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This page was generated on 2021-08-03 12:06:49 -0400 (Tue, 03 Aug 2021).

CHECK results for MAIT on merida1

To the developers/maintainers of the MAIT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAIT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1010/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAIT 1.27.0  (landing page)
Pol Sola-Santos
Snapshot Date: 2021-08-02 14:50:09 -0400 (Mon, 02 Aug 2021)
URL: https://git.bioconductor.org/packages/MAIT
Branch: master
Last Commit: a42ed1d
Last Changed Date: 2021-05-19 12:08:43 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  NO, package depends on 'CAMERA' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MAIT
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAIT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAIT_1.27.0.tar.gz
StartedAt: 2021-08-03 03:54:03 -0400 (Tue, 03 Aug 2021)
EndedAt: 2021-08-03 04:02:44 -0400 (Tue, 03 Aug 2021)
EllapsedTime: 521.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MAIT.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAIT.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAIT_1.27.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MAIT.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.27.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for ‘bin’
See ‘/Users/biocbuild/bbs-3.14-bioc/meat/MAIT.Rcheck/00install.out’ for details.
* 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 ‘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 ‘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 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", "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 (user + system) or elapsed time > 5s
                      user system elapsed
classifRatioClasses 22.207  0.217  22.682
ovClassifRatio      21.342  0.211  21.582
Validation          20.962  0.236  21.251
parameters          20.775  0.193  21.044
ovClassifRatioTable 20.060  0.195  20.315
* 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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MAIT.Rcheck/00check.log’
for details.



Installation output

MAIT.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAIT
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘MAIT’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
multiple methods tables found for ‘bin’ 
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: multiple methods tables found for ‘bin’
** testing if installed package can be loaded from final location
Warning: multiple methods tables found for ‘bin’
** testing if installed package keeps a record of temporary installation path
* DONE (MAIT)

Tests output


Example timings

MAIT.Rcheck/MAIT-Ex.timings

nameusersystemelapsed
Biotransformations1.5210.0891.612
LSDResults1.3100.0611.373
MAITbuilder0.0260.0060.031
Validation20.962 0.23621.251
classNum0.0050.0030.007
classes0.0060.0040.010
classifRatioClasses22.207 0.21722.682
featureID1.2950.0171.313
featureInfo1.1530.0061.160
featureSigID1.2570.0091.267
getScoresTable1.3160.0801.397
identifyMetabolites1.9780.0222.003
loadings3.4030.0303.440
metaboliteTable1.9790.0322.015
method0.0030.0020.005
model3.2280.0403.270
models1.1130.0071.121
ovClassifRatio21.342 0.21121.582
ovClassifRatioTable20.060 0.19520.315
parameters20.775 0.19321.044
pcaLoadings1.2500.0091.260
pcaModel1.2480.0101.301
pcaScores1.3150.0281.345
peakAggregation0.0120.0030.015
peakAnnotation000
plotBoxplot1.4140.0121.470
plotHeatmap3.5580.0353.598
plotPCA1.2360.0071.244
plotPLS3.0630.0193.086
plsLoadings3.1310.0233.157
plsModel3.1330.0193.157
plsScores3.1730.0273.204
pvalues1.2090.0081.220
pvaluesCorrection1.2160.0051.223
rawData0.0050.0030.008
resultsPath1.1090.0061.115
sampleProcessing0.0010.0010.001
scores3.2880.0833.374
sigPeaksTable1.3710.0181.391
spectralSigFeatures1.2110.0061.220