Back to Multiple platform build/check report for BioC 3.7 experimental data

BUILD report for RnaSeqTutorial on malbec2

This page was generated on 2018-10-16 14:17:51 -0400 (Tue, 16 Oct 2018).

Package 272/342HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnaSeqTutorial 0.18.0
Nicolas Delhomme
Snapshot Date: 2018-10-16 07:35:22 -0400 (Tue, 16 Oct 2018)
URL: https://git.bioconductor.org/packages/RnaSeqTutorial
Branch: RELEASE_3_7
Last Commit: a4cc7d9
Last Changed Date: 2018-04-30 10:31:27 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK [ ERROR ] skipped 

Summary

Package: RnaSeqTutorial
Version: 0.18.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RnaSeqTutorial
StartedAt: 2018-10-16 09:26:32 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 09:27:38 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 66.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RnaSeqTutorial
###
##############################################################################
##############################################################################


* checking for file ‘RnaSeqTutorial/DESCRIPTION’ ... OK
* preparing ‘RnaSeqTutorial’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: easyRNASeq
Warning: Package 'RnaSeqTutorial' is deprecated and will be removed from
  Bioconductor version 3.8
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 object is masked from ‘package:easyRNASeq’:

    basename

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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: BiocParallel
Loading required package: Biostrings
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: XVector

Attaching package: ‘Biostrings’

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

    strsplit

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
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: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

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

    rowRanges


Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    type

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

    type

The following objects are masked from ‘package:base’:

    aperm, apply

Loading required package: BSgenome
Loading required package: rtracklayer

Error: processing vignette 'RnaSeqTutorial.Rnw' failed with diagnostics:
 chunk 16 (label = Exon Transcript object transformation) 
Error : The 'universe' argument of the RangedData() constructor function is
  defunct.
Execution halted