BioC 3.0: CHECK report for MAIT on oaxaca

Package: MAIT

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MAIT_1.0.0.tar.gz

StartedAt: 2015-04-10 00:54:40 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:01:21 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 401.9 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 --no-multiarch MAIT_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/MAIT.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.0.0’
* 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 ... [21s/23s] 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 ... [158s/169s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
Validation          21.966  0.157  23.638
parameters          21.945  0.121  23.035
classifRatioClasses 21.743  0.108  22.449
ovClassifRatio      21.612  0.115  22.267
ovClassifRatioTable 20.712  0.111  21.568
* 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
  ‘/Users/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	1.472	0.028	1.505
LSDResults	0.801	0.008	0.826
MAITbuilder	0.032	0.004	0.036
Validation	21.966	0.157	23.638
classNum	0.005	0.003	0.008
classes	0.005	0.004	0.009
classifRatioClasses	21.743	0.108	22.449
featureID	0.812	0.006	0.869
featureInfo	0.790	0.005	0.821
featureSigID	0.809	0.006	0.878
getScoresTable	0.706	0.024	1.565
identifyMetabolites	1.817	0.020	1.844
loadings	2.814	0.038	3.059
metaboliteTable	1.819	0.032	1.907
method	0.005	0.003	0.008
model	2.456	0.037	2.544
models	0.701	0.007	0.713
ovClassifRatio	21.612	0.115	22.267
ovClassifRatioTable	20.712	0.111	21.568
parameters	21.945	0.121	23.035
pcaLoadings	0.914	0.016	0.944
pcaModel	0.947	0.015	0.979
pcaScores	0.948	0.020	0.982
peakAggregation	0.012	0.005	0.017
peakAnnotation	0.001	0.000	0.000
plotBoxplot	1.175	0.031	1.276
plotHeatmap	4.565	0.182	4.938
plotPCA	0.737	0.015	1.428
plotPLS	1.994	0.025	2.575
plsLoadings	1.651	0.027	2.920
plsModel	2.428	0.030	2.835
plsScores	2.259	0.028	2.310
pvalues	0.766	0.007	0.776
pvaluesCorrection	0.785	0.008	0.794
rawData	0.005	0.006	0.011
resultsPath	0.797	0.009	0.808
sampleProcessing	0.000	0.000	0.001
scores	2.543	0.057	2.662
sigPeaksTable	1.064	0.013	1.146
spectralSigFeatures	0.815	0.008	0.847