BioC 2.13: CHECK report for lumi on perceval

Package: lumi

Version: 2.14.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.14.2.tar.gz

StartedAt: 2014-04-05 02:22:12 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:39:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 1061.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/lumi.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.14.2’
* 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 ... [54s/55s] OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 ‘:::’ import not declared from: ‘bigmemoryExtras’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... NOTE
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:39-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘hdrcde’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘IlluminaAnnotation.Rnw’, ‘lumi_VST_evaluation.Rnw’, ‘lumi.Rnw’,
  ‘methylationAnalysis.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [481s/513s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
lumiMethyStatus       179.257 25.709 222.283
getNuIDMappingInfo     36.668  0.306  41.282
nuID2RefSeqID          31.892  0.221  32.639
nuID2EntrezID          29.893  0.218  30.677
getChipInfo            13.342  0.689  15.488
plotGammaFit           11.835  1.483  13.464
methylationCall        11.022  1.660  13.066
gammaFitEM             10.137  0.064  10.795
nuID2targetID           9.564  0.348  10.019
targetID2nuID           9.292  0.333   9.789
nuID2IlluminaID         9.158  0.343   9.712
nuID2probeID            8.863  0.318   9.411
probeID2nuID            8.740  0.323   9.224
MAplot-methods          7.731  0.125   8.218
adjColorBias.quantile   5.324  0.073   5.826
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
Warning: replacing previous import by ‘nleqslv::nleqslv’ when loading ‘lumi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘methylumi’
Warning: replacing previous import by ‘nleqslv::nleqslv’ when loading ‘lumi’
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	4.420	0.113	4.784
MAplot-methods	7.731	0.125	8.218
addAnnotationInfo	0.092	0.015	0.110
addControlData2lumi	0.003	0.002	0.005
addNuID2lumi	0.019	0.006	0.029
adjColorBias.quantile	5.324	0.073	5.826
adjColorBias.ssn	0.959	0.040	1.037
bgAdjust	0.112	0.018	0.132
bgAdjustMethylation	0.352	0.036	0.397
boxplot-MethyLumiM-methods	1.731	0.065	1.860
boxplot-methods	0.269	0.036	0.316
boxplotColorBias	1.568	0.054	1.871
density-methods	0.119	0.035	0.155
detectOutlier	0.126	0.025	0.151
detectionCall	0.193	0.047	0.241
estimateBeta	0.152	0.019	0.171
estimateIntensity	1.153	0.030	1.319
estimateLumiCV	0.136	0.029	0.176
estimateM	0.852	0.066	0.944
estimateMethylationBG	0.283	0.020	0.336
example.lumi	0.116	0.027	0.163
example.lumiMethy	0.083	0.014	0.099
example.methyTitration	0.206	0.025	0.274
gammaFitEM	10.137	0.064	10.795
getChipInfo	13.342	0.689	15.488
getControlData	1.219	0.105	1.514
getControlProbe	0.203	0.017	0.229
getControlType	0.223	0.014	0.255
getNuIDMappingInfo	36.668	0.306	41.282
hist-methods	0.226	0.030	0.308
id2seq	0.063	0.006	0.069
inverseVST	1.192	0.053	1.754
is.nuID	0.094	0.012	0.109
lumiB	0.167	0.019	0.191
lumiExpresso	0.540	0.059	0.648
lumiMethyB	0.068	0.010	0.089
lumiMethyC	3.614	0.168	4.639
lumiMethyN	0.122	0.020	0.144
lumiMethyStatus	179.257	25.709	222.283
lumiN	0.871	0.065	1.029
lumiQ	0.402	0.038	0.449
lumiR	0.003	0.005	0.007
lumiR.batch	0.002	0.004	0.006
lumiT	0.605	0.049	0.763
methylationCall	11.022	1.660	13.066
normalizeMethylation.quantile	0.346	0.046	0.417
normalizeMethylation.ssn	0.384	0.055	0.447
nuID2EntrezID	29.893	0.218	30.677
nuID2IlluminaID	9.158	0.343	9.712
nuID2RefSeqID	31.892	0.221	32.639
nuID2probeID	8.863	0.318	9.411
nuID2targetID	9.564	0.348	10.019
pairs-methods	2.328	0.150	2.510
plot-methods	3.196	0.140	3.439
plotCDF	0.191	0.032	0.224
plotColorBias1D	0.398	0.040	0.451
plotColorBias2D	0.429	0.021	0.457
plotControlData	0.267	0.020	0.304
plotDensity	0.141	0.031	0.175
plotGammaFit	11.835	1.483	13.464
plotHousekeepingGene	0.274	0.020	0.298
plotSampleRelation	1.197	0.039	1.253
plotStringencyGene	0.292	0.016	0.340
plotVST	0.704	0.059	0.816
probeID2nuID	8.740	0.323	9.224
produceGEOPlatformFile	0.111	0.005	0.117
produceGEOSubmissionFile	0.109	0.006	0.130
produceMethylationGEOSubmissionFile	0.003	0.004	0.007
seq2id	0.096	0.006	0.103
targetID2nuID	9.292	0.333	9.789
vst	0.870	0.058	0.934