Back to Multiple platform build/check report for BioC 3.11
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

BUILD report for BayesPeak on tokay2

This page was generated on 2020-10-17 11:56:07 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BayesPeak PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 122/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BayesPeak 1.40.0
Jonathan Cairns
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BayesPeak
Branch: RELEASE_3_11
Last Commit: f72780e
Last Changed Date: 2020-04-27 14:21:54 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK [ ERROR ] skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: BayesPeak
Version: 1.40.0
Command: chmod a+r BayesPeak -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BayesPeak
StartedAt: 2020-10-16 20:09:05 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 20:09:33 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 28.4 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r BayesPeak -R && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data BayesPeak
###
##############################################################################
##############################################################################


* checking for file 'BayesPeak/DESCRIPTION' ... OK
* preparing 'BayesPeak':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'BayesPeak.Rnw' using Sweave
Loading required package: IRanges
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    windows

Warning: Package 'BayesPeak' is deprecated and will be removed from Bioconductor
  version 3.12
Warning in summarize.peaks(raw.output, method = "lowerbound", exclude.jobs = unreliable.jobs) :
  No enrichment found on at PP > 0.5 on the following chromosomes: chr1, chr10, chr11, chr12, chr13, chr14, chr15, chr17, chr18, chr19, chr2, chr20, chr21, chr22, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chrM, chrX, chrY

Error: processing vignette 'BayesPeak.Rnw' failed with diagnostics:
 chunk 22 (label = OF4) 
Error : RangedData objects are defunct. Please migrate your code to use GRanges
  or GRangesList objects instead. See IMPORTANT NOTE in ?RangedData

--- failed re-building 'BayesPeak.Rnw'

SUMMARY: processing the following file failed:
  'BayesPeak.Rnw'

Error: Vignette re-building failed.
Execution halted