette 'rMAT.Rnw' failed with diagnostics:
 chunk 8 (label = COMPUTING rMAT SCORES) 
Error : RangedData objects are deprecated and the "lapply" method for
  RangedData objects is now defunct. Please migrate your code to use
  GRanges or GRangesList objects instead. See IMPORTANT NOTE in
  ?RangedData

--- failed re-building ‘rMAT.Rnw’

SUMMARY: processing the following file failed:
  ‘rMAT.Rnw’

Error: Vignette re-building failed.
Execution halted