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BioC 2.12: CHECK report for lumi on george2

This page was generated on 2013-10-09 09:37:21 -0700 (Wed, 09 Oct 2013).

Package 375/671HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.12.0
Pan Du
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/lumi
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: lumi
Version: 2.12.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.12.0.tar.gz
StartedAt: 2013-10-09 02:58:18 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:17:27 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1148.4 seconds
RetCode: 0
Status:  OK 
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.12.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lumi’ can be installed ... [55s/56s] OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    7.9Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... NOTE
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:44-47: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [10m/10m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
lumiMethyStatus       266.253  0.040 268.321
getNuIDMappingInfo     47.995  0.060  48.586
nuID2RefSeqID          39.779  0.016  40.061
nuID2EntrezID          37.950  0.024  38.304
plotGammaFit           18.285  0.000  18.295
methylationCall        17.465  0.016  17.485
getChipInfo            16.965  0.300  17.602
gammaFitEM             16.261  0.000  16.382
probeID2nuID           12.161  0.040  12.348
nuID2IlluminaID        11.225  0.028  11.493
nuID2targetID          11.229  0.008  11.402
nuID2probeID           11.160  0.012  11.245
targetID2nuID          10.676  0.012  10.693
MAplot-methods          8.597  0.084   8.724
adjColorBias.quantile   6.160  0.072   6.263
LumiBatch-class         5.536  0.100   5.667
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck/00check.log’
for details.

lumi.Rcheck/00install.out:

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘nleqslv’ when loading ‘nleqslv’
Warning: ignoring .First.lib() for package ‘lumi’
* DONE (lumi)

lumi.Rcheck/lumi-Ex.timings:

nameusersystemelapsed
LumiBatch-class5.5360.1005.667
MAplot-methods8.5970.0848.724
addAnnotationInfo0.9760.0080.996
addControlData2lumi0.0120.0040.015
addNuID2lumi0.0160.0040.019
adjColorBias.quantile6.1600.0726.263
adjColorBias.ssn2.2440.0082.260
bgAdjust0.1240.0080.132
bgAdjustMethylation0.4840.0000.485
boxplot-MethyLumiM-methods1.0040.0001.005
boxplot-methods0.3400.0040.341
boxplotColorBias2.9040.0082.914
density-methods0.1520.0080.163
detectOutlier0.1880.0080.195
detectionCall0.2320.0200.255
estimateBeta1.2600.0121.271
estimateIntensity0.4320.0040.438
estimateLumiCV0.1520.0080.158
estimateM0.9840.0040.990
estimateMethylationBG1.4360.0041.441
example.lumi0.1280.0040.131
example.lumiMethy0.0880.0040.095
example.methyTitration0.2160.0080.224
gammaFitEM16.261 0.00016.382
getChipInfo16.965 0.30017.602
getControlData1.5730.0681.640
getControlProbe0.2800.0160.295
getControlType0.2840.0000.283
getNuIDMappingInfo47.995 0.06048.586
hist-methods0.1440.0120.156
id2seq0.0080.0000.008
inverseVST1.4600.0121.476
is.nuID0.0880.0000.085
lumiB0.2040.0040.208
lumiExpresso1.5520.0041.579
lumiMethyB0.0720.0000.072
lumiMethyC2.8280.0042.834
lumiMethyN0.1400.0040.143
lumiMethyStatus266.253 0.040268.321
lumiN1.1120.0081.158
lumiQ0.4680.0080.474
lumiR0.0280.0000.030
lumiR.batch0.0080.0000.005
lumiT0.7240.0360.760
methylationCall17.465 0.01617.485
normalizeMethylation.quantile0.4040.0080.411
normalizeMethylation.ssn0.4720.0080.477
nuID2EntrezID37.950 0.02438.304
nuID2IlluminaID11.225 0.02811.493
nuID2RefSeqID39.779 0.01640.061
nuID2probeID11.160 0.01211.245
nuID2targetID11.229 0.00811.402
pairs-methods2.5200.0282.771
plot-methods4.6760.0284.708
plotCDF0.2440.0080.253
plotColorBias1D0.4120.0120.433
plotColorBias2D0.2880.0080.299
plotControlData0.3490.0040.349
plotDensity0.1640.0000.162
plotGammaFit18.285 0.00018.295
plotHousekeepingGene0.3120.0040.318
plotSampleRelation1.4040.0081.421
plotStringencyGene0.2840.0040.289
plotVST0.7400.0360.779
probeID2nuID12.161 0.04012.348
produceGEOPlatformFile0.2680.0000.268
produceGEOSubmissionFile0.0080.0000.008
produceMethylationGEOSubmissionFile0.0080.0000.009
seq2id0.0080.0000.011
targetID2nuID10.676 0.01210.693
vst2.3120.0122.326