BioC 3.1: CHECK report for MAIT on zin2

Package: MAIT

Version: 1.2.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.2.1.tar.gz

StartedAt: 2015-10-09 03:07:03 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:11:40 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 277.5 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/MAIT.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.2.1’
* 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 ... [10s/15s] 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 ... [115s/129s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatioTable 16.646  0.041  16.808
classifRatioClasses 16.583  0.050  16.864
ovClassifRatio      16.332  0.065  16.577
parameters          16.329  0.052  16.608
Validation          15.638  0.074  24.169
* 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
  ‘/home/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	0.909	0.010	1.862
LSDResults	0.558	0.000	0.953
MAITbuilder	0.027	0.000	0.027
Validation	15.638	0.074	24.169
classNum	0.004	0.000	0.004
classes	0.005	0.000	0.005
classifRatioClasses	16.583	0.050	16.864
featureID	0.566	0.004	0.570
featureInfo	0.623	0.000	0.623
featureSigID	0.601	0.000	0.607
getScoresTable	0.677	0.008	0.691
identifyMetabolites	1.235	0.012	1.246
loadings	1.910	0.008	1.930
metaboliteTable	1.340	0.004	1.373
method	0.004	0.000	0.004
model	1.897	0.008	1.915
models	0.600	0.000	0.624
ovClassifRatio	16.332	0.065	16.577
ovClassifRatioTable	16.646	0.041	16.808
parameters	16.329	0.052	16.608
pcaLoadings	0.642	0.004	0.661
pcaModel	0.608	0.000	0.608
pcaScores	0.660	0.000	0.659
peakAggregation	0.008	0.000	0.011
peakAnnotation	0.001	0.000	0.001
plotBoxplot	0.792	0.004	0.811
plotHeatmap	2.802	0.008	2.831
plotPCA	0.652	0.004	0.680
plotPLS	1.750	0.004	1.789
plsLoadings	1.937	0.008	1.945
plsModel	1.704	0.001	1.707
plsScores	1.654	0.004	1.669
pvalues	0.507	0.000	0.507
pvaluesCorrection	0.518	0.000	0.519
rawData	0.004	0.000	0.003
resultsPath	0.521	0.004	0.524
sampleProcessing	0	0	0
scores	1.750	0.008	1.800
sigPeaksTable	0.700	0.000	0.708
spectralSigFeatures	0.563	0.000	0.573