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This page was generated on 2021-07-30 12:05:04 -0400 (Fri, 30 Jul 2021).

CHECK results for MAIT on riesling1

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: 2021-07-29 14:50:07 -0400 (Thu, 29 Jul 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: D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAIT.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MAIT_1.27.0.tar.gz
StartedAt: 2021-07-30 01:07:59 -0400 (Fri, 30 Jul 2021)
EndedAt: 2021-07-30 01:15:53 -0400 (Fri, 30 Jul 2021)
EllapsedTime: 474.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MAIT.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MAIT.install-out.txt --library=D:\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MAIT_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.14-bioc/meat/MAIT.Rcheck'
* using R version 4.1.0 (2021-05-18)
* 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 '1.27.0'
* 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 whether package 'MAIT' can be installed ... WARNING
Found the following significant warnings:
  Warning: multiple methods tables found for 'bin'
See 'D:/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
* 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
* 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
parameters          7.53   0.06    7.59
Validation          7.33   0.03    7.36
classifRatioClasses 7.30   0.03    7.33
ovClassifRatioTable 6.97   0.06    7.03
ovClassifRatio      6.96   0.06    7.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Validation          7.83   0.07    7.89
classifRatioClasses 7.73   0.04    7.78
ovClassifRatio      7.53   0.00    7.53
parameters          7.52   0.00    7.52
ovClassifRatioTable 7.51   0.00    7.53
* 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
  'D:/biocbuild/bbs-3.14-bioc/meat/MAIT.Rcheck/00check.log'
for details.



Installation output

MAIT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MAIT_1.27.0.tar.gz && rm -rf MAIT.buildbin-libdir && mkdir MAIT.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MAIT.buildbin-libdir MAIT_1.27.0.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MAIT_1.27.0.zip && rm MAIT_1.27.0.tar.gz MAIT_1.27.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2186k  100 2186k    0     0  6006k      0 --:--:-- --:--:-- --:--:-- 5990k

install for i386

* 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
  converting help for package 'MAIT'
    finding HTML links ... done
    Biotransformations                      html  
    Database                                html  
    FisherLSD                               html  
    LSDResults                              html  
    MAIT-class                              html  
    finding level-2 HTML links ... done

    MAIT.FeatureData-class                  html  
    MAIT.FeatureInfo-class                  html  
    MAIT.Parameters-class                   html  
    MAIT.PhenoData-class                    html  
    MAIT.RawData-class                      html  
    MAIT.Validation-class                   html  
    MAIT_dataSet                            html  
    MAITbuilder                             html  
    PCAplot3d                               html  
    PLSDA                                   html  
    SearchCand                              html  
    Validation                              html  
    annotateBiotransf                       html  
    biotransformationsTable                 html  
    classNum                                html  
    classes                                 html  
    classifRatioClasses                     html  
    featureID                               html  
    featureInfo                             html  
    featureSigID                            html  
    getScoresTable                          html  
    identifyMetabolites                     html  
    inBetween                               html  
    loadings                                html  
    metaboliteTable                         html  
    method                                  html  
    model                                   html  
    models                                  html  
    negAdducts                              html  
    ovClassifRatio                          html  
    ovClassifRatioTable                     html  
    parameters                              html  
    pcaLoadings                             html  
    pcaModel                                html  
    pcaScores                               html  
    peakAggregation                         html  
    peakAnnotation                          html  
    plotBoxplot                             html  
    plotHeatmap                             html  
    plotPCA                                 html  
    plotPLS                                 html  
    plsLoadings                             html  
    plsModel                                html  
    plsScores                               html  
    posAdducts                              html  
    project                                 html  
    pvalues                                 html  
    pvaluesCorrection                       html  
    rawData                                 html  
    removeOnePeakSpectra                    html  
    resultsPath                             html  
    retrieveSpectrum                        html  
    sampleProcessing                        html  
    scores                                  html  
    selectK                                 html  
    selectPLScomp                           html  
    sigPeaksTable                           html  
    spectralAnova                           html  
    spectralFUN                             html  
    spectralKruskal                         html  
    spectralSigFeatures                     html  
    spectralTStudent                        html  
    spectralWelch                           html  
    spectralWilcox                          html  
    successRatio                            html  
    writeExcelTable                         html  
    writeParameterTable                     html  
** 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

install for x64

* installing *source* package 'MAIT' ...
** testing if installed package can be loaded
Warning: multiple methods tables found for 'bin'
* MD5 sums
packaged installation of 'MAIT' as MAIT_1.27.0.zip
* DONE (MAIT)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'MAIT' successfully unpacked and MD5 sums checked

Tests output


Example timings

MAIT.Rcheck/examples_i386/MAIT-Ex.timings

nameusersystemelapsed
Biotransformations0.510.020.53
LSDResults0.420.030.45
MAITbuilder0.010.000.01
Validation7.330.037.36
classNum000
classes0.000.020.02
classifRatioClasses7.300.037.33
featureID0.440.000.43
featureInfo0.430.010.46
featureSigID0.440.000.44
getScoresTable0.470.020.48
identifyMetabolites0.740.050.78
loadings1.480.031.52
metaboliteTable0.750.010.77
method000
model1.400.071.47
models0.420.000.42
ovClassifRatio6.960.067.03
ovClassifRatioTable6.970.067.03
parameters7.530.067.59
pcaLoadings0.420.020.46
pcaModel0.450.010.47
pcaScores0.420.050.47
peakAggregation0.000.020.01
peakAnnotation000
plotBoxplot0.500.040.55
plotHeatmap1.550.031.59
plotPCA0.440.020.45
plotPLS1.420.061.49
plsLoadings1.420.021.44
plsModel1.420.001.43
plsScores1.430.011.44
pvalues0.450.020.47
pvaluesCorrection0.480.000.48
rawData000
resultsPath0.440.000.44
sampleProcessing000
scores1.440.031.49
sigPeaksTable0.500.020.51
spectralSigFeatures0.440.000.44

MAIT.Rcheck/examples_x64/MAIT-Ex.timings

nameusersystemelapsed
Biotransformations0.600.040.65
LSDResults0.50.00.5
MAITbuilder0.010.000.01
Validation7.830.077.89
classNum000
classes0.020.000.02
classifRatioClasses7.730.047.78
featureID0.470.000.47
featureInfo0.480.000.48
featureSigID0.470.000.47
getScoresTable0.490.020.50
identifyMetabolites0.810.000.81
loadings1.660.051.71
metaboliteTable0.760.010.78
method0.020.000.01
model1.570.031.61
models0.440.020.46
ovClassifRatio7.530.007.53
ovClassifRatioTable7.510.007.53
parameters7.520.007.52
pcaLoadings0.470.010.48
pcaModel0.470.020.50
pcaScores0.470.020.50
peakAggregation0.000.010.02
peakAnnotation000
plotBoxplot0.500.060.56
plotHeatmap1.420.051.50
plotPCA0.500.020.52
plotPLS1.560.041.61
plsLoadings1.560.031.59
plsModel1.530.021.55
plsScores1.520.031.54
pvalues0.450.000.46
pvaluesCorrection0.460.000.45
rawData000
resultsPath0.430.000.44
sampleProcessing000
scores1.580.061.64
sigPeaksTable0.50.00.5
spectralSigFeatures1.030.001.03