Package: lumi

Version: 2.32.0

Command: /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_2.32.0.tar.gz

StartedAt: 2018-10-16 22:18:04 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:25:46 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 461.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 3

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/lumi.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.32.0’
* 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 61.386  4.188  66.047
getChipInfo      5.105  0.284   5.476
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/lumi.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘lumi’ ...
** 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
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	1.596	0.121	1.730
MAplot-methods	4.464	0.067	4.579
addAnnotationInfo	0.084	0.006	0.090
addControlData2lumi	0.002	0.000	0.002
addNuID2lumi	0.002	0.000	0.002
adjColorBias.quantile	1.588	0.064	1.671
adjColorBias.ssn	0.465	0.013	0.481
bgAdjust	0.095	0.004	0.100
bgAdjustMethylation	0.196	0.008	0.210
boxplot-MethyLumiM-methods	0.567	0.023	0.597
boxplot-methods	0.085	0.007	0.097
boxplotColorBias	0.177	0.028	0.207
density-methods	0.079	0.004	0.085
detectOutlier	0.094	0.005	0.102
detectionCall	0.158	0.008	0.168
estimateBeta	0.194	0.008	0.207
estimateIntensity	0.851	0.013	0.867
estimateLumiCV	0.114	0.005	0.121
estimateM	0.496	0.021	0.520
estimateMethylationBG	0.149	0.008	0.158
example.lumi	0.091	0.005	0.096
example.lumiMethy	0.054	0.003	0.057
example.methyTitration	0.184	0.007	0.195
gammaFitEM	3.066	0.313	3.396
getChipInfo	5.105	0.284	5.476
getControlData	0.004	0.000	0.004
getControlProbe	0.003	0.000	0.003
getControlType	0.003	0.000	0.003
getNuIDMappingInfo	1.588	0.071	1.664
hist-methods	0.140	0.007	0.149
id2seq	0.001	0.000	0.002
inverseVST	0.482	0.007	0.489
is.nuID	0.003	0.000	0.003
lumiB	0.166	0.007	0.173
lumiExpresso	0.306	0.012	0.318
lumiMethyB	0.077	0.004	0.082
lumiMethyC	1.107	0.056	1.172
lumiMethyN	0.088	0.006	0.094
lumiMethyStatus	61.386	4.188	66.047
lumiN	0.478	0.019	0.503
lumiQ	0.328	0.018	0.348
lumiR	0.002	0.001	0.002
lumiR.batch	0.002	0.000	0.002
lumiT	0.349	0.014	0.371
methylationCall	3.694	0.242	3.994
normalizeMethylation.quantile	0.216	0.012	0.230
normalizeMethylation.ssn	0.194	0.008	0.204
nuID2EntrezID	1.282	0.033	1.336
nuID2IlluminaID	4.749	0.099	4.910
nuID2RefSeqID	1.213	0.026	1.251
nuID2probeID	4.039	0.069	4.134
nuID2targetID	3.962	0.058	4.044
pairs-methods	0.945	0.045	1.000
plot-methods	2.316	0.035	2.377
plotCDF	0.156	0.009	0.168
plotColorBias1D	0.315	0.013	0.331
plotColorBias2D	0.217	0.006	0.225
plotControlData	0.003	0.000	0.004
plotDensity	0.125	0.007	0.133
plotGammaFit	4.089	0.254	4.372
plotHousekeepingGene	0.003	0.001	0.004
plotSampleRelation	1.656	0.010	1.680
plotStringencyGene	0.002	0.000	0.002
plotVST	0.355	0.014	0.375
probeID2nuID	4.028	0.062	4.121
produceGEOPlatformFile	0.001	0.000	0.001
produceGEOSubmissionFile	0.001	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.003	0.000	0.003
targetID2nuID	3.928	0.061	4.019
vst	0.282	0.008	0.293