BioC 3.1: CHECK report for MAIT on morelia

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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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/MAIT.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.2.1’
* 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 ... [13s/14s] 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 ... [138s/139s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
Validation          19.531  0.869  20.557
ovClassifRatioTable 19.076  0.675  19.792
ovClassifRatio      18.385  0.933  19.370
classifRatioClasses 18.550  0.759  19.331
parameters          18.029  0.753  18.814
* 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-3.1-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	0.940	0.030	1.018
LSDResults	0.691	0.005	0.696
MAITbuilder	0.039	0.004	0.043
Validation	19.531	0.869	20.557
classNum	0.012	0.002	0.015
classes	0.006	0.002	0.008
classifRatioClasses	18.550	0.759	19.331
featureID	0.703	0.087	0.790
featureInfo	0.613	0.003	0.615
featureSigID	0.631	0.004	0.634
getScoresTable	0.680	0.030	0.712
identifyMetabolites	1.452	0.101	1.555
loadings	2.043	0.135	2.206
metaboliteTable	1.573	0.110	1.686
method	0.004	0.002	0.007
model	2.107	0.090	2.204
models	0.588	0.032	0.622
ovClassifRatio	18.385	0.933	19.370
ovClassifRatioTable	19.076	0.675	19.792
parameters	18.029	0.753	18.814
pcaLoadings	0.785	0.049	0.837
pcaModel	0.691	0.056	0.749
pcaScores	0.713	0.022	0.739
peakAggregation	0.012	0.002	0.014
peakAnnotation	0	0	0
plotBoxplot	0.956	0.045	1.008
plotHeatmap	3.675	0.267	3.960
plotPCA	0.760	0.036	0.799
plotPLS	2.278	0.166	2.450
plsLoadings	1.888	0.136	2.028
plsModel	1.889	0.062	1.957
plsScores	1.768	0.093	1.866
pvalues	0.598	0.006	0.604
pvaluesCorrection	0.665	0.003	0.669
rawData	0.003	0.002	0.004
resultsPath	0.662	0.066	0.729
sampleProcessing	0.000	0.000	0.001
scores	2.003	0.072	2.083
sigPeaksTable	0.788	0.039	0.827
spectralSigFeatures	0.554	0.005	0.558

BioC 3.1: CHECK report for MAIT on morelia

Summary

Command output