Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

BUILD report for recount on tokay1

This page was generated on 2019-04-13 11:26:57 -0400 (Sat, 13 Apr 2019).

Package 1280/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.8.2
Leonardo Collado-Torres
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/recount
Branch: RELEASE_3_8
Last Commit: ecd06f4
Last Changed Date: 2019-02-14 11:52:47 -0400 (Thu, 14 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS 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  ERROR  skipped  skipped 

Summary

Package: recount
Version: 1.8.2
Command: chmod a+r recount -R && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data recount
StartedAt: 2019-04-12 23:02:30 -0400 (Fri, 12 Apr 2019)
EndedAt: 2019-04-12 23:03:41 -0400 (Fri, 12 Apr 2019)
EllapsedTime: 71.0 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r recount -R && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data recount
###
##############################################################################
##############################################################################


* checking for file 'recount/DESCRIPTION' ... OK
* preparing 'recount':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning in citation("BiocParallel") :
  no date field in DESCRIPTION file of package 'BiocParallel'
Warning in citation("BiocParallel") :
  could not determine year for 'BiocParallel' from package DESCRIPTION file
Warning in citation("BiocStyle") :
  no date field in DESCRIPTION file of package 'BiocStyle'
Warning in citation("BiocStyle") :
  could not determine year for 'BiocStyle' from package DESCRIPTION file
Warning in citation("EnsDb.Hsapiens.v79") :
  no date field in DESCRIPTION file of package 'EnsDb.Hsapiens.v79'
Warning in citation("org.Hs.eg.db") :
  no date field in DESCRIPTION file of package 'org.Hs.eg.db'
Writing 31 Bibtex entries ... OK
Results written to file 'quickstartRef.bib'
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
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, 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: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: GenomeInfoDb
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

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Quitting from lines 292-300 (recount-quickstart.Rmd) 
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
cannot open URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Execution halted