BioC 3.2: CHECK report for MAIT on linux1.bioconductor.org

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: 2015-10-27 05:13:49 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:17:37 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 228.2 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 3.2.2 (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 ‘1.4.0’
* 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 ... [12s/12s] 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 ... [108s/108s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ovClassifRatio      16.945  0.036  16.992
classifRatioClasses 16.225  0.076  16.396
parameters          14.547  0.032  14.580
Validation          14.257  0.040  14.299
ovClassifRatioTable 13.602  0.040  13.643
* 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
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	1.167	0.016	1.185
LSDResults	0.562	0.004	0.567
MAITbuilder	0.017	0.000	0.018
Validation	14.257	0.040	14.299
classNum	0.000	0.004	0.003
classes	0.004	0.000	0.004
classifRatioClasses	16.225	0.076	16.396
featureID	0.497	0.004	0.502
featureInfo	0.489	0.004	0.492
featureSigID	0.644	0.000	0.645
getScoresTable	0.753	0.020	0.773
identifyMetabolites	1.039	0.008	1.056
loadings	1.577	0.004	1.580
metaboliteTable	1.270	0.004	1.275
method	0.004	0.000	0.004
model	1.483	0.004	1.487
models	0.425	0.000	0.426
ovClassifRatio	16.945	0.036	16.992
ovClassifRatioTable	13.602	0.040	13.643
parameters	14.547	0.032	14.580
pcaLoadings	0.742	0.004	0.746
pcaModel	0.488	0.000	0.488
pcaScores	0.493	0.000	0.493
peakAggregation	0.005	0.004	0.009
peakAnnotation	0.000	0.000	0.001
plotBoxplot	0.591	0.004	0.595
plotHeatmap	2.444	0.008	2.452
plotPCA	0.487	0.000	0.487
plotPLS	1.751	0.000	1.751
plsLoadings	1.763	0.000	1.763
plsModel	2.204	0.012	2.216
plsScores	1.739	0.000	1.739
pvalues	0.551	0.000	0.551
pvaluesCorrection	0.444	0.000	0.444
rawData	0.004	0.000	0.004
resultsPath	0.439	0.000	0.439
sampleProcessing	0	0	0
scores	2.147	0.008	2.155
sigPeaksTable	0.923	0.000	0.936
spectralSigFeatures	0.578	0.008	0.587