methylumi 2.19.3
Sean Davis
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/methylumi | | Last Changed Rev: 118066 / Revision: 121152 | | Last Changed Date: 2016-06-01 10:54:08 -0700 (Wed, 01 Jun 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | [ 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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### rm -rf methylumi.buildbin-libdir && mkdir methylumi.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.4/bioc/src/contrib/methylumi_2.19.3.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=methylumi.buildbin-libdir --merge-multiarch methylumi_2.19.3.tar.gz && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL methylumi_2.19.3.zip && rm methylumi_2.19.3.tar.gz methylumi_2.19.3.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
1 5616k 1 87355 0 0 41195 0 0:02:19 0:00:02 0:02:17 41263
12 5616k 12 712k 0 0 217k 0 0:00:25 0:00:03 0:00:22 218k
100 5616k 100 5616k 0 0 1472k 0 0:00:03 0:00:03 --:--:-- 1474k
install for i386
* 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 2016-09-19 21:14:34 2016-09-19 21:14:35
2 2016-09-19 21:14:35 2016-09-19 21:14:35
3 2016-09-19 21:14:35 21:14:37
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 *source* package 'methylumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylumi' as methylumi_2.19.3.zip
* DONE (methylumi)
* installing to library 'D:/biocbld/bbs-3.4-bioc/R/library'
package 'methylumi' successfully unpacked and MD5 sums checked