BioC 3.2: CHECK report for MAIT on oaxaca

Package: MAIT

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAIT_1.4.0.tar.gz

StartedAt: 2016-04-23 01:40:09 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:45:28 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 319.0 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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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 3.2.4 (2016-03-10)
* 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/17s] 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 ... [151s/165s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatioTable 21.560  0.104  21.853
parameters          20.001  0.107  28.128
Validation          19.817  0.192  20.284
classifRatioClasses 18.548  0.146  19.178
ovClassifRatio      18.546  0.123  19.264
plotHeatmap          9.993  0.196  10.779
* 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
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	1.041	0.030	1.086
LSDResults	0.681	0.006	0.687
MAITbuilder	0.026	0.002	0.029
Validation	19.817	0.192	20.284
classNum	0.004	0.002	0.007
classes	0.005	0.003	0.009
classifRatioClasses	18.548	0.146	19.178
featureID	0.706	0.007	0.713
featureInfo	0.770	0.003	0.777
featureSigID	0.796	0.005	0.808
getScoresTable	0.825	0.022	0.851
identifyMetabolites	1.654	0.016	1.672
loadings	2.481	0.036	2.581
metaboliteTable	1.547	0.022	1.570
method	0.004	0.002	0.006
model	2.090	0.031	2.127
models	0.724	0.003	0.728
ovClassifRatio	18.546	0.123	19.264
ovClassifRatioTable	21.560	0.104	21.853
parameters	20.001	0.107	28.128
pcaLoadings	0.902	0.016	0.949
pcaModel	0.942	0.017	0.974
pcaScores	0.882	0.018	0.916
peakAggregation	0.012	0.005	0.016
peakAnnotation	0.001	0.000	0.001
plotBoxplot	1.110	0.032	1.252
plotHeatmap	9.993	0.196	10.779
plotPCA	0.926	0.017	0.951
plotPLS	2.534	0.027	2.579
plsLoadings	2.495	0.027	2.567
plsModel	2.421	0.032	2.557
plsScores	2.477	0.034	2.540
pvalues	0.790	0.007	0.797
pvaluesCorrection	0.801	0.007	0.810
rawData	0.004	0.005	0.010
resultsPath	0.875	0.009	0.894
sampleProcessing	0.001	0.000	0.001
scores	2.506	0.048	2.896
sigPeaksTable	1.012	0.011	1.889
spectralSigFeatures	0.750	0.007	0.797