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BUILD report for SeqGSEA on merida2

This page was generated on 2019-04-09 13:28:05 -0400 (Tue, 09 Apr 2019).

Package 1465/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SeqGSEA 1.23.4
Xi Wang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SeqGSEA
Branch: master
Last Commit: e8eba9b
Last Changed Date: 2018-12-13 14:48:46 -0400 (Thu, 13 Dec 2018)
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  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: SeqGSEA
Version: 1.23.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SeqGSEA
StartedAt: 2019-04-08 20:34:38 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:36:53 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 135.3 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 SeqGSEA
###
##############################################################################
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* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* preparing ‘SeqGSEA’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: Biobase
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, 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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
Warning: executing %dopar% sequentially: no parallel backend registered
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning: closing unused connection 6 (<-localhost:11064)
Warning: closing unused connection 5 (<-localhost:11064)
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.
Warning in .local(object, ...) :
  in estimateDispersions: sharingMode=='gene-est-only' will cause inflated numbers of false positives unless you have many replicates.

Error: processing vignette 'SeqGSEA.Rnw' failed with diagnostics:
 chunk 38 (label = main_gsea_DE) 
Error in getBM(values = ensembl.genes, attributes = c("ensembl_gene_id",  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 
Please report this on the support site at http://support.bioconductor.org
Execution halted