Package: MAIT

Version: 1.18.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MAIT_1.18.0.tar.gz

StartedAt: 2019-10-16 02:50:36 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:56:49 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 373.1 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MAIT_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MAIT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.18.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
classifRatioClasses 21.406  0.044  21.460
Validation          16.418  0.064  16.496
ovClassifRatioTable 15.890  0.048  15.948
ovClassifRatio      15.232  0.044  15.286
parameters          14.575  0.040  14.620
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MAIT.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MAIT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MAIT’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.329	0.040	1.902
LSDResults	0.973	0.000	0.973
MAITbuilder	0.028	0.000	0.028
Validation	16.418	0.064	16.496
classNum	0.005	0.000	0.005
classes	0.006	0.000	0.006
classifRatioClasses	21.406	0.044	21.460
featureID	1.142	0.004	1.148
featureInfo	0.824	0.000	0.825
featureSigID	0.801	0.004	0.805
getScoresTable	1.206	0.012	1.291
identifyMetabolites	2.340	0.008	2.464
loadings	2.372	0.036	2.440
metaboliteTable	1.201	0.008	1.209
method	0.000	0.003	0.003
model	2.041	0.012	2.053
models	0.820	0.004	0.823
ovClassifRatio	15.232	0.044	15.286
ovClassifRatioTable	15.890	0.048	15.948
parameters	14.575	0.040	14.620
pcaLoadings	1.262	0.004	1.269
pcaModel	1.252	0.000	1.253
pcaScores	1.230	0.012	1.241
peakAggregation	0.015	0.000	0.014
peakAnnotation	0	0	0
plotBoxplot	1.410	0.000	1.411
plotHeatmap	3.781	0.008	3.790
plotPCA	1.255	0.000	1.255
plotPLS	3.03	0.00	3.03
plsLoadings	2.315	0.012	2.327
plsModel	3.116	0.008	3.125
plsScores	3.089	0.001	3.093
pvalues	1.207	0.000	1.208
pvaluesCorrection	1.208	0.000	1.207
rawData	0.001	0.004	0.006
resultsPath	1.174	0.000	1.174
sampleProcessing	0	0	0
scores	2.629	0.000	2.630
sigPeaksTable	1.351	0.000	1.351
spectralSigFeatures	1.159	0.004	1.163