BioC 3.3: CHECK report for MAIT on linux2.bioconductor.org

Package: MAIT

Version: 1.5.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.5.0.tar.gz

StartedAt: 2015-10-27 05:22:11 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:26:03 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 232.3 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MAIT_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MAIT.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.0’
* 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 ... [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [115s/115s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
parameters          17.367  0.063  17.456
ovClassifRatio      16.305  0.036  16.342
ovClassifRatioTable 15.957  0.053  16.017
classifRatioClasses 14.958  0.044  15.003
Validation          14.429  0.060  14.493
* 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-3.3-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	1.172	0.016	1.188
LSDResults	0.752	0.000	0.751
MAITbuilder	0.031	0.000	0.032
Validation	14.429	0.060	14.493
classNum	0.003	0.000	0.003
classes	0.003	0.000	0.003
classifRatioClasses	14.958	0.044	15.003
featureID	0.533	0.000	0.533
featureInfo	0.645	0.004	0.649
featureSigID	0.496	0.004	0.501
getScoresTable	0.781	0.016	0.797
identifyMetabolites	1.559	0.012	1.571
loadings	2.378	0.008	2.386
metaboliteTable	1.286	0.016	1.302
method	0.005	0.000	0.005
model	2.005	0.012	2.017
models	0.648	0.004	0.652
ovClassifRatio	16.305	0.036	16.342
ovClassifRatioTable	15.957	0.053	16.017
parameters	17.367	0.063	17.456
pcaLoadings	0.548	0.000	0.548
pcaModel	0.767	0.000	0.768
pcaScores	0.756	0.004	0.761
peakAggregation	0.014	0.000	0.013
peakAnnotation	0	0	0
plotBoxplot	0.606	0.000	0.606
plotHeatmap	2.802	0.016	2.818
plotPCA	0.752	0.000	0.752
plotPLS	1.586	0.004	1.604
plsLoadings	1.506	0.004	1.511
plsModel	1.544	0.004	1.549
plsScores	1.800	0.000	1.803
pvalues	0.639	0.000	0.647
pvaluesCorrection	0.709	0.000	0.709
rawData	0.005	0.000	0.006
resultsPath	0.675	0.000	0.675
sampleProcessing	0	0	0
scores	2.323	0.016	2.359
sigPeaksTable	0.531	0.004	1.059
spectralSigFeatures	0.58	0.00	0.58