BioC 3.2: CHECK report for MAIT on perceval

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAIT_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MAIT.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.4.0’
* 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 ... [15s/17s] 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 ... [150s/153s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
parameters          20.421  0.289  20.716
classifRatioClasses 20.263  0.329  20.630
ovClassifRatio      20.132  0.286  20.424
Validation          20.154  0.175  20.461
ovClassifRatioTable 20.079  0.201  20.286
plotHeatmap          5.351  0.246   5.697
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MAIT.Rcheck/00check.log’
for details.

* installing *source* package ‘MAIT’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
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
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.185	0.043	1.237
LSDResults	0.697	0.010	0.707
MAITbuilder	0.028	0.008	0.036
Validation	20.154	0.175	20.461
classNum	0.005	0.007	0.012
classes	0.005	0.005	0.010
classifRatioClasses	20.263	0.329	20.630
featureID	0.723	0.016	0.740
featureInfo	0.714	0.009	0.723
featureSigID	0.714	0.011	0.724
getScoresTable	0.784	0.032	0.816
identifyMetabolites	1.529	0.048	1.859
loadings	2.678	0.064	2.769
metaboliteTable	1.628	0.050	1.678
method	0.005	0.009	0.012
model	2.862	0.048	2.928
models	0.708	0.012	0.721
ovClassifRatio	20.132	0.286	20.424
ovClassifRatioTable	20.079	0.201	20.286
parameters	20.421	0.289	20.716
pcaLoadings	0.875	0.034	0.917
pcaModel	0.862	0.022	0.892
pcaScores	0.867	0.027	0.900
peakAggregation	0.011	0.009	0.020
peakAnnotation	0.001	0.000	0.000
plotBoxplot	1.146	0.042	1.206
plotHeatmap	5.351	0.246	5.697
plotPCA	0.838	0.022	2.225
plotPLS	2.386	0.045	3.373
plsLoadings	2.364	0.031	2.405
plsModel	2.396	0.040	2.444
plsScores	2.319	0.037	2.364
pvalues	0.673	0.008	0.682
pvaluesCorrection	0.690	0.008	0.698
rawData	0.005	0.007	0.010
resultsPath	0.697	0.008	0.705
sampleProcessing	0.001	0.000	0.000
scores	2.542	0.074	2.633
sigPeaksTable	0.912	0.018	0.929
spectralSigFeatures	0.706	0.011	0.718

BioC 3.2: CHECK report for MAIT on perceval

Summary

Command output