BioC 3.5: CHECK report for lumi on oaxaca

Package: lumi

Version: 2.27.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.27.3.tar.gz

StartedAt: 2017-03-04 05:02:41 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 05:08:58 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 377.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.27.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.27.3’
* 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 ... OK
* 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 56.719  6.710  63.446
getChipInfo      4.763  0.205   5.835
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.5-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	2.009	0.055	2.064
MAplot-methods	3.636	0.038	4.346
addAnnotationInfo	0.434	0.004	0.438
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.001	0.000	0.000
adjColorBias.quantile	1.305	0.025	1.347
adjColorBias.ssn	1.177	0.018	1.197
bgAdjust	0.071	0.009	0.081
bgAdjustMethylation	0.283	0.010	0.293
boxplot-MethyLumiM-methods	0.479	0.012	0.492
boxplot-methods	0.077	0.005	0.082
boxplotColorBias	0.185	0.013	0.198
density-methods	0.103	0.004	0.107
detectOutlier	0.088	0.004	0.092
detectionCall	0.259	0.011	0.271
estimateBeta	0.226	0.011	0.239
estimateIntensity	0.179	0.008	0.187
estimateLumiCV	0.084	0.005	0.089
estimateM	0.889	0.017	0.906
estimateMethylationBG	0.214	0.002	0.216
example.lumi	0.080	0.007	0.086
example.lumiMethy	0.061	0.003	0.063
example.methyTitration	0.178	0.009	0.186
gammaFitEM	2.869	0.016	3.021
getChipInfo	4.763	0.205	5.835
getControlData	0.002	0.000	0.002
getControlProbe	0.001	0.000	0.002
getControlType	0.002	0.000	0.002
getNuIDMappingInfo	1.189	0.052	1.259
hist-methods	0.122	0.007	0.130
id2seq	0.001	0.000	0.001
inverseVST	0.778	0.018	0.813
is.nuID	0.001	0.000	0.001
lumiB	0.192	0.008	0.200
lumiExpresso	1.059	0.017	1.075
lumiMethyB	0.061	0.004	0.065
lumiMethyC	1.388	0.030	1.422
lumiMethyN	0.078	0.003	0.081
lumiMethyStatus	56.719	6.710	63.446
lumiN	0.465	0.016	0.500
lumiQ	0.218	0.014	0.236
lumiR	0	0	0
lumiR.batch	0.001	0.000	0.001
lumiT	0.282	0.013	0.302
methylationCall	3.107	0.365	3.473
normalizeMethylation.quantile	0.139	0.009	0.148
normalizeMethylation.ssn	0.206	0.007	0.213
nuID2EntrezID	1.077	0.035	1.113
nuID2IlluminaID	4.544	0.090	4.637
nuID2RefSeqID	1.247	0.029	1.277
nuID2probeID	4.689	0.082	4.775
nuID2targetID	3.487	0.064	3.553
pairs-methods	0.764	0.032	0.844
plot-methods	1.715	0.029	1.765
plotCDF	0.173	0.007	0.180
plotColorBias1D	0.285	0.009	0.296
plotColorBias2D	0.289	0.005	0.295
plotControlData	0.002	0.000	0.002
plotDensity	0.161	0.009	0.171
plotGammaFit	4.137	0.577	4.717
plotHousekeepingGene	0.002	0.000	0.001
plotSampleRelation	0.987	0.038	1.027
plotStringencyGene	0.002	0.000	0.002
plotVST	0.311	0.014	0.329
probeID2nuID	3.635	0.098	3.734
produceGEOPlatformFile	0.001	0.001	0.001
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.001	0.001	0.001
targetID2nuID	3.725	0.074	3.799
vst	0.222	0.014	0.237