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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MAIT.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.3.1’
* 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 ... [18s/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 ... [153s/154s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatio      21.073  0.345  21.519
ovClassifRatioTable 20.729  0.355  21.109
classifRatioClasses 20.398  0.421  20.868
Validation          20.190  0.243  20.447
parameters          19.456  0.418  19.882
plotHeatmap          4.959  0.306   5.367
* 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	1.237	0.051	1.305
LSDResults	0.734	0.010	0.744
MAITbuilder	0.043	0.005	0.047
Validation	20.190	0.243	20.447
classNum	0.005	0.007	0.012
classes	0.005	0.005	0.010
classifRatioClasses	20.398	0.421	20.868
featureID	0.635	0.020	0.655
featureInfo	0.626	0.011	0.638
featureSigID	0.689	0.007	0.697
getScoresTable	0.747	0.038	0.785
identifyMetabolites	1.515	0.030	1.546
loadings	2.720	0.071	2.807
metaboliteTable	1.680	0.060	1.751
method	0.004	0.006	0.011
model	3.206	0.065	3.317
models	0.693	0.011	0.719
ovClassifRatio	21.073	0.345	21.519
ovClassifRatioTable	20.729	0.355	21.109
parameters	19.456	0.418	19.882
pcaLoadings	0.821	0.024	0.852
pcaModel	0.806	0.022	0.833
pcaScores	0.802	0.026	0.835
peakAggregation	0.010	0.005	0.015
peakAnnotation	0	0	0
plotBoxplot	1.080	0.041	1.137
plotHeatmap	4.959	0.306	5.367
plotPCA	0.847	0.022	0.887
plotPLS	2.588	0.045	2.654
plsLoadings	2.416	0.044	2.477
plsModel	2.472	0.050	2.537
plsScores	2.489	0.038	2.566
pvalues	0.657	0.008	0.665
pvaluesCorrection	0.630	0.006	0.637
rawData	0.004	0.005	0.009
resultsPath	0.661	0.006	0.672
sampleProcessing	0.001	0.000	0.001
scores	2.615	0.081	2.725
sigPeaksTable	0.894	0.018	0.921
spectralSigFeatures	0.666	0.010	0.677

BioC 3.2: CHECK report for MAIT on perceval

Summary

Command output