BioC 2.11: CHECK report for lumi on pitt

Package: lumi

Version: 2.9.4

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.9.4.tar.gz

StartedAt: 2012-06-21 01:19:12 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:36:36 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 1043.5 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/lumi.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.9.4'
* 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 whether package 'lumi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    7.8Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: MethyLumiM2GenoSet.Rd:22-24: Dropping empty section \details
prepare_Rd: MethyLumiM2GenoSet.Rd:28-30: Dropping empty section \references
prepare_Rd: MethyLumiM2GenoSet.Rd:38-40: Dropping empty section \examples
prepare_Rd: export.methyGenoSet.Rd:28-30: Dropping empty section \details
prepare_Rd: export.methyGenoSet.Rd:31-34: Dropping empty section \value
prepare_Rd: export.methyGenoSet.Rd:35-37: Dropping empty section \references
prepare_Rd: export.methyGenoSet.Rd:42-44: Dropping empty section \seealso
prepare_Rd: export.methyGenoSet.Rd:45-48: Dropping empty section \examples
prepare_Rd: getChrInfo.Rd:25-27: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:31-33: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:40-42: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:43-46: Dropping empty section \examples
prepare_Rd: smoothMethyData.Rd:31-33: Dropping empty section \details
prepare_Rd: smoothMethyData.Rd:42-44: Dropping empty section \note
prepare_Rd: smoothMethyData.Rd:37-38: Dropping empty section \references
prepare_Rd: smoothMethyData.Rd:48-50: Dropping empty section \seealso
prepare_Rd: smoothMethyData.Rd:51-53: 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* 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 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/lumi.Rcheck/00check.log'
for details.

* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'image' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'IlluminaAnnotation.Rnw' 
   'lumi.Rnw' 
   'lumi_VST_evaluation.Rnw' 
   'methylationAnalysis.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'

* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	1.204	0.068	1.496
MAplot-methods	9.752	0.391	10.802
MethyGenoSet-class	0.000	0.000	0.001
addAnnotationInfo	0.197	0.011	0.231
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	4.213	0.810	5.169
adjColorBias.ssn	1.645	0.213	1.877
bgAdjust	0.158	0.013	0.172
bgAdjustMethylation	0.939	0.106	1.054
boxplot-MethyLumiM-methods	5.280	0.232	5.576
boxplot-methods	0.344	0.026	0.376
boxplotColorBias	1.194	0.149	1.351
density-methods	0.176	0.017	0.193
detectOutlier	0.208	0.046	0.256
detectionCall	0.303	0.024	0.335
estimateBeta	0.280	0.044	0.441
estimateIntensity	2.235	0.263	2.522
estimateLumiCV	0.220	0.022	0.243
estimateM	2.671	0.222	2.999
estimateMethylationBG	0.423	0.061	0.512
example.lumi	0.151	0.009	0.165
example.lumiMethy	0.197	0.012	0.215
example.methyTitration	0.339	0.021	0.373
gammaFitEM	9.904	7.788	18.769
getChipInfo	6.985	0.877	8.497
getControlData	1.071	0.087	1.174
getControlProbe	0.189	0.007	0.198
getControlType	0.183	0.013	0.197
getNuIDMappingInfo	41.453	0.220	42.199
hist-methods	0.222	0.020	0.245
id2seq	0.002	0.000	0.002
inverseVST	0.638	0.124	0.773
is.nuID	0.001	0.000	0.001
lumiB	0.160	0.014	0.175
lumiExpresso	0.639	0.110	0.758
lumiMethyB	0.195	0.013	0.209
lumiMethyC	3.500	0.800	4.425
lumiMethyN	0.246	0.019	0.272
lumiMethyStatus	184.515	139.112	336.210
lumiN	1.113	0.170	1.300
lumiQ	0.519	0.084	0.889
lumiR	0.000	0.000	0.001
lumiR.batch	0	0	0
lumiT	0.776	0.125	0.916
methylationCall	11.367	7.713	19.468
normalizeMethylation.quantile	1.275	0.141	1.435
normalizeMethylation.ssn	0.488	0.086	0.580
nuID2EntrezID	22.195	0.116	22.544
nuID2IlluminaID	6.998	0.353	7.545
nuID2RefSeqID	27.087	0.135	27.945
nuID2probeID	6.285	0.325	6.648
nuID2targetID	6.317	0.319	6.721
pairs-methods	1.950	0.268	2.249
plot-methods	4.197	0.248	4.484
plotCDF	0.269	0.028	0.300
plotColorBias1D	0.716	0.070	0.797
plotColorBias2D	0.388	0.023	0.413
plotControlData	0.459	0.018	0.487
plotDensity	0.290	0.016	0.307
plotGammaFit	13.239	7.322	21.586
plotHousekeepingGene	0.351	0.009	0.362
plotSampleRelation	1.466	0.039	1.517
plotStringencyGene	0.323	0.008	0.335
plotVST	0.687	0.100	0.799
probeID2nuID	6.399	0.324	6.785
produceGEOPlatformFile	0.000	0.001	0.001
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	5.594	0.318	5.989
vst	0.825	0.112	0.958

Summary

Command output