Package: lumi

Version: 2.38.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings lumi_2.38.0.tar.gz

StartedAt: 2020-04-15 00:22:45 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:30:08 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 443.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings lumi_2.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/lumi.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 51.056  0.036  51.218
getChipInfo      5.056  0.120   5.705
MAplot-methods   5.024  0.020   5.064
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/lumi.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL lumi
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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)

name	user	system	elapsed
LumiBatch-class	2.356	0.080	2.446
MAplot-methods	5.024	0.020	5.064
addAnnotationInfo	0.052	0.004	0.056
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	0.920	0.012	0.930
adjColorBias.ssn	0.416	0.000	0.416
bgAdjust	0.104	0.004	0.108
bgAdjustMethylation	0.976	0.004	0.981
boxplot-MethyLumiM-methods	0.680	0.012	0.694
boxplot-methods	0.148	0.008	0.160
boxplotColorBias	0.168	0.004	0.175
density-methods	0.124	0.004	0.125
detectOutlier	0.136	0.004	0.143
detectionCall	0.212	0.008	0.217
estimateBeta	0.236	0.000	0.237
estimateIntensity	0.272	0.000	0.269
estimateLumiCV	0.144	0.004	0.148
estimateM	0.676	0.000	0.682
estimateMethylationBG	0.120	0.000	0.118
example.lumi	0.076	0.004	0.077
example.lumiMethy	0.072	0.000	0.075
example.methyTitration	0.200	0.008	0.210
gammaFitEM	2.840	0.004	2.859
getChipInfo	5.056	0.120	5.705
getControlData	0.000	0.000	0.001
getControlProbe	0.004	0.000	0.001
getControlType	0.000	0.000	0.001
getNuIDMappingInfo	1.024	0.040	1.062
hist-methods	0.108	0.000	0.109
id2seq	0	0	0
inverseVST	0.612	0.004	0.621
is.nuID	0.004	0.000	0.001
lumiB	0.136	0.000	0.137
lumiExpresso	0.392	0.004	0.401
lumiMethyB	0.080	0.012	0.094
lumiMethyC	3.052	0.020	3.073
lumiMethyN	0.084	0.000	0.090
lumiMethyStatus	51.056	0.036	51.218
lumiN	0.564	0.000	0.585
lumiQ	0.368	0.012	0.380
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.468	0.004	0.474
methylationCall	3.180	0.000	3.183
normalizeMethylation.quantile	0.236	0.000	0.234
normalizeMethylation.ssn	0.196	0.000	0.197
nuID2EntrezID	0.956	0.004	0.961
nuID2IlluminaID	3.924	0.004	3.933
nuID2RefSeqID	1.456	0.004	1.465
nuID2probeID	3.964	0.000	3.981
nuID2targetID	3.896	0.004	3.918
pairs-methods	0.904	0.012	0.919
plot-methods	2.424	0.016	2.445
plotCDF	0.136	0.004	0.143
plotColorBias1D	0.236	0.004	0.244
plotColorBias2D	1.328	0.004	1.333
plotControlData	0.000	0.000	0.001
plotDensity	0.144	0.004	0.146
plotGammaFit	2.956	0.004	2.977
plotHousekeepingGene	0.000	0.000	0.001
plotSampleRelation	0.712	0.000	0.713
plotStringencyGene	0.000	0.000	0.001
plotVST	0.344	0.008	0.353
probeID2nuID	4.308	0.000	4.312
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.004	0.000	0.001
targetID2nuID	4.036	0.000	4.053
vst	0.168	0.004	0.172