BioC 3.3: CHECK report for MAIT on morelia

Package: MAIT

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAIT_1.5.0.tar.gz

StartedAt: 2015-10-22 07:51:02 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 07:54:39 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 217.1 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MAIT.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.5.0’
* 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 ... [12s/13s] 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 ... [102s/103s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatio      15.835  0.123  16.009
ovClassifRatioTable 15.003  0.112  15.135
Validation          14.924  0.140  15.106
classifRatioClasses 12.948  0.116  13.099
parameters          12.511  0.142  12.669
* 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-3.3-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	0.708	0.020	0.761
LSDResults	0.448	0.005	0.454
MAITbuilder	0.018	0.001	0.019
Validation	14.924	0.140	15.106
classNum	0.005	0.003	0.007
classes	0.005	0.002	0.007
classifRatioClasses	12.948	0.116	13.099
featureID	0.509	0.003	0.513
featureInfo	0.439	0.004	0.444
featureSigID	0.465	0.003	0.467
getScoresTable	0.507	0.015	0.522
identifyMetabolites	1.121	0.007	1.133
loadings	1.744	0.029	1.828
metaboliteTable	1.410	0.018	1.434
method	0.004	0.002	0.006
model	2.034	0.028	2.067
models	0.654	0.004	0.659
ovClassifRatio	15.835	0.123	16.009
ovClassifRatioTable	15.003	0.112	15.135
parameters	12.511	0.142	12.669
pcaLoadings	0.522	0.011	0.535
pcaModel	0.533	0.011	0.544
pcaScores	0.632	0.012	0.647
peakAggregation	0.007	0.001	0.009
peakAnnotation	0	0	0
plotBoxplot	0.665	0.024	0.693
plotHeatmap	3.032	0.162	3.198
plotPCA	0.507	0.011	0.520
plotPLS	1.421	0.019	1.442
plsLoadings	1.363	0.018	1.384
plsModel	1.416	0.019	1.436
plsScores	1.447	0.020	1.470
pvalues	0.444	0.003	0.448
pvaluesCorrection	0.458	0.002	0.461
rawData	0.003	0.001	0.004
resultsPath	0.501	0.003	0.504
sampleProcessing	0.001	0.000	0.000
scores	1.519	0.038	1.562
sigPeaksTable	0.603	0.006	0.609
spectralSigFeatures	0.445	0.002	0.447