Multiple platform build/check report for BioC 3.9 - CHECK report for lumi on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.36.0’
* 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 ... 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 ... WARNING
Package unavailable to check Rd xrefs: ‘hdrcde’
Missing link or links in documentation object 'lumiN.Rd':
  ‘[vsn]{vsn}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘IlluminaAnnotation.R’, ‘IlluminaAnnotation.pdf’, ‘lumi.R’,
    ‘lumi.pdf’, ‘lumi_VST_evaluation.R’, ‘lumi_VST_evaluation.pdf’,
    ‘methylationAnalysis.R’, ‘methylationAnalysis.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 71.492 13.701  85.236
getChipInfo      8.086  0.601   8.774
plotGammaFit     6.606  0.857   7.464
nuID2IlluminaID  6.667  0.201   6.868
targetID2nuID    5.605  0.130   5.735
nuID2probeID     5.321  0.124   5.446
probeID2nuID     5.241  0.113   5.354
MAplot-methods   5.178  0.164   5.344
nuID2targetID    5.009  0.118   5.129
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL lumi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘lumi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lumi)

Tests output

Example timings

name	user	system	elapsed
LumiBatch-class	2.343	0.289	2.632
MAplot-methods	5.178	0.164	5.344
addAnnotationInfo	0.073	0.010	0.082
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.000	0.001	0.001
adjColorBias.quantile	1.139	0.099	1.240
adjColorBias.ssn	0.510	0.020	0.531
bgAdjust	0.117	0.013	0.130
bgAdjustMethylation	0.254	0.052	0.306
boxplot-MethyLumiM-methods	1.412	0.040	1.451
boxplot-methods	0.092	0.008	0.100
boxplotColorBias	0.170	0.039	0.209
density-methods	0.106	0.011	0.117
detectOutlier	0.165	0.037	0.203
detectionCall	0.185	0.027	0.212
estimateBeta	0.197	0.019	0.216
estimateIntensity	0.266	0.026	0.292
estimateLumiCV	0.135	0.014	0.150
estimateM	0.756	0.051	0.807
estimateMethylationBG	0.192	0.017	0.208
example.lumi	0.115	0.018	0.134
example.lumiMethy	0.073	0.009	0.083
example.methyTitration	0.32	0.03	0.35
gammaFitEM	3.790	0.933	4.724
getChipInfo	8.086	0.601	8.774
getControlData	0.002	0.001	0.002
getControlProbe	0.002	0.001	0.002
getControlType	0.001	0.001	0.002
getNuIDMappingInfo	1.563	0.121	1.686
hist-methods	0.131	0.012	0.143
id2seq	0.001	0.000	0.001
inverseVST	0.879	0.066	0.945
is.nuID	0.001	0.000	0.002
lumiB	0.105	0.008	0.113
lumiExpresso	0.247	0.027	0.275
lumiMethyB	0.060	0.006	0.066
lumiMethyC	1.638	0.213	1.852
lumiMethyN	0.102	0.004	0.107
lumiMethyStatus	71.492	13.701	85.236
lumiN	0.508	0.031	0.538
lumiQ	0.418	0.042	0.464
lumiR	0.000	0.001	0.001
lumiR.batch	0	0	0
lumiT	0.404	0.027	0.435
methylationCall	3.353	0.742	4.095
normalizeMethylation.quantile	0.205	0.026	0.232
normalizeMethylation.ssn	0.237	0.034	0.271
nuID2EntrezID	1.340	0.037	1.377
nuID2IlluminaID	6.667	0.201	6.868
nuID2RefSeqID	1.878	0.070	1.949
nuID2probeID	5.321	0.124	5.446
nuID2targetID	5.009	0.118	5.129
pairs-methods	1.096	0.120	1.218
plot-methods	2.286	0.065	2.357
plotCDF	0.183	0.023	0.206
plotColorBias1D	0.392	0.030	0.422
plotColorBias2D	0.259	0.012	0.271
plotControlData	0.002	0.000	0.001
plotDensity	0.150	0.011	0.161
plotGammaFit	6.606	0.857	7.464
plotHousekeepingGene	0.001	0.000	0.001
plotSampleRelation	1.000	0.016	1.016
plotStringencyGene	0.002	0.001	0.002
plotVST	0.553	0.044	0.599
probeID2nuID	5.241	0.113	5.354
produceGEOPlatformFile	0.000	0.001	0.001
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.001	0.001	0.002
targetID2nuID	5.605	0.130	5.735
vst	0.433	0.031	0.463

CHECK report for lumi on celaya2

Summary

Command output

Installation output

Tests output

Example timings