BioC 3.4: CHECK report for lumi on morelia

Package: lumi

Version: 2.26.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.26.4.tar.gz

StartedAt: 2017-04-15 04:17:48 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 04:25:02 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 433.3 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 lumi_2.26.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/lumi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.26.4’
* 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 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 ... OK
* checking installed package size ... OK
* 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘IRanges’ ‘bigmemoryExtras’
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘bigmemoryExtras’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 64.841  5.101  69.991
getChipInfo      5.732  0.222   6.522
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.137	0.053	2.192
MAplot-methods	4.057	0.045	4.412
addAnnotationInfo	0.065	0.004	0.069
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.099	0.040	1.270
adjColorBias.ssn	0.636	0.013	0.881
bgAdjust	0.092	0.006	0.098
bgAdjustMethylation	0.646	0.012	0.659
boxplot-MethyLumiM-methods	1.049	0.015	1.065
boxplot-methods	0.122	0.006	0.128
boxplotColorBias	0.208	0.012	0.220
density-methods	0.099	0.005	0.104
detectOutlier	0.106	0.004	0.126
detectionCall	0.534	0.010	0.544
estimateBeta	0.113	0.011	0.124
estimateIntensity	0.156	0.008	0.166
estimateLumiCV	0.117	0.007	0.125
estimateM	0.648	0.015	0.664
estimateMethylationBG	0.686	0.003	0.690
example.lumi	0.103	0.009	0.111
example.lumiMethy	0.065	0.002	0.067
example.methyTitration	0.204	0.013	0.217
gammaFitEM	3.571	0.270	3.860
getChipInfo	5.732	0.222	6.522
getControlData	0.002	0.001	0.003
getControlProbe	0.002	0.000	0.002
getControlType	0.002	0.000	0.002
getNuIDMappingInfo	1.345	0.055	1.441
hist-methods	0.162	0.011	0.200
id2seq	0.001	0.000	0.001
inverseVST	0.463	0.009	0.482
is.nuID	0.002	0.001	0.002
lumiB	0.137	0.007	0.145
lumiExpresso	0.334	0.014	0.348
lumiMethyB	0.064	0.004	0.069
lumiMethyC	1.784	0.037	1.845
lumiMethyN	0.086	0.003	0.090
lumiMethyStatus	64.841	5.101	69.991
lumiN	0.934	0.020	0.999
lumiQ	0.260	0.016	0.281
lumiR	0.001	0.000	0.001
lumiR.batch	0.001	0.000	0.000
lumiT	0.328	0.014	0.349
methylationCall	3.767	0.275	4.048
normalizeMethylation.quantile	0.163	0.010	0.172
normalizeMethylation.ssn	0.248	0.007	0.254
nuID2EntrezID	1.224	0.041	1.889
nuID2IlluminaID	4.817	0.097	4.915
nuID2RefSeqID	1.487	0.035	1.522
nuID2probeID	3.889	0.064	3.955
nuID2targetID	4.222	0.066	4.291
pairs-methods	1.199	0.042	1.246
plot-methods	1.858	0.032	1.929
plotCDF	0.148	0.009	0.171
plotColorBias1D	0.252	0.008	0.262
plotColorBias2D	0.218	0.005	0.224
plotControlData	0.002	0.000	0.003
plotDensity	0.133	0.009	0.143
plotGammaFit	3.717	0.289	4.009
plotHousekeepingGene	0.003	0.000	0.003
plotSampleRelation	0.851	0.013	0.887
plotStringencyGene	0.002	0.000	0.002
plotVST	0.333	0.012	0.372
probeID2nuID	3.926	0.070	3.999
produceGEOPlatformFile	0.001	0.000	0.000
produceGEOSubmissionFile	0.001	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.001	0.000	0.002
targetID2nuID	4.395	0.077	4.476
vst	0.357	0.013	0.370