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BioC 3.2: BUILD report for flowCore on oaxaca

This page was generated on 2015-10-27 17:38:22 -0400 (Tue, 27 Oct 2015).

Package 354/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowCore 1.36.0
M.Jiang
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/flowCore
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  ERROR  skipped 
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  ERROR  skipped  skipped 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  ERROR  skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: flowCore
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data flowCore
StartedAt: 2015-10-26 20:54:53 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 20:55:57 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 64.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data flowCore
###
##############################################################################
##############################################################################


* checking for file ‘flowCore/DESCRIPTION’ ... OK
* preparing ‘flowCore’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: lattice
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Warning in KernSmooth::bkde2D(x, bandwidth = bandwidth, gridsize = nbin,  :
  Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: gridExtra
Warning in .load_gs(output = path, files = files) :
  Boost serialization format is to be deprecated. Try to resave it with 'google protocol buffer' (lib = 'PB')!
loading R object...
loading tree object...
Done
..done!
replicating filter 'NonDebris' across samples!
..done!
replicating filter 'defaultPolygonGate' across samples!
replicating filter 'defaultRectangleGate' across samples!
replicating filter 'defaultQuadGate' across samples!
..done!
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: grid
sROC 0.1-2 loaded
Error : object ‘drvkde’ is not exported by 'namespace:ks'
In addition: Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: GLX extension missing on server
2: In fun(libname, pkgname) : Error in 'rgl_init'

Error: processing vignette 'HowTo-flowCore.Rnw' failed with diagnostics:
 chunk 60 (label = openCyto-nonDebris) 
Error : package or namespace load failed for ‘openCyto’
Execution halted