Package: MAIT

Version: 1.20.0

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_1.20.0.tar.gz

StartedAt: 2020-04-15 03:32:04 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:39:06 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 421.2 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_1.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MAIT.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.20.0’
* 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
parameters          22.128  0.134  22.663
ovClassifRatio      20.802  0.142  21.167
Validation          20.435  0.239  20.848
ovClassifRatioTable 20.372  0.134  20.724
classifRatioClasses 19.787  0.161  20.128
plotHeatmap          9.689  0.335   9.909
* 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-3.10-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/3.6/Resources/library’
* installing *source* package ‘MAIT’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’ 
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 from temporary location
Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘xcms::plot’ by ‘graphics::plot’ when loading ‘CAMERA’
** testing if installed package keeps a record of temporary installation path
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.964	0.040	2.021
LSDResults	1.153	0.030	1.190
MAITbuilder	0.027	0.006	0.035
Validation	20.435	0.239	20.848
classNum	0.005	0.006	0.011
classes	0.006	0.005	0.011
classifRatioClasses	19.787	0.161	20.128
featureID	1.225	0.007	1.244
featureInfo	1.209	0.009	1.222
featureSigID	1.234	0.009	1.254
getScoresTable	1.174	0.031	1.213
identifyMetabolites	2.407	0.021	2.440
loadings	3.096	0.078	3.217
metaboliteTable	2.189	0.040	2.243
method	0.005	0.005	0.010
model	3.204	0.063	3.280
models	1.167	0.012	1.186
ovClassifRatio	20.802	0.142	21.167
ovClassifRatioTable	20.372	0.134	20.724
parameters	22.128	0.134	22.663
pcaLoadings	1.258	0.026	1.303
pcaModel	1.381	0.024	1.450
pcaScores	1.280	0.028	1.329
peakAggregation	0.013	0.006	0.019
peakAnnotation	0	0	0
plotBoxplot	1.493	0.075	1.588
plotHeatmap	9.689	0.335	9.909
plotPCA	1.402	0.033	1.462
plotPLS	2.916	0.032	2.973
plsLoadings	3.088	0.037	3.152
plsModel	2.927	0.036	3.003
plsScores	3.041	0.044	3.110
pvalues	1.308	0.010	1.365
pvaluesCorrection	1.251	0.010	1.282
rawData	0.004	0.004	0.012
resultsPath	1.046	0.008	1.067
sampleProcessing	0.000	0.000	0.001
scores	2.493	0.069	2.564
sigPeaksTable	1.109	0.013	1.127
spectralSigFeatures	0.945	0.007	0.954