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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MAIT.Rcheck’
* using R version 3.2.2 (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 ‘1.4.0’
* 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/16s] 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 ... [147s/154s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatioTable 21.158  0.125  21.345
Validation          20.999  0.171  21.224
classifRatioClasses 20.127  0.142  20.333
parameters          19.979  0.154  25.620
ovClassifRatio      19.871  0.126  20.113
* 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	1.110	0.026	1.158
LSDResults	0.755	0.003	0.766
MAITbuilder	0.029	0.001	0.029
Validation	20.999	0.171	21.224
classNum	0.004	0.002	0.006
classes	0.005	0.002	0.006
classifRatioClasses	20.127	0.142	20.333
featureID	0.825	0.004	0.833
featureInfo	0.796	0.004	0.811
featureSigID	0.784	0.004	0.788
getScoresTable	0.865	0.024	0.894
identifyMetabolites	1.550	0.018	1.569
loadings	2.467	0.031	2.539
metaboliteTable	1.688	0.021	1.711
method	0.005	0.002	0.008
model	2.403	0.031	2.452
models	0.730	0.003	0.733
ovClassifRatio	19.871	0.126	20.113
ovClassifRatioTable	21.158	0.125	21.345
parameters	19.979	0.154	25.620
pcaLoadings	0.697	0.016	1.389
pcaModel	0.823	0.014	0.840
pcaScores	0.809	0.015	0.827
peakAggregation	0.011	0.002	0.013
peakAnnotation	0.000	0.000	0.001
plotBoxplot	0.965	0.026	1.014
plotHeatmap	4.038	0.182	4.255
plotPCA	0.739	0.011	0.752
plotPLS	2.339	0.029	2.374
plsLoadings	2.047	0.026	2.078
plsModel	2.019	0.021	2.044
plsScores	1.916	0.023	1.944
pvalues	0.609	0.005	0.614
pvaluesCorrection	0.618	0.004	0.622
rawData	0.003	0.001	0.004
resultsPath	0.753	0.003	0.756
sampleProcessing	0.000	0.000	0.001
scores	2.343	0.043	2.394
sigPeaksTable	0.989	0.010	0.999
spectralSigFeatures	0.652	0.004	0.657

BioC 3.2: CHECK report for MAIT on oaxaca

Summary

Command output