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BUILD report for CellMapper on veracruz1

This page was generated on 2018-04-12 13:43:26 -0400 (Thu, 12 Apr 2018).

Package 195/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellMapper 1.4.0
Brad Nelms
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/CellMapper
Branch: RELEASE_3_6
Last Commit: 19d7d16
Last Changed Date: 2017-10-30 12:41:21 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: CellMapper
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CellMapper
StartedAt: 2018-04-11 22:48:32 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:49:43 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 71.5 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CellMapper
###
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* checking for file ‘CellMapper/DESCRIPTION’ ... OK
* preparing ‘CellMapper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
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, cbind, colMeans, colSums, colnames, 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: AnnotationHub
snapshotDate(): 2017-10-30
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/170’
snapshotDate(): 2017-10-30
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/170’
* Running CellMapper with query gene(s) '2571'...

see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/171’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/172’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/173’
* Running CellMapper on 'Dataset 1' with query gene(s) '3856'...

* Running CellMapper on 'Dataset 2' with query gene(s) '3856'...

* Running CellMapper on 'Dataset 3' with query gene(s) '3856'...

* Pooling results...

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")'.


Attaching package: ‘Biobase’

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

    cache

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

    cache

* Scaling the data matrix...

* Computing the singular-value decomposition of the data matrix...

* Preparing data for CellMapper...

* Running CellMapper with query gene(s) '1000_at'...

see ?HumanAffyData and browseVignettes('HumanAffyData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/177’
* Scaling the data matrix...

* Computing the singular-value decomposition of the data matrix...

* Preparing data for CellMapper...

see ?HumanAffyData and browseVignettes('HumanAffyData') for documentation
loading from cache ‘/Users/biocbuild//.ExperimentHub/176’
Warning in load(cache(getHub(x))) : lzma decoder corrupt data

Error: processing vignette 'CellMapper.Rnw' failed with diagnostics:
 chunk 26 
Error : failed to load resource
  name: EH176
  title: GEO accession data GSE64985 as an ExpressionSet
  reason: error reading from connection
Execution halted