BioC 3.0: CHECK report for MAIT on perceval

Package: MAIT

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MAIT_1.0.0.tar.gz

StartedAt: 2015-04-10 03:13:27 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:21:16 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 469.2 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MAIT_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MAIT.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAIT’ version ‘1.0.0’
* 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 ‘MAIT’ can be installed ... [27s/29s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [178s/181s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
parameters          23.953  0.331  24.648
Validation          23.621  0.243  24.176
ovClassifRatioTable 23.364  0.269  23.770
classifRatioClasses 23.116  0.326  23.658
ovClassifRatio      23.097  0.253  24.371
plotHeatmap          5.296  0.319   5.739
* 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
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/MAIT.Rcheck/00check.log’
for details.

* installing *source* package ‘MAIT’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘scores’ in package ‘MAIT’
Creating a new generic function for ‘loadings’ in package ‘MAIT’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.844	0.049	1.894
LSDResults	0.793	0.009	0.804
MAITbuilder	0.033	0.005	0.037
Validation	23.621	0.243	24.176
classNum	0.005	0.005	0.010
classes	0.006	0.004	0.011
classifRatioClasses	23.116	0.326	23.658
featureID	0.831	0.013	0.851
featureInfo	0.782	0.009	0.796
featureSigID	0.856	0.008	0.874
getScoresTable	0.876	0.037	0.926
identifyMetabolites	1.903	0.030	1.947
loadings	3.018	0.062	3.122
metaboliteTable	1.983	0.047	2.227
method	0.005	0.006	0.036
model	3.394	0.069	3.540
models	0.845	0.013	1.008
ovClassifRatio	23.097	0.253	24.371
ovClassifRatioTable	23.364	0.269	23.770
parameters	23.953	0.331	24.648
pcaLoadings	0.953	0.027	0.989
pcaModel	1.009	0.026	1.043
pcaScores	0.964	0.033	1.012
peakAggregation	0.013	0.008	0.021
peakAnnotation	0.001	0.000	0.001
plotBoxplot	1.258	0.053	1.346
plotHeatmap	5.296	0.319	5.739
plotPCA	1.001	0.026	1.037
plotPLS	2.649	0.048	2.708
plsLoadings	2.757	0.051	2.827
plsModel	2.812	0.047	2.874
plsScores	2.637	0.047	2.695
pvalues	0.792	0.010	0.803
pvaluesCorrection	0.785	0.007	0.797
rawData	0.004	0.004	0.008
resultsPath	0.775	0.008	0.784
sampleProcessing	0.000	0.000	0.001
scores	2.860	0.089	2.976
sigPeaksTable	1.013	0.014	1.038
spectralSigFeatures	0.826	0.010	0.871