Package: rMAT

Version: 3.34.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rMAT

StartedAt: 2019-10-15 20:02:16 -0400 (Tue, 15 Oct 2019)

EndedAt: 2019-10-15 20:03:01 -0400 (Tue, 15 Oct 2019)

EllapsedTime: 45.2 seconds

RetCode: 1

Status:  ERROR

PackageFile: None

PackageFileSize: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data rMAT
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* 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 /private/tmp/RtmpccYWgm/Rinstd9af42337ab2/rMAT/extdata/Sc03b_MR_v04_10000.bpmap
Reading Sequence Information from /private/tmp/RtmpccYWgm/Rinstd9af42337ab2/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