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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_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.6.2’
* 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 for sufficient/correct file permissions ... 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 ‘/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
compareFactors             47.121  1.050  51.940
selectModel                36.293  0.194  39.932
compareModels              34.668  0.168  38.049
regressCovariates          22.294  0.211  22.530
predict                    17.596  0.915  18.560
runEnrichmentAnalysis      17.285  0.555  17.860
plotFactorScatters         11.036  0.413  11.465
plotEnrichmentDetailed     10.593  0.836  11.560
plotVarianceExplained      10.151  0.386  10.588
plotWeightsHeatmap          9.727  0.400  10.143
calculateVarianceExplained  9.641  0.455  10.119
plotEnrichment              8.822  0.783   9.627
plotFactorBeeswarm          8.803  0.442   9.257
clusterSamples              8.485  0.421   8.917
plotWeights                 8.408  0.294   8.719
plotEnrichmentHeatmap       7.861  0.677   8.551
plotTopWeights              8.234  0.252   8.497
plotEnrichmentBars          7.885  0.563  11.834
trainCurveFactors           7.886  0.436   8.334
plotDataOverview            7.752  0.359  12.617
plotFactorHist              7.458  0.287   7.795
plotFactorScatter           7.450  0.266   7.728
impute                      7.117  0.550   7.684
trainCurveELBO              7.233  0.274   7.518
plotFactorCor               7.087  0.408   7.504
DataOptions                 6.079  0.273   6.373
plotDataScatter             5.363  0.302   5.701
ImputedData                 5.071  0.218   5.296
factorNames                 4.917  0.300   5.220
* 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
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck/00check.log’
for details.

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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
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)