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### Running command:
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###   /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.

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###
### Running command:
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###   /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)