BioC 3.2: CHECK report for MAIT on zin1

Package: MAIT

Version: 1.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.4.0.tar.gz

StartedAt: 2016-04-23 02:24:04 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:27:47 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 223.7 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/MAIT.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.4.0’
* 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 ... [10s/10s] 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 ... [114s/115s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
Validation          16.592  0.052  16.774
classifRatioClasses 16.172  0.048  16.274
ovClassifRatioTable 15.856  0.040  15.900
parameters          15.823  0.052  15.952
ovClassifRatio      15.662  0.056  15.907
* 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-3.2-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	0.902	0.004	0.910
LSDResults	0.565	0.004	0.572
MAITbuilder	0.022	0.000	0.023
Validation	16.592	0.052	16.774
classNum	0.004	0.000	0.004
classes	0.005	0.000	0.005
classifRatioClasses	16.172	0.048	16.274
featureID	0.633	0.000	0.636
featureInfo	0.619	0.000	0.619
featureSigID	0.564	0.000	0.564
getScoresTable	0.625	0.012	0.639
identifyMetabolites	1.255	0.004	1.262
loadings	1.836	0.004	2.041
metaboliteTable	1.265	0.008	1.273
method	0.004	0.000	0.003
model	1.870	0.004	1.894
models	0.573	0.000	0.581
ovClassifRatio	15.662	0.056	15.907
ovClassifRatioTable	15.856	0.040	15.900
parameters	15.823	0.052	15.952
pcaLoadings	0.607	0.004	0.611
pcaModel	0.61	0.00	0.61
pcaScores	0.666	0.004	0.669
peakAggregation	0.005	0.004	0.012
peakAnnotation	0.001	0.000	0.001
plotBoxplot	0.758	0.008	0.772
plotHeatmap	2.717	0.008	2.747
plotPCA	0.620	0.000	0.622
plotPLS	2.041	0.000	2.040
plsLoadings	1.793	0.000	1.794
plsModel	1.711	0.004	1.720
plsScores	1.694	0.008	1.702
pvalues	0.601	0.000	0.601
pvaluesCorrection	0.563	0.000	0.563
rawData	0.004	0.000	0.004
resultsPath	0.555	0.004	0.561
sampleProcessing	0.001	0.000	0.001
scores	1.865	0.008	1.872
sigPeaksTable	0.674	0.000	0.673
spectralSigFeatures	0.557	0.000	0.569