BioC 3.5: CHECK report for MAIT on tokay2

Package: MAIT

Version: 1.9.0

Command: rm -rf MAIT.buildbin-libdir MAIT.Rcheck && mkdir MAIT.buildbin-libdir MAIT.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MAIT.buildbin-libdir MAIT_1.9.0.tar.gz >MAIT.Rcheck\00install.out 2>&1 && cp MAIT.Rcheck\00install.out MAIT-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MAIT.buildbin-libdir --install="check:MAIT-install.out" --force-multiarch --no-vignettes --timings MAIT_1.9.0.tar.gz

StartedAt: 2017-04-19 00:31:34 -0400 (Wed, 19 Apr 2017)

EndedAt: 2017-04-19 00:41:16 -0400 (Wed, 19 Apr 2017)

EllapsedTime: 582.4 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MAIT.buildbin-libdir MAIT.Rcheck && mkdir MAIT.buildbin-libdir MAIT.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MAIT.buildbin-libdir MAIT_1.9.0.tar.gz >MAIT.Rcheck\00install.out 2>&1 && cp MAIT.Rcheck\00install.out MAIT-install.out  && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MAIT.buildbin-libdir --install="check:MAIT-install.out" --force-multiarch --no-vignettes --timings MAIT_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MAIT.Rcheck'
* using R version 3.4.0 RC (2017-04-13 r72510)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAIT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAIT' version '1.9.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
Validation          17.63   0.11   18.36
classifRatioClasses 15.63   0.16   15.78
ovClassifRatio      15.00   0.03   15.03
ovClassifRatioTable 13.48   0.12   13.61
parameters          12.93   0.08   13.00
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
classifRatioClasses 23.58   0.06   23.64
Validation          20.32   0.05   20.39
ovClassifRatio      18.28   0.08   18.36
ovClassifRatioTable 17.64   0.06   17.70
parameters          16.62   0.06   16.69
model                5.00   0.11    5.11
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MAIT.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'MAIT' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MAIT' as MAIT_1.9.0.zip
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.81	0.04	2.13
LSDResults	0.87	0.01	0.89
MAITbuilder	0.03	0.02	0.05
Validation	17.63	0.11	18.36
classNum	0.00	0.01	0.01
classes	0.01	0.00	0.02
classifRatioClasses	15.63	0.16	15.78
featureID	0.68	0.00	0.69
featureInfo	0.71	0.00	0.70
featureSigID	0.43	0.01	0.45
getScoresTable	0.46	0.04	0.49
identifyMetabolites	1.22	0.01	1.23
loadings	2.34	0.05	2.50
metaboliteTable	1.31	0.03	1.34
method	0.00	0.01	0.02
model	2.70	0.04	2.73
models	0.45	0.00	0.45
ovClassifRatio	15.00	0.03	15.03
ovClassifRatioTable	13.48	0.12	13.61
parameters	12.93	0.08	13.00
pcaLoadings	0.43	0.03	0.47
pcaModel	0.47	0.02	0.48
pcaScores	0.47	0.03	0.50
peakAggregation	0.02	0.00	0.02
peakAnnotation	0	0	0
plotBoxplot	0.51	0.05	0.56
plotHeatmap	3.33	0.53	3.86
plotPCA	0.77	0.03	0.80
plotPLS	2.37	0.05	2.43
plsLoadings	1.70	0.03	1.74
plsModel	1.95	0.02	1.97
plsScores	1.57	0.01	1.57
pvalues	0.39	0.00	0.39
pvaluesCorrection	0.39	0.02	0.41
rawData	0	0	0
resultsPath	0.39	0.01	0.41
sampleProcessing	0	0	0
scores	2.06	0.10	2.15
sigPeaksTable	0.69	0.03	0.72
spectralSigFeatures	0.49	0.00	0.48

name	user	system	elapsed
Biotransformations	1.95	0.00	1.95
LSDResults	0.64	0.00	0.65
MAITbuilder	0.01	0.01	0.03
Validation	20.32	0.05	20.39
classNum	0.00	0.02	0.02
classes	0.01	0.00	0.01
classifRatioClasses	23.58	0.06	23.64
featureID	0.89	0.01	0.91
featureInfo	0.89	0.00	0.89
featureSigID	0.83	0.00	0.83
getScoresTable	0.86	0.00	0.86
identifyMetabolites	2.12	0.05	2.17
loadings	2.91	0.02	2.92
metaboliteTable	2.08	0.03	2.11
method	0.00	0.01	0.01
model	5.00	0.11	5.11
models	0.82	0.02	0.83
ovClassifRatio	18.28	0.08	18.36
ovClassifRatioTable	17.64	0.06	17.70
parameters	16.62	0.06	16.69
pcaLoadings	0.89	0.03	0.92
pcaModel	0.55	0.02	0.57
pcaScores	0.58	0.03	0.60
peakAggregation	0.01	0.00	0.02
peakAnnotation	0	0	0
plotBoxplot	0.63	0.06	0.83
plotHeatmap	3.99	0.47	4.46
plotPCA	0.86	0.03	0.89
plotPLS	2.50	0.02	2.51
plsLoadings	2.22	0.01	2.24
plsModel	2.14	0.07	2.20
plsScores	1.93	0.03	1.97
pvalues	0.47	0.00	0.47
pvaluesCorrection	0.66	0.00	0.65
rawData	0.02	0.00	0.02
resultsPath	0.62	0.00	0.63
sampleProcessing	0	0	0
scores	2.14	0.01	2.16
sigPeaksTable	0.83	0.02	0.85
spectralSigFeatures	0.64	0.00	0.64