BioC 2.13: CHECK report for lumi on zin1

Package: lumi

Version: 2.14.2

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.14.2.tar.gz

StartedAt: 2014-04-05 02:11:20 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:19:58 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 518.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/lumi.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.14.2’
* 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 ... [30s/30s] OK
* checking installed package size ... NOTE
  installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... WARNING
‘::’ or ‘:::’ import not declared from: ‘bigmemoryExtras’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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: 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:39-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘hdrcde’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘IlluminaAnnotation.Rnw’, ‘lumi.Rnw’, ‘lumi_VST_evaluation.Rnw’,
  ‘methylationAnalysis.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [212s/213s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lumiMethyStatus    99.978  0.008 100.742
nuID2RefSeqID       9.281  0.004   9.299
getNuIDMappingInfo  8.249  0.188   8.463
nuID2EntrezID       6.476  0.004   6.492
plotGammaFit        5.960  0.008   6.005
methylationCall     5.945  0.004   6.032
getChipInfo         5.824  0.120   6.012
gammaFitEM          5.477  0.004   5.498
MAplot-methods      5.100  0.020   5.129
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/lumi.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
LumiBatch-class	2.201	0.024	2.228
MAplot-methods	5.100	0.020	5.129
addAnnotationInfo	0.060	0.000	0.061
addControlData2lumi	0.004	0.000	0.004
addNuID2lumi	0.008	0.000	0.009
adjColorBias.quantile	2.280	0.020	2.303
adjColorBias.ssn	0.604	0.004	0.610
bgAdjust	0.084	0.000	0.086
bgAdjustMethylation	0.580	0.004	0.584
boxplot-MethyLumiM-methods	0.652	0.000	0.656
boxplot-methods	0.192	0.004	0.197
boxplotColorBias	0.784	0.000	0.784
density-methods	0.104	0.000	0.105
detectOutlier	0.100	0.008	0.108
detectionCall	0.164	0.004	0.167
estimateBeta	0.488	0.004	0.492
estimateIntensity	0.268	0.004	0.271
estimateLumiCV	0.116	0.000	0.115
estimateM	0.968	0.008	0.978
estimateMethylationBG	0.568	0.004	0.597
example.lumi	0.092	0.004	0.096
example.lumiMethy	0.060	0.004	0.067
example.methyTitration	0.188	0.004	0.190
gammaFitEM	5.477	0.004	5.498
getChipInfo	5.824	0.120	6.012
getControlData	0.752	0.032	0.786
getControlProbe	0.148	0.012	0.161
getControlType	0.172	0.000	0.171
getNuIDMappingInfo	8.249	0.188	8.463
hist-methods	0.136	0.004	0.143
id2seq	0.000	0.000	0.003
inverseVST	1.120	0.008	1.133
is.nuID	0.000	0.000	0.002
lumiB	0.080	0.000	0.082
lumiExpresso	0.288	0.000	0.287
lumiMethyB	0.060	0.000	0.062
lumiMethyC	1.628	0.008	1.640
lumiMethyN	0.104	0.000	0.104
lumiMethyStatus	99.978	0.008	100.742
lumiN	0.580	0.004	0.590
lumiQ	0.284	0.004	0.314
lumiR	0.004	0.000	0.001
lumiR.batch	0.004	0.000	0.001
lumiT	0.448	0.004	0.456
methylationCall	5.945	0.004	6.032
normalizeMethylation.quantile	0.220	0.000	0.222
normalizeMethylation.ssn	0.240	0.000	0.244
nuID2EntrezID	6.476	0.004	6.492
nuID2IlluminaID	3.936	0.004	3.947
nuID2RefSeqID	9.281	0.004	9.299
nuID2probeID	4.244	0.012	4.262
nuID2targetID	3.608	0.008	3.622
pairs-methods	0.968	0.008	0.975
plot-methods	2.161	0.008	2.170
plotCDF	0.188	0.000	0.187
plotColorBias1D	0.76	0.00	0.76
plotColorBias2D	0.204	0.000	0.206
plotControlData	0.152	0.004	0.159
plotDensity	0.112	0.004	0.119
plotGammaFit	5.960	0.008	6.005
plotHousekeepingGene	0.160	0.000	0.163
plotSampleRelation	0.852	0.000	0.855
plotStringencyGene	0.148	0.000	0.147
plotVST	0.412	0.000	0.415
probeID2nuID	3.712	0.016	3.828
produceGEOPlatformFile	0.032	0.000	0.030
produceGEOSubmissionFile	0.028	0.004	0.029
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.032	0.000	0.031
targetID2nuID	4.369	0.004	4.566
vst	0.400	0.000	0.405