Package: lumi

Version: 2.36.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings lumi_2.36.0.tar.gz

StartedAt: 2019-10-16 02:47:44 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:54:55 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 431.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings lumi_2.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.36.0’
* 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 47.505  0.072  47.605
MAplot-methods   5.857  0.000   5.886
getChipInfo      5.412  0.176   6.687
* checking PDF version of manual ... OK
* DONE

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

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL lumi
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

name	user	system	elapsed
LumiBatch-class	1.680	0.052	1.738
MAplot-methods	5.857	0.000	5.886
addAnnotationInfo	0.076	0.004	0.080
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	0.966	0.004	0.971
adjColorBias.ssn	0.509	0.004	0.512
bgAdjust	0.104	0.008	0.118
bgAdjustMethylation	0.183	0.004	0.188
boxplot-MethyLumiM-methods	0.661	0.012	0.673
boxplot-methods	0.135	0.000	0.137
boxplotColorBias	0.943	0.007	0.956
density-methods	0.126	0.001	0.126
detectOutlier	0.127	0.003	0.131
detectionCall	0.218	0.007	0.233
estimateBeta	0.219	0.004	0.227
estimateIntensity	0.268	0.000	0.269
estimateLumiCV	0.139	0.000	0.140
estimateM	0.681	0.012	0.699
estimateMethylationBG	0.160	0.000	0.161
example.lumi	0.108	0.000	0.109
example.lumiMethy	0.079	0.000	0.078
example.methyTitration	0.247	0.004	0.250
gammaFitEM	2.953	0.000	2.956
getChipInfo	5.412	0.176	6.687
getControlData	0.001	0.000	0.002
getControlProbe	0.001	0.000	0.001
getControlType	0.001	0.000	0.001
getNuIDMappingInfo	1.466	0.008	1.496
hist-methods	0.154	0.004	0.158
id2seq	0.001	0.000	0.001
inverseVST	1.405	0.000	1.432
is.nuID	0.001	0.000	0.000
lumiB	0.118	0.000	0.119
lumiExpresso	0.301	0.004	0.317
lumiMethyB	0.078	0.000	0.077
lumiMethyC	1.115	0.004	1.119
lumiMethyN	0.110	0.000	0.112
lumiMethyStatus	47.505	0.072	47.605
lumiN	0.384	0.000	0.407
lumiQ	0.236	0.000	0.236
lumiR	0	0	0
lumiR.batch	0.000	0.000	0.001
lumiT	0.383	0.000	0.383
methylationCall	2.196	0.000	2.195
normalizeMethylation.quantile	0.19	0.00	0.19
normalizeMethylation.ssn	0.210	0.001	0.210
nuID2EntrezID	1.101	0.007	1.108
nuID2IlluminaID	4.936	0.017	4.954
nuID2RefSeqID	0.907	0.000	0.907
nuID2probeID	3.530	0.004	3.534
nuID2targetID	3.151	0.000	3.151
pairs-methods	0.891	0.012	0.904
plot-methods	1.636	0.008	1.645
plotCDF	0.133	0.004	0.137
plotColorBias1D	0.235	0.000	0.235
plotColorBias2D	0.170	0.004	0.174
plotControlData	0.001	0.000	0.001
plotDensity	0.112	0.000	0.112
plotGammaFit	3.228	0.004	3.235
plotHousekeepingGene	0.001	0.000	0.001
plotSampleRelation	0.810	0.004	0.813
plotStringencyGene	0.001	0.000	0.001
plotVST	0.457	0.004	0.461
probeID2nuID	4.650	0.004	4.654
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	4.398	0.008	4.410
vst	0.339	0.004	0.342