BioC 2.14: CHECK report for lumi on zin2

Package: lumi

Version: 2.16.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.16.0.tar.gz

StartedAt: 2014-10-08 00:46:53 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:55:27 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 513.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/lumi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘2.16.0’
* 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 ... [29s/30s] OK
* checking installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.4Mb
* 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
Packages unavailable to check Rd xrefs: ‘bigmemoryExtras’, ‘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 files in ‘vignettes’ ... OK
* checking examples ... [190s/192s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lumiMethyStatus    85.225  0.008  85.553
nuID2RefSeqID       8.149  0.016   8.184
getNuIDMappingInfo  7.764  0.028   8.043
nuID2EntrezID       6.801  0.000   6.876
getChipInfo         5.328  0.092   6.098
plotGammaFit        5.133  0.004   5.178
* 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-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’
** 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’
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.485	0.032	2.524
MAplot-methods	4.620	0.016	4.648
addAnnotationInfo	0.06	0.00	0.06
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.888	0.012	1.900
adjColorBias.ssn	0.984	0.000	0.985
bgAdjust	0.076	0.004	0.079
bgAdjustMethylation	0.228	0.004	0.233
boxplot-MethyLumiM-methods	1.016	0.000	1.016
boxplot-methods	0.112	0.004	0.113
boxplotColorBias	0.568	0.000	0.569
density-methods	0.096	0.004	0.100
detectOutlier	0.456	0.000	0.457
detectionCall	0.156	0.000	0.156
estimateBeta	0.112	0.000	0.112
estimateIntensity	0.548	0.000	0.550
estimateLumiCV	0.108	0.000	0.110
estimateM	0.980	0.004	0.983
estimateMethylationBG	0.188	0.000	0.190
example.lumi	0.076	0.004	0.081
example.lumiMethy	0.436	0.000	0.436
example.methyTitration	0.192	0.004	0.196
gammaFitEM	4.517	0.000	4.534
getChipInfo	5.328	0.092	6.098
getControlData	0.004	0.000	0.005
getControlProbe	0.004	0.000	0.004
getControlType	0.004	0.004	0.005
getNuIDMappingInfo	7.764	0.028	8.043
hist-methods	0.12	0.00	0.12
id2seq	0.004	0.000	0.001
inverseVST	0.608	0.008	0.619
is.nuID	0.000	0.000	0.001
lumiB	0.084	0.004	0.086
lumiExpresso	0.281	0.000	0.279
lumiMethyB	0.080	0.000	0.081
lumiMethyC	1.944	0.008	1.956
lumiMethyN	0.084	0.000	0.086
lumiMethyStatus	85.225	0.008	85.553
lumiN	0.564	0.000	0.583
lumiQ	0.276	0.000	0.277
lumiR	0	0	0
lumiR.batch	0.000	0.000	0.001
lumiT	0.412	0.004	0.417
methylationCall	4.872	0.004	4.969
normalizeMethylation.quantile	0.192	0.000	0.194
normalizeMethylation.ssn	0.228	0.000	0.228
nuID2EntrezID	6.801	0.000	6.876
nuID2IlluminaID	4.256	0.012	4.279
nuID2RefSeqID	8.149	0.016	8.184
nuID2probeID	4.060	0.004	4.136
nuID2targetID	4.400	0.016	4.433
pairs-methods	0.988	0.008	0.998
plot-methods	2.080	0.020	2.133
plotCDF	0.160	0.000	0.159
plotColorBias1D	0.792	0.000	0.794
plotColorBias2D	0.220	0.004	0.228
plotControlData	0.004	0.000	0.004
plotDensity	0.124	0.004	0.147
plotGammaFit	5.133	0.004	5.178
plotHousekeepingGene	0.004	0.000	0.003
plotSampleRelation	0.808	0.000	0.811
plotStringencyGene	0.000	0.000	0.003
plotVST	0.376	0.004	0.381
probeID2nuID	4.032	0.008	4.044
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.004	0.000	0.001
seq2id	0.000	0.000	0.001
targetID2nuID	4.512	0.008	4.527
vst	0.328	0.004	0.330

BioC 2.14: CHECK report for lumi on zin2

Summary

Command output