methylumi 2.14.0
Sean Davis
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/methylumi | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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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 methylumi
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* 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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 2015-10-08 18:57:42 2015-10-08 18:57:44
2 2015-10-08 18:57:45 2015-10-08 18:57:45
3 2015-10-08 18:57:46 18:57:47
command
1 methylumIDAT(barcodes = getBarcodes())
2 Subset of 27578 features.
3 methylumi.bgcorr(x = methylumIDAT(getBarcodes()))
* building ‘methylumi_2.14.0.tar.gz’