##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MOFA.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MOFA_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/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
regressCovariates      24.464  0.004  24.498
compareModels          20.528  0.056  23.628
compareFactors         19.052  0.752  26.182
selectModel            18.876  0.056  21.995
predict                18.764  0.140  18.927
runEnrichmentAnalysis  15.708  0.440  16.191
plotEnrichmentDetailed  7.392  0.652   8.068
plotWeightsHeatmap      6.568  0.132   6.715
plotEnrichmentHeatmap   6.208  0.324   6.540
plotFactorScatters      6.480  0.044   6.535
plotEnrichment          5.844  0.296   6.155
plotEnrichmentBars      5.556  0.412   5.976
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MOFA
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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)