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BUILD report for htSeqTools on celaya2

This page was generated on 2019-10-16 13:02:45 -0400 (Wed, 16 Oct 2019).

Package 773/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
htSeqTools 1.32.0
Oscar Reina
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/htSeqTools
Branch: RELEASE_3_9
Last Commit: 8bb3e67
Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019)
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 [ ERROR ] skipped  skipped 

Summary

Package: htSeqTools
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data htSeqTools
StartedAt: 2019-10-15 23:35:55 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 23:37:04 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 68.9 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/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
--- re-building ‘htSeqTools.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: 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 object is masked from ‘package:base’:

    expand.grid

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

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: rtracklayer
Warning: Package 'htSeqTools' is deprecated and will be removed from
  Bioconductor version 3.10
Warning in showList(object, showFunction, print.classinfo = TRUE) :
  Note that starting with BioC 3.7, the class attribute of all
  GRangesList **instances** needs to be set to
  "CompressedGRangesList". Please update this object with
  'updateObject(object, verbose=TRUE)' and re-serialize it.
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData
Warning:   RangedData objects are deprecated. Please migrate your code to
  use GRanges or GRangesList objects instead. See IMPORTANT NOTE
  in ?RangedData

Error: processing vignette 'htSeqTools.Rnw' failed with diagnostics:
 chunk 6 (label = qcontrol1) 
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 ‘htSeqTools.Rnw’

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

Error: Vignette re-building failed.
Execution halted