Multiple platform build/check report for BioC 3.11 - 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_2.39.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.39.0’
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
lumiMethyStatus 105.628 13.607 119.348
getChipInfo       8.712  0.672   9.447
plotGammaFit      8.326  0.861   9.187
gammaFitEM        6.041  0.844   6.895
nuID2IlluminaID   6.662  0.199   6.861
methylationCall   5.876  0.862   6.740
targetID2nuID     5.790  0.129   5.948
nuID2targetID     5.648  0.132   5.780
nuID2probeID      5.513  0.136   5.649
probeID2nuID      5.018  0.104   5.123
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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	2.988	0.232	3.221
MAplot-methods	4.460	0.129	4.594
addAnnotationInfo	0.082	0.012	0.094
addControlData2lumi	0.000	0.001	0.001
addNuID2lumi	0	0	0
adjColorBias.quantile	1.147	0.137	1.289
adjColorBias.ssn	1.707	0.073	1.783
bgAdjust	0.098	0.013	0.111
bgAdjustMethylation	0.166	0.024	0.191
boxplot-MethyLumiM-methods	1.529	0.046	1.577
boxplot-methods	0.118	0.013	0.132
boxplotColorBias	0.190	0.043	0.233
density-methods	0.093	0.009	0.103
detectOutlier	0.119	0.017	0.137
detectionCall	0.171	0.018	0.190
estimateBeta	0.300	0.038	0.339
estimateIntensity	0.321	0.026	0.351
estimateLumiCV	0.133	0.012	0.144
estimateM	0.750	0.047	0.797
estimateMethylationBG	0.227	0.034	0.260
example.lumi	0.108	0.011	0.120
example.lumiMethy	0.074	0.004	0.079
example.methyTitration	0.269	0.015	0.285
gammaFitEM	6.041	0.844	6.895
getChipInfo	8.712	0.672	9.447
getControlData	0.002	0.001	0.003
getControlProbe	0.002	0.001	0.003
getControlType	0.002	0.001	0.002
getNuIDMappingInfo	2.152	0.154	2.309
hist-methods	0.171	0.014	0.186
id2seq	0.001	0.000	0.002
inverseVST	0.630	0.025	0.655
is.nuID	0.002	0.000	0.002
lumiB	0.141	0.013	0.154
lumiExpresso	0.392	0.025	0.418
lumiMethyB	0.090	0.007	0.097
lumiMethyC	1.825	0.123	1.966
lumiMethyN	0.125	0.011	0.135
lumiMethyStatus	105.628	13.607	119.348
lumiN	0.579	0.046	0.626
lumiQ	0.390	0.027	0.421
lumiR	0	0	0
lumiR.batch	0.000	0.000	0.001
lumiT	0.476	0.056	0.539
methylationCall	5.876	0.862	6.740
normalizeMethylation.quantile	0.274	0.037	0.311
normalizeMethylation.ssn	0.239	0.028	0.271
nuID2EntrezID	1.716	0.096	1.812
nuID2IlluminaID	6.662	0.199	6.861
nuID2RefSeqID	1.959	0.070	2.029
nuID2probeID	5.513	0.136	5.649
nuID2targetID	5.648	0.132	5.780
pairs-methods	1.185	0.135	1.323
plot-methods	2.547	0.100	2.667
plotCDF	0.197	0.020	0.217
plotColorBias1D	0.431	0.029	0.464
plotColorBias2D	0.223	0.010	0.235
plotControlData	0.001	0.000	0.002
plotDensity	0.160	0.012	0.172
plotGammaFit	8.326	0.861	9.187
plotHousekeepingGene	0.002	0.001	0.003
plotSampleRelation	1.186	0.025	1.212
plotStringencyGene	0.001	0.001	0.002
plotVST	0.600	0.056	0.661
probeID2nuID	5.018	0.104	5.123
produceGEOPlatformFile	0.001	0.001	0.001
produceGEOSubmissionFile	0.001	0.001	0.000
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	5.790	0.129	5.948
vst	0.260	0.020	0.281

CHECK report for lumi on celaya2

Summary

Command output

Installation output

Tests output

Example timings