BioC 3.6: CHECK report for lumi on malbec1

Package: lumi

Version: 2.29.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.29.0.tar.gz

StartedAt: 2017-08-16 00:21:53 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:27:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 365.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.29.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.29.0’
* 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 53.648  0.008  53.697
plotGammaFit     6.020  0.024   6.047
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.140	0.036	2.175
MAplot-methods	4.164	0.024	4.189
addAnnotationInfo	0.072	0.000	0.071
addControlData2lumi	0	0	0
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.628	0.004	1.636
adjColorBias.ssn	0.476	0.004	0.482
bgAdjust	0.076	0.000	0.076
bgAdjustMethylation	0.220	0.000	0.224
boxplot-MethyLumiM-methods	0.544	0.004	0.549
boxplot-methods	0.104	0.000	0.104
boxplotColorBias	0.680	0.008	0.689
density-methods	0.088	0.000	0.087
detectOutlier	0.092	0.000	0.091
detectionCall	0.168	0.004	0.171
estimateBeta	0.148	0.000	0.151
estimateIntensity	0.172	0.000	0.173
estimateLumiCV	0.092	0.000	0.090
estimateM	0.476	0.000	0.477
estimateMethylationBG	0.160	0.000	0.161
example.lumi	0.076	0.000	0.078
example.lumiMethy	0.056	0.000	0.055
example.methyTitration	0.176	0.004	0.182
gammaFitEM	4.292	0.000	4.298
getChipInfo	4.380	0.136	4.818
getControlData	0.000	0.000	0.002
getControlProbe	0.004	0.000	0.001
getControlType	0.000	0.000	0.001
getNuIDMappingInfo	1.100	0.012	1.112
hist-methods	0.120	0.000	0.117
id2seq	0.000	0.000	0.001
inverseVST	0.660	0.004	0.667
is.nuID	0.000	0.000	0.001
lumiB	0.124	0.000	0.125
lumiExpresso	0.460	0.008	0.480
lumiMethyB	0.124	0.000	0.125
lumiMethyC	1.772	0.004	1.778
lumiMethyN	0.088	0.000	0.093
lumiMethyStatus	53.648	0.008	53.697
lumiN	0.540	0.008	0.559
lumiQ	0.256	0.000	0.257
lumiR	0	0	0
lumiR.batch	0.000	0.000	0.001
lumiT	0.336	0.008	0.347
methylationCall	3.704	0.000	3.706
normalizeMethylation.quantile	0.152	0.000	0.150
normalizeMethylation.ssn	0.168	0.000	0.168
nuID2EntrezID	0.976	0.008	0.983
nuID2IlluminaID	4.780	0.004	4.785
nuID2RefSeqID	0.908	0.000	0.906
nuID2probeID	3.376	0.008	3.385
nuID2targetID	3.876	0.000	3.878
pairs-methods	0.872	0.012	0.886
plot-methods	2.004	0.004	2.009
plotCDF	0.136	0.004	0.143
plotColorBias1D	0.360	0.004	0.360
plotColorBias2D	0.256	0.000	0.256
plotControlData	0.000	0.000	0.001
plotDensity	0.144	0.000	0.146
plotGammaFit	6.020	0.024	6.047
plotHousekeepingGene	0.000	0.000	0.002
plotSampleRelation	0.604	0.016	0.618
plotStringencyGene	0.000	0.000	0.001
plotVST	0.296	0.004	0.298
probeID2nuID	3.164	0.000	3.167
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.000	0.000	0.001
targetID2nuID	3.308	0.000	3.310
vst	0.292	0.000	0.292