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BUILD report for RcwlPipelines on tokay1

This page was generated on 2019-10-21 12:41:57 -0400 (Mon, 21 Oct 2019).

Package 1373/1800HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RcwlPipelines 1.1.13
Qiang Hu
Snapshot Date: 2019-10-20 17:01:46 -0400 (Sun, 20 Oct 2019)
URL: https://git.bioconductor.org/packages/RcwlPipelines
Branch: master
Last Commit: 84405e7
Last Changed Date: 2019-10-11 15:09:15 -0400 (Fri, 11 Oct 2019)
malbec1 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RcwlPipelines
Version: 1.1.13
Command: chmod a+r RcwlPipelines -R && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RcwlPipelines
StartedAt: 2019-10-21 00:24:04 -0400 (Mon, 21 Oct 2019)
EndedAt: 2019-10-21 00:25:06 -0400 (Mon, 21 Oct 2019)
EllapsedTime: 62.1 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   chmod a+r RcwlPipelines -R && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data RcwlPipelines
###
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* checking for file 'RcwlPipelines/DESCRIPTION' ... OK
* preparing 'RcwlPipelines':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'RcwlPipelines.Rmd' using rmarkdown
Loading required package: Rcwl
Loading required package: yaml
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
c:\python27\lib\site-packages\cwltool\__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
Loading required package: BiocFileCache
Loading required package: dbplyr
Quitting from lines 48-50 (RcwlPipelines.Rmd) 
Quitting from lines 48-50 (RcwlPipelines.Rmd) 
Error: processing vignette 'RcwlPipelines.Rmd' failed with diagnostics:
object 'con' not found
--- failed re-building 'RcwlPipelines.Rmd'

SUMMARY: processing the following file failed:
  'RcwlPipelines.Rmd'

Error: Vignette re-building failed.
Execution halted