Package: MAIT

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAIT_1.14.0.tar.gz

StartedAt: 2018-10-16 22:20:37 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:27:38 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 421.3 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 --install=check:MAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAIT_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MAIT.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’
* 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 ... 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 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 ... NOTE
Biotransformations: no visible global function definition for ‘data’
Biotransformations: no visible binding for global variable ‘MAITtables’
Biotransformations: no visible global function definition for
  ‘read.csv’
Biotransformations: no visible global function definition for
  ‘read.csv2’
PLSDA: no visible global function definition for ‘predict’
Validation: no visible global function definition for ‘predict’
Validation: no visible global function definition for ‘sd’
Validation: no visible global function definition for ‘rainbow’
Validation: no visible global function definition for ‘png’
Validation: no visible global function definition for ‘boxplot’
Validation: no visible global function definition for ‘legend’
Validation: no visible global function definition for ‘title’
Validation: no visible global function definition for ‘dev.off’
Validation: no visible binding for global variable ‘sd’
computeSpectra: no visible global function definition for ‘cor’
identifyMetabolites: no visible global function definition for ‘data’
identifyMetabolites: no visible binding for global variable
  ‘MAITtables’
identifyMetabolites: no visible global function definition for
  ‘read.csv’
identifyMetabolites: no visible global function definition for
  ‘write.table’
metaboliteTable: no visible global function definition for
  ‘write.table’
peakAggregation: no visible global function definition for
  ‘write.table’
peakAnnotation: no visible global function definition for ‘data’
peakAnnotation: no visible binding for global variable ‘MAITtables’
peakAnnotation: no visible global function definition for ‘read.csv2’
plotBoxplot: no visible global function definition for ‘png’
plotBoxplot: no visible global function definition for ‘boxplot’
plotBoxplot: no visible global function definition for ‘title’
plotBoxplot: no visible global function definition for ‘dev.off’
plotHeatmap: no visible global function definition for ‘p.adjust’
plotHeatmap : distCor: no visible global function definition for
  ‘as.dist’
plotHeatmap : distCor: no visible global function definition for ‘cor’
plotHeatmap : hclustWard: no visible global function definition for
  ‘hclust’
plotHeatmap: no visible global function definition for
  ‘colorRampPalette’
plotHeatmap: no visible global function definition for ‘png’
plotHeatmap: no visible global function definition for ‘legend’
plotHeatmap: no visible global function definition for ‘dev.off’
plotPCA: no visible global function definition for ‘prcomp’
plotPCA: no visible global function definition for ‘png’
plotPCA: no visible global function definition for ‘plot’
plotPCA: no visible global function definition for ‘legend’
plotPCA: no visible global function definition for ‘dev.off’
plotPLS: no visible global function definition for ‘png’
plotPLS: no visible global function definition for ‘plot’
plotPLS: no visible global function definition for ‘legend’
plotPLS: no visible global function definition for ‘dev.off’
sigPeaksTable: no visible global function definition for ‘p.adjust’
sigPeaksTable: no visible global function definition for ‘aggregate’
sigPeaksTable: no visible binding for global variable ‘median’
sigPeaksTable: no visible global function definition for ‘write.csv’
spectralAnova: no visible global function definition for ‘lm’
spectralAnova: no visible global function definition for ‘anova’
spectralAnova: no visible global function definition for ‘p.adjust’
spectralFUN: no visible global function definition for ‘p.adjust’
spectralKruskal: no visible global function definition for
  ‘kruskal.test’
spectralKruskal: no visible global function definition for ‘p.adjust’
spectralTStudent: no visible global function definition for ‘lm’
spectralTStudent: no visible global function definition for ‘t.test’
spectralTStudent: no visible global function definition for ‘p.adjust’
spectralWelch: no visible global function definition for ‘lm’
spectralWelch: no visible global function definition for ‘t.test’
spectralWelch: no visible global function definition for ‘p.adjust’
spectralWilcox: no visible global function definition for ‘lm’
spectralWilcox: no visible global function definition for ‘wilcox.test’
spectralWilcox: no visible global function definition for ‘p.adjust’
writeExcelTable: no visible global function definition for ‘write.csv’
writeParameterTable: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  MAITtables aggregate anova as.dist boxplot colorRampPalette cor data
  dev.off hclust kruskal.test legend lm median p.adjust plot png prcomp
  predict rainbow read.csv read.csv2 sd t.test title wilcox.test
  write.csv write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png",
             "rainbow")
  importFrom("graphics", "boxplot", "legend", "plot", "title")
  importFrom("stats", "aggregate", "anova", "as.dist", "cor", "hclust",
             "kruskal.test", "lm", "median", "p.adjust", "prcomp",
             "predict", "sd", "t.test", "wilcox.test")
  importFrom("utils", "data", "read.csv", "read.csv2", "write.csv",
             "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
Validation          19.293  0.202  19.731
ovClassifRatioTable 19.085  0.152  19.459
parameters          19.017  0.173  19.431
classifRatioClasses 18.749  0.137  19.052
ovClassifRatio      18.535  0.167  18.894
plotHeatmap         10.213  0.331  10.643
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/MAIT.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MAIT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MAIT’ ...
** R
** data
** inst
** byte-compile and prepare 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	1.348	0.075	1.445
LSDResults	1.124	0.014	1.139
MAITbuilder	0.019	0.002	0.021
Validation	19.293	0.202	19.731
classNum	0.006	0.004	0.010
classes	0.006	0.002	0.007
classifRatioClasses	18.749	0.137	19.052
featureID	1.223	0.011	1.249
featureInfo	1.031	0.005	1.047
featureSigID	1.067	0.004	1.081
getScoresTable	1.291	0.031	1.332
identifyMetabolites	2.426	0.028	2.476
loadings	3.133	0.070	3.232
metaboliteTable	2.178	0.041	2.244
method	0.005	0.007	0.014
model	3.046	0.068	3.145
models	1.017	0.010	1.039
ovClassifRatio	18.535	0.167	18.894
ovClassifRatioTable	19.085	0.152	19.459
parameters	19.017	0.173	19.431
pcaLoadings	1.292	0.030	1.326
pcaModel	1.359	0.035	1.422
pcaScores	1.293	0.032	1.337
peakAggregation	0.014	0.008	0.023
peakAnnotation	0.001	0.001	0.002
plotBoxplot	1.393	0.056	1.458
plotHeatmap	10.213	0.331	10.643
plotPCA	1.368	0.027	1.410
plotPLS	3.239	0.042	3.330
plsLoadings	3.051	0.038	3.124
plsModel	2.981	0.032	3.049
plsScores	2.965	0.035	3.029
pvalues	1.139	0.008	1.154
pvaluesCorrection	1.063	0.008	1.076
rawData	0.005	0.006	0.011
resultsPath	1.030	0.007	1.042
sampleProcessing	0.000	0.000	0.001
scores	2.849	0.074	2.941
sigPeaksTable	1.159	0.015	1.182
spectralSigFeatures	0.955	0.005	0.965