Multiple platform build/check report for BioC 3.10 - CHECK report for lumi on merida1

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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_2.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/lumi.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.38.0’
* 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 48.433  4.663  53.444
getChipInfo      4.925  0.257   5.259
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.10-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
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’
** testing if installed package keeps a record of temporary installation path
* DONE (lumi)

Tests output

Example timings

name	user	system	elapsed
LumiBatch-class	2.637	0.143	2.795
MAplot-methods	4.246	0.069	4.352
addAnnotationInfo	0.053	0.002	0.055
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	0.831	0.068	0.902
adjColorBias.ssn	0.471	0.028	0.504
bgAdjust	0.106	0.005	0.112
bgAdjustMethylation	0.918	0.015	0.936
boxplot-MethyLumiM-methods	0.664	0.021	0.692
boxplot-methods	0.135	0.015	0.150
boxplotColorBias	0.167	0.021	0.190
density-methods	0.122	0.004	0.128
detectOutlier	0.133	0.014	0.150
detectionCall	0.174	0.009	0.185
estimateBeta	0.215	0.008	0.224
estimateIntensity	0.230	0.011	0.243
estimateLumiCV	0.114	0.006	0.125
estimateM	0.587	0.022	0.613
estimateMethylationBG	0.130	0.006	0.136
example.lumi	0.102	0.012	0.114
example.lumiMethy	0.054	0.001	0.056
example.methyTitration	0.208	0.008	0.216
gammaFitEM	2.829	0.284	3.130
getChipInfo	4.925	0.257	5.259
getControlData	0.001	0.000	0.002
getControlProbe	0.001	0.000	0.001
getControlType	0.001	0.000	0.001
getNuIDMappingInfo	1.298	0.055	1.364
hist-methods	0.126	0.005	0.133
id2seq	0.001	0.000	0.001
inverseVST	0.501	0.010	0.514
is.nuID	0.001	0.000	0.001
lumiB	0.101	0.004	0.105
lumiExpresso	0.405	0.013	0.418
lumiMethyB	0.067	0.004	0.072
lumiMethyC	2.805	0.048	2.872
lumiMethyN	0.095	0.006	0.101
lumiMethyStatus	48.433	4.663	53.444
lumiN	0.492	0.018	0.520
lumiQ	0.325	0.013	0.343
lumiR	0	0	0
lumiR.batch	0.001	0.000	0.001
lumiT	0.366	0.015	0.388
methylationCall	2.942	0.281	3.251
normalizeMethylation.quantile	0.187	0.019	0.206
normalizeMethylation.ssn	0.165	0.014	0.179
nuID2EntrezID	1.154	0.036	1.195
nuID2IlluminaID	4.310	0.099	4.443
nuID2RefSeqID	1.424	0.034	1.472
nuID2probeID	3.945	0.071	4.045
nuID2targetID	4.179	0.066	4.283
pairs-methods	0.965	0.051	1.029
plot-methods	2.164	0.038	2.233
plotCDF	0.147	0.007	0.158
plotColorBias1D	0.228	0.009	0.239
plotColorBias2D	0.320	0.008	0.334
plotControlData	0.001	0.001	0.002
plotDensity	0.127	0.007	0.135
plotGammaFit	3.863	0.266	4.170
plotHousekeepingGene	0.001	0.000	0.001
plotSampleRelation	0.824	0.010	0.840
plotStringencyGene	0.001	0.000	0.001
plotVST	0.361	0.017	0.382
probeID2nuID	3.788	0.059	3.875
produceGEOPlatformFile	0.001	0.000	0.000
produceGEOSubmissionFile	0.000	0.001	0.001
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.000	0.000	0.001
targetID2nuID	3.895	0.070	3.987
vst	0.216	0.006	0.224

CHECK report for lumi on merida1

Summary

Command output

Installation output

Tests output

Example timings