BioC 2.14: CHECK report for lumi on morelia

Package: lumi

Version: 2.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.16.0.tar.gz

StartedAt: 2014-10-07 23:46:11 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:56:16 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 604.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/lumi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ... [35s/35s] OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.2Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [235s/238s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lumiMethyStatus    91.285  7.586  99.611
getNuIDMappingInfo 17.705  0.087  17.841
nuID2RefSeqID      14.868  0.053  14.933
nuID2EntrezID       9.969  0.046  10.021
getChipInfo         6.066  0.259   6.593
methylationCall     5.284  0.318   5.705
plotGammaFit        5.303  0.265   5.574
targetID2nuID       5.163  0.106   5.382
nuID2IlluminaID     5.096  0.107   5.208
nuID2targetID       4.984  0.103   5.095
* 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
  ‘/Users/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	3.164	0.040	3.207
MAplot-methods	4.628	0.042	4.680
addAnnotationInfo	0.070	0.004	0.074
addControlData2lumi	0	0	0
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	2.065	0.039	2.121
adjColorBias.ssn	1.113	0.012	1.219
bgAdjust	0.102	0.008	0.110
bgAdjustMethylation	0.292	0.007	0.300
boxplot-MethyLumiM-methods	1.134	0.016	1.152
boxplot-methods	0.121	0.006	0.127
boxplotColorBias	1.050	0.016	1.067
density-methods	0.112	0.011	0.123
detectOutlier	0.121	0.009	0.131
detectionCall	0.183	0.018	0.201
estimateBeta	0.125	0.004	0.131
estimateIntensity	0.566	0.009	0.575
estimateLumiCV	0.128	0.011	0.140
estimateM	1.075	0.014	1.091
estimateMethylationBG	0.248	0.005	0.253
example.lumi	0.10	0.01	0.11
example.lumiMethy	0.057	0.003	0.060
example.methyTitration	0.205	0.011	0.215
gammaFitEM	4.780	0.191	4.995
getChipInfo	6.066	0.259	6.593
getControlData	0.005	0.001	0.005
getControlProbe	0.004	0.001	0.004
getControlType	0.003	0.001	0.004
getNuIDMappingInfo	17.705	0.087	17.841
hist-methods	0.174	0.012	0.186
id2seq	0.001	0.000	0.001
inverseVST	0.758	0.023	0.781
is.nuID	0.001	0.000	0.002
lumiB	0.103	0.007	0.110
lumiExpresso	0.309	0.016	0.325
lumiMethyB	0.486	0.008	0.494
lumiMethyC	1.672	0.060	1.737
lumiMethyN	0.079	0.002	0.081
lumiMethyStatus	91.285	7.586	99.611
lumiN	0.664	0.021	0.714
lumiQ	0.679	0.018	0.702
lumiR	0.001	0.000	0.001
lumiR.batch	0.001	0.000	0.000
lumiT	0.406	0.022	0.436
methylationCall	5.284	0.318	5.705
normalizeMethylation.quantile	0.236	0.014	0.251
normalizeMethylation.ssn	0.689	0.011	0.702
nuID2EntrezID	9.969	0.046	10.021
nuID2IlluminaID	5.096	0.107	5.208
nuID2RefSeqID	14.868	0.053	14.933
nuID2probeID	4.100	0.099	4.201
nuID2targetID	4.984	0.103	5.095
pairs-methods	1.033	0.039	1.077
plot-methods	2.146	0.031	2.204
plotCDF	0.170	0.013	0.184
plotColorBias1D	0.427	0.011	0.443
plotColorBias2D	0.318	0.005	0.325
plotControlData	0.004	0.001	0.005
plotDensity	0.175	0.014	0.189
plotGammaFit	5.303	0.265	5.574
plotHousekeepingGene	0.004	0.001	0.005
plotSampleRelation	0.980	0.012	1.005
plotStringencyGene	0.003	0.001	0.003
plotVST	0.409	0.014	0.432
probeID2nuID	4.811	0.103	4.981
produceGEOPlatformFile	0.001	0.001	0.001
produceGEOSubmissionFile	0.001	0.000	0.000
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.001	0.001	0.001
targetID2nuID	5.163	0.106	5.382
vst	0.398	0.011	0.410

BioC 2.14: CHECK report for lumi on morelia

Summary

Command output