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CHECK report for MOFA on machv2

This page was generated on 2020-10-17 11:58:59 -0400 (Sat, 17 Oct 2020).

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 1116/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA 1.4.0
Britta Velten
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MOFA
Branch: RELEASE_3_11
Last Commit: baf2eef
Last Changed Date: 2020-04-27 15:25:02 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MOFA
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MOFA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MOFA_1.4.0.tar.gz
StartedAt: 2020-10-17 03:12:05 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:23:37 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 691.4 seconds
RetCode: 0
Status:  OK 
CheckDir: MOFA.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MOFA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MOFA_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MOFA.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOFA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA’ version ‘1.4.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MOFA’ 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 ... 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              52.355  0.187  55.808
compareFactors             49.468  1.604  53.953
selectModel                46.952  0.215  50.484
regressCovariates          27.055  0.245  27.326
runEnrichmentAnalysis      18.423  1.101  19.577
predict                    17.124  0.992  18.274
plotEnrichmentDetailed     10.083  1.126  11.212
plotEnrichment              8.015  1.107   9.127
plotFactorScatters          8.535  0.425   8.965
plotEnrichmentBars          7.726  0.813   8.543
plotEnrichmentHeatmap       7.412  0.727   8.145
plotWeightsHeatmap          6.363  0.463   6.831
clusterSamples              6.193  0.599   6.797
plotTopWeights              5.709  0.700   6.417
calculateVarianceExplained  5.681  0.604   6.301
getTrainData                5.742  0.335   6.081
plotFactorBeeswarm          5.365  0.670   6.042
plotVarianceExplained       5.605  0.402   6.011
plotWeights                 5.318  0.359   5.680
trainCurveFactors           4.916  0.514   5.445
plotDataOverview            4.756  0.566   5.327
plotFactorScatter           4.832  0.431   5.267
plotFactorHist              4.830  0.422   5.255
trainCurveELBO              4.596  0.527   5.191
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/MOFA.Rcheck/00check.log’
for details.



Installation output

MOFA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MOFA
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MOFA’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** 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 (MOFA)

Tests output


Example timings

MOFA.Rcheck/MOFA-Ex.timings

nameusersystemelapsed
DataOptions4.3070.3684.687
Dimensions2.7250.2853.012
Expectations2.6740.2722.948
FeatureIntercepts2.7530.3343.114
ImputedData3.0350.3563.393
InputData2.9260.2173.145
ModelOptions2.5190.2122.732
Status2.5150.2152.734
TrainData2.8180.2603.083
TrainOptions2.5610.2322.797
TrainStats2.5230.2702.796
calculateVarianceExplained5.6810.6046.301
clusterSamples6.1930.5996.797
compareFactors49.468 1.60453.953
compareModels52.355 0.18755.808
createMOFAobject2.6070.2422.853
factorNames2.8210.2973.118
featureNames0.7990.0410.840
getCovariates4.1110.1904.306
getDefaultDataOptions0.0210.0000.021
getDefaultModelOptions1.9270.1822.110
getDefaultTrainOptions0.0200.0010.021
getDimensions2.7050.3043.012
getELBO2.5600.2132.773
getExpectations2.7470.3393.088
getFactors2.5800.2602.841
getImputedData3.6690.8134.484
getTrainData5.7420.3356.081
getWeights2.6070.2852.893
impute4.2940.4904.786
loadModel2.6460.3723.019
makeExampleData0.0470.0020.048
plotDataHeatmap2.6700.3593.034
plotDataOverview4.7560.5665.327
plotDataScatter3.9610.1564.119
plotEnrichment8.0151.1079.127
plotEnrichmentBars7.7260.8138.543
plotEnrichmentDetailed10.083 1.12611.212
plotEnrichmentHeatmap7.4120.7278.145
plotFactorBeeswarm5.3650.6706.042
plotFactorCor4.1010.5644.669
plotFactorHist4.8300.4225.255
plotFactorScatter4.8320.4315.267
plotFactorScatters8.5350.4258.965
plotTopWeights5.7090.7006.417
plotVarianceExplained5.6050.4026.011
plotWeights5.3180.3595.680
plotWeightsHeatmap6.3630.4636.831
predict17.124 0.99218.274
prepareMOFA2.0240.0842.110
qualityControl3.2340.3223.557
regressCovariates27.055 0.24527.326
runEnrichmentAnalysis18.423 1.10119.577
runMOFA0.5980.0010.601
sampleNames0.9500.0861.037
selectModel46.952 0.21550.484
subsetFactors2.0640.2112.279
subsetSamples2.0650.1712.237
subsetViews2.6630.3943.063
trainCurveELBO4.5960.5275.191
trainCurveFactors4.9160.5145.445
viewNames1.1170.0271.147