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BioC 3.2: BUILD report for methylumi on oaxaca

This page was generated on 2015-08-24 10:56:05 -0700 (Mon, 24 Aug 2015).

Package 616/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylumi 2.15.2
Sean Davis
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi
Last Changed Rev: 105672 / Revision: 107696
Last Changed Date: 2015-06-30 12:49:07 -0700 (Tue, 30 Jun 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS 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: 2.15.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data methylumi
StartedAt: 2015-08-23 18:05:57 -0700 (Sun, 23 Aug 2015)
EndedAt: 2015-08-23 18:12:04 -0700 (Sun, 23 Aug 2015)
EllapsedTime: 367.4 seconds
RetCode: 0
Status:  OK 
PackageFile: methylumi_2.15.2.tar.gz
PackageFileSize: 5.89 MiB

Command output

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


* checking for file ‘methylumi/DESCRIPTION’ ... OK
* preparing ‘methylumi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
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 2015-08-23 18:11:58 2015-08-23 18:12:00
2 2015-08-23 18:12:00 2015-08-23 18:12:00
3 2015-08-23 18:12:01            18:12:02
                                            command
1            methylumIDAT(barcodes = getBarcodes())
2                         Subset of 27578 features.
3 methylumi.bgcorr(x = methylumIDAT(getBarcodes()))
* building ‘methylumi_2.15.2.tar.gz’