BioC 3.0: CHECK report for MAIT on zin1

Package: MAIT

Version: 1.0.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.0.0.tar.gz

StartedAt: 2015-04-10 01:32:47 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:38:02 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 314.9 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/MAIT.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.0.0’
* 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 ... [17s/19s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [134s/139s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatioTable 19.237  0.096  20.012
ovClassifRatio      18.657  0.040  18.806
parameters          18.514  0.052  18.939
Validation          18.281  0.036  18.586
classifRatioClasses 18.145  0.036  18.318
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/MAIT.Rcheck/00check.log’
for details.

* installing *source* package ‘MAIT’ ...
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.256	0.008	1.335
LSDResults	0.704	0.000	0.710
MAITbuilder	0.028	0.000	0.029
Validation	18.281	0.036	18.586
classNum	0.004	0.000	0.004
classes	0.004	0.000	0.004
classifRatioClasses	18.145	0.036	18.318
featureID	0.692	0.004	0.749
featureInfo	0.700	0.008	0.726
featureSigID	0.708	0.000	0.792
getScoresTable	0.753	0.020	0.794
identifyMetabolites	1.504	0.004	1.794
loadings	2.048	0.000	2.136
metaboliteTable	1.580	0.024	1.748
method	0.004	0.000	0.005
model	2.272	0.016	2.378
models	0.708	0.000	0.709
ovClassifRatio	18.657	0.040	18.806
ovClassifRatioTable	19.237	0.096	20.012
parameters	18.514	0.052	18.939
pcaLoadings	0.748	0.000	0.800
pcaModel	0.768	0.000	0.792
pcaScores	0.720	0.008	0.729
peakAggregation	0.008	0.004	0.011
peakAnnotation	0.004	0.000	0.001
plotBoxplot	0.944	0.004	1.155
plotHeatmap	2.928	0.036	3.248
plotPCA	0.756	0.000	1.064
plotPLS	2.052	0.008	2.318
plsLoadings	1.872	0.000	1.879
plsModel	1.948	0.000	2.338
plsScores	2.040	0.020	2.188
pvalues	0.721	0.000	0.723
pvaluesCorrection	0.660	0.004	0.663
rawData	0.004	0.000	0.004
resultsPath	0.668	0.008	0.733
sampleProcessing	0	0	0
scores	2.124	0.012	2.237
sigPeaksTable	0.924	0.004	0.971
spectralSigFeatures	0.728	0.000	0.772