BioC 3.2: CHECK report for MAIT on oaxaca

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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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.3.1’
* 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 ... [16s/18s] 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 ... [149s/161s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
parameters          22.105  0.139  22.888
classifRatioClasses 21.247  0.130  23.753
Validation          20.997  0.170  22.120
ovClassifRatioTable 20.424  0.111  21.314
ovClassifRatio      19.478  0.102  20.827
plotHeatmap          4.642  0.174   5.067
* 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	1.138	0.025	1.191
LSDResults	0.718	0.004	0.723
MAITbuilder	0.036	0.002	0.038
Validation	20.997	0.170	22.120
classNum	0.005	0.002	0.007
classes	0.006	0.002	0.008
classifRatioClasses	21.247	0.130	23.753
featureID	0.786	0.009	0.798
featureInfo	0.761	0.005	0.780
featureSigID	0.813	0.004	0.915
getScoresTable	0.839	0.022	0.902
identifyMetabolites	1.703	0.014	1.888
loadings	2.220	0.034	2.304
metaboliteTable	1.567	0.015	1.591
method	0.003	0.001	0.004
model	2.271	0.031	2.317
models	0.726	0.004	0.733
ovClassifRatio	19.478	0.102	20.827
ovClassifRatioTable	20.424	0.111	21.314
parameters	22.105	0.139	22.888
pcaLoadings	0.908	0.014	1.205
pcaModel	0.909	0.012	0.932
pcaScores	0.956	0.017	0.985
peakAggregation	0.012	0.003	0.014
peakAnnotation	0.001	0.000	0.001
plotBoxplot	1.148	0.030	1.238
plotHeatmap	4.642	0.174	5.067
plotPCA	0.930	0.012	0.957
plotPLS	2.575	0.026	2.677
plsLoadings	2.059	0.024	2.612
plsModel	1.867	0.019	2.142
plsScores	1.916	0.021	2.199
pvalues	0.659	0.004	0.814
pvaluesCorrection	0.541	0.003	0.619
rawData	0.004	0.001	0.025
resultsPath	0.725	0.003	0.871
sampleProcessing	0.001	0.000	0.019
scores	2.011	0.046	2.972
sigPeaksTable	0.770	0.009	0.974
spectralSigFeatures	0.697	0.003	1.678

BioC 3.2: CHECK report for MAIT on oaxaca

Summary

Command output