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BioC 3.2: INSTALL report for methylumi on perceval

This page was generated on 2015-10-27 17:33:59 -0400 (Tue, 27 Oct 2015).

Package 637/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.16.0
Sean Davis
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/methylumi
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  OK  WARNINGS UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: methylumi
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylumi
StartedAt: 2015-10-26 20:28:31 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 20:29:10 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 38.9 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL methylumi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’
* installing *source* package ‘methylumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** help
*** installing help indices
** building package indices
3 HumanMethylation27 samples found
0 HumanMethylation450 samples found
Attempting to extract protocolData() from list...
Determining chip type from IDAT protocolData...
Note: method with signature ‘methylData#character’ chosen for function ‘sampleNames<-’,
 target signature ‘MethyLumiQC#character’.
 "eSet#ANY" would also be valid
Background mean & SD estimated from 24156 probes
Loading required package: MASS

Attaching package: ‘MASS’

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

    select

Background mean & SD estimated from 31000 probes
HumanMethylation27 data encountered, skipping...

Object Information:
MethyLumiSet (storageMode: lockedEnvironment)
assayData: 27578 features, 3 samples 
  element names: betas, methylated, methylated.OOB, pvals, unmethylated, unmethylated.OOB 
protocolData: none
phenoData
  sampleNames: 5318317007_A 5318317007_B 5318317007_C
  varLabels: barcode mu.Cy3 ... offset.Cy5 (9 total)
  varMetadata: labelDescription
featureData
  featureNames: cg00000292 cg00002426 ... cg27665659 (27578 total)
  fvarLabels: Probe_ID DESIGN COLOR_CHANNEL
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: IlluminaHumanMethylation27k 
Major Operation History:
            submitted            finished
1 2015-10-26 20:28:50 2015-10-26 20:28:52
2 2015-10-26 20:28:52 2015-10-26 20:28:52
3 2015-10-26 20:28:52            20:28:53
                                            command
1            methylumIDAT(barcodes = getBarcodes())
2                         Subset of 27578 features.
3 methylumi.bgcorr(x = methylumIDAT(getBarcodes()))
** installing vignettes
   ‘methylumi.Rnw’ 
   ‘methylumi450k.Rnw’ 
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (methylumi)