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CHECK report for MOFA on tokay1

This page was generated on 2021-05-06 12:32:19 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MOFA package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1133/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA 1.6.2  (landing page)
Britta Velten
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MOFA
Branch: RELEASE_3_12
Last Commit: 0ae14cf
Last Changed Date: 2021-02-08 07:46:11 -0400 (Mon, 08 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: MOFA
Version: 1.6.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MOFA_1.6.2.tar.gz
StartedAt: 2021-05-06 04:46:15 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:55:01 -0400 (Thu, 06 May 2021)
EllapsedTime: 525.5 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: MOFA.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MOFA_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MOFA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MOFA' version '1.6.2'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MOFA' can be installed ... WARNING
Found the following significant warnings:
  Warning: Please use MOFA2 instead of MOFA.  Package 'MOFA' is deprecated and
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotEnrichmentDetailed: no visible binding for global variable
  'pathway'
plotEnrichmentDetailed: no visible binding for global variable
  'feature.statistic'
Undefined global functions or variables:
  feature.statistic pathway
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'PCGSE'
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
compareModels              22.36   0.05   25.40
selectModel                20.25   0.11   23.38
compareFactors             18.43   0.48   51.94
predict                    16.98   0.91   17.89
runEnrichmentAnalysis      16.22   0.79   17.04
regressCovariates          15.89   0.13   16.01
plotFactorScatters          9.25   0.47    9.72
plotEnrichmentDetailed      7.81   0.88    8.70
plotEnrichment              6.42   0.87    7.55
calculateVarianceExplained  6.22   0.77    8.98
plotEnrichmentHeatmap       5.92   0.62    6.55
plotWeightsHeatmap          6.01   0.48    6.50
plotEnrichmentBars          5.39   0.47    5.86
getTrainData                4.92   0.42    5.35
DataOptions                 4.00   0.28    8.99
* 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, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck/00check.log'
for details.



Installation output

MOFA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MOFA
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
* installing *source* package 'MOFA' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MOFA'
    finding HTML links ... done
    DataOptions                             html  
    Dimensions                              html  
    Expectations                            html  
    FeatureIntercepts                       html  
    ImputedData                             html  
    InputData                               html  
    MOFA                                    html  
    MOFAmodel                               html  
    ModelOptions                            html  
    Status                                  html  
    TrainData                               html  
    TrainOptions                            html  
    TrainStats                              html  
    calculateVarianceExplained              html  
    clusterSamples                          html  
    compareFactors                          html  
    compareModels                           html  
    createMOFAobject                        html  
    finding level-2 HTML links ... done

    factorNames                             html  
    featureNames                            html  
    getCovariates                           html  
    getDefaultDataOptions                   html  
    getDefaultModelOptions                  html  
    getDefaultTrainOptions                  html  
    getDimensions                           html  
    getELBO                                 html  
    getExpectations                         html  
    getFactors                              html  
    getImputedData                          html  
    getTrainData                            html  
    getWeights                              html  
    impute                                  html  
    loadModel                               html  
    makeExampleData                         html  
    plotDataHeatmap                         html  
    plotDataOverview                        html  
    plotDataScatter                         html  
    plotEnrichment                          html  
    plotEnrichmentBars                      html  
    plotEnrichmentDetailed                  html  
    plotEnrichmentHeatmap                   html  
    plotFactorBeeswarm                      html  
    plotFactorCor                           html  
    plotFactorHist                          html  
    plotFactorScatter                       html  
    plotFactorScatters                      html  
    plotTopWeights                          html  
    plotVarianceExplained                   html  
    plotWeights                             html  
    plotWeightsHeatmap                      html  
    predict                                 html  
    prepareMOFA                             html  
    qualityControl                          html  
    regressCovariates                       html  
    runEnrichmentAnalysis                   html  
    runMOFA                                 html  
    sampleNames                             html  
    selectModel                             html  
    subsetFactors                           html  
    subsetSamples                           html  
    subsetViews                             html  
    trainCurveELBO                          html  
    trainCurveFactors                       html  
    viewNames                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Please use MOFA2 instead of MOFA.  Package 'MOFA' is deprecated and
  will be removed from Bioconductor version 3.13. Please see
  replacement package MOFA2.
** testing if installed package can be loaded from final location
Warning: Please use MOFA2 instead of MOFA.  Package 'MOFA' is deprecated and
  will be removed from Bioconductor version 3.13. Please see
  replacement package MOFA2.
** testing if installed package keeps a record of temporary installation path
* DONE (MOFA)
Making 'packages.html' ... done

Tests output


Example timings

MOFA.Rcheck/MOFA-Ex.timings

nameusersystemelapsed
DataOptions4.000.288.99
Dimensions2.250.322.56
Expectations1.920.172.09
FeatureIntercepts1.970.192.16
ImputedData2.570.232.80
InputData2.140.202.34
ModelOptions2.040.242.28
Status2.750.222.97
TrainData1.850.202.05
TrainOptions2.150.232.39
TrainStats2.000.222.22
calculateVarianceExplained6.220.778.98
clusterSamples3.850.564.41
compareFactors18.43 0.4851.94
compareModels22.36 0.0525.40
createMOFAobject1.780.113.40
factorNames1.270.241.50
featureNames0.570.120.70
getCovariates3.160.173.39
getDefaultDataOptions0.010.000.01
getDefaultModelOptions1.480.141.62
getDefaultTrainOptions000
getDimensions1.650.281.93
getELBO2.170.182.34
getExpectations2.130.252.38
getFactors2.240.452.69
getImputedData2.440.422.86
getTrainData4.920.425.35
getWeights2.720.503.22
impute3.190.693.88
loadModel1.980.312.30
makeExampleData0.050.000.04
plotDataHeatmap2.670.503.17
plotDataOverview3.550.754.30
plotDataScatter3.610.494.09
plotEnrichment6.420.877.55
plotEnrichmentBars5.390.475.86
plotEnrichmentDetailed7.810.888.70
plotEnrichmentHeatmap5.920.626.55
plotFactorBeeswarm4.430.344.78
plotFactorCor2.950.133.08
plotFactorHist3.350.393.74
plotFactorScatter3.640.504.14
plotFactorScatters9.250.479.72
plotTopWeights4.090.484.57
plotVarianceExplained4.410.364.77
plotWeights4.470.354.81
plotWeightsHeatmap6.010.486.50
predict16.98 0.9117.89
prepareMOFA1.280.171.46
qualityControl2.120.422.54
regressCovariates15.89 0.1316.01
runEnrichmentAnalysis16.22 0.7917.04
runMOFA0.390.000.39
sampleNames0.660.000.66
selectModel20.25 0.1123.38
subsetFactors1.560.111.67
subsetSamples2.390.222.61
subsetViews1.520.271.78
trainCurveELBO3.160.483.64
trainCurveFactors2.880.413.28
viewNames0.680.000.69