BioC 3.1: CHECK report for MAIT on petty

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAIT_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.2.1’
* 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 ... [21s/29s] 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 ... [198s/220s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
parameters          29.374  0.294  33.674
classifRatioClasses 28.536  0.441  30.364
Validation          26.674  0.253  29.386
ovClassifRatioTable 25.470  0.303  28.163
ovClassifRatio      23.727  0.275  27.264
plotHeatmap          7.927  0.345   9.114
* 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	1.368	0.043	1.687
LSDResults	0.801	0.006	0.840
MAITbuilder	0.039	0.003	0.042
Validation	26.674	0.253	29.386
classNum	0.006	0.005	0.013
classes	0.008	0.005	0.013
classifRatioClasses	28.536	0.441	30.364
featureID	0.975	0.014	0.989
featureInfo	0.799	0.007	0.806
featureSigID	1.011	0.008	1.029
getScoresTable	1.139	0.040	1.246
identifyMetabolites	2.078	0.036	2.615
loadings	3.210	0.061	3.765
metaboliteTable	1.794	0.036	2.185
method	0.006	0.005	0.011
model	3.187	0.062	3.812
models	0.823	0.014	0.840
ovClassifRatio	23.727	0.275	27.264
ovClassifRatioTable	25.470	0.303	28.163
parameters	29.374	0.294	33.674
pcaLoadings	1.322	0.032	1.510
pcaModel	1.261	0.031	1.560
pcaScores	1.272	0.036	1.387
peakAggregation	0.018	0.011	0.030
peakAnnotation	0.002	0.000	0.001
plotBoxplot	1.662	0.054	1.947
plotHeatmap	7.927	0.345	9.114
plotPCA	1.171	0.027	1.320
plotPLS	3.416	0.046	3.830
plsLoadings	3.001	0.046	4.410
plsModel	3.022	0.047	3.361
plsScores	3.035	0.049	3.499
pvalues	1.061	0.008	1.124
pvaluesCorrection	0.946	0.006	0.995
rawData	0.006	0.004	0.011
resultsPath	0.920	0.007	0.965
sampleProcessing	0.001	0.000	0.001
scores	3.454	0.078	3.957
sigPeaksTable	1.236	0.015	1.309
spectralSigFeatures	1.000	0.007	1.018

BioC 3.1: CHECK report for MAIT on petty

Summary

Command output