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BioC 3.2: INSTALL report for methylumi on windows1.bioconductor.org

This page was generated on 2015-10-27 17:28:53 -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: C:\cygwin64\bin\curl.exe -O http://linux1.bioconductor.org/BBS/3.2/bioc/src/contrib/methylumi_2.16.0.tar.gz && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch methylumi_2.16.0.tar.gz && rm methylumi_2.16.0.tar.gz
StartedAt: 2015-10-26 20:16:28 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 20:17:06 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 38.4 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin64\bin\curl.exe -O http://linux1.bioconductor.org/BBS/3.2/bioc/src/contrib/methylumi_2.16.0.tar.gz && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch methylumi_2.16.0.tar.gz && rm methylumi_2.16.0.tar.gz
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 5610k  100 5610k    0     0   150M      0 --:--:-- --:--:-- --:--:--  176M

install for i386

* installing to library 'C:/biocbld/bbs-3.2-bioc/R/library'
* installing *source* package 'methylumi' ...
** R
** data
** inst
** preparing package for lazy loading
** 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 20:16:43 2015-10-26 20:16:44
2 2015-10-26 20:16:44 2015-10-26 20:16:44
3 2015-10-26 20:16:44            20:16:44
                                            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

install for x64

* installing to library 'C:/biocbld/bbs-3.2-bioc/R/library'
* installing *source* package 'methylumi' ...
** testing if installed package can be loaded
* DONE (methylumi)