##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MOFA2_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.9.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MOFA2’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.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
.plot_factors_vs_cov_1d: no visible binding for global variable
  ‘value.factor’
.plot_factors_vs_cov_1d: no visible binding for global variable
  ‘value_scaled’
.plot_factors_vs_cov_1d: no visible binding for global variable
  ‘value.covariate’
.plot_factors_vs_cov_1d: no visible binding for global variable ‘value’
.plot_factors_vs_cov_2d: no visible binding for global variable
  ‘value.factor’
.set_xax: no visible binding for global variable ‘value’
add_mofa_factors_to_seurat: no visible global function definition for
  ‘CreateDimReducObject’
create_mofa_from_SingleCellExperiment: no visible global function
  definition for ‘colData’
get_interpolated_factors: no visible binding for global variable ‘L1’
get_interpolated_factors: no visible binding for global variable ‘L2’
get_interpolated_factors: no visible binding for global variable
  ‘value’
get_interpolated_factors: no visible binding for global variable
  ‘covariate’
get_interpolated_factors: no visible binding for global variable
  ‘covariate_value’
get_interpolated_factors: no visible binding for global variable
  ‘sample_id’
interpolate_factors: no visible binding for global variable ‘.’
plot_alignment: no visible binding for global variable ‘group’
plot_alignment: no visible binding for global variable ‘value.warped’
plot_alignment: no visible binding for global variable
  ‘value.unaligned’
plot_contribution_scores: no visible binding for global variable ‘view’
plot_data_overview: no visible binding for global variable ‘view’
plot_data_overview: no visible binding for global variable ‘ptotal’
plot_data_overview: no visible binding for global variable ‘ntotal’
plot_data_overview: no visible binding for global variable ‘group’
plot_dimred: no visible binding for global variable ‘.’
plot_enrichment_detailed: no visible binding for global variable
  ‘pathway’
plot_enrichment_detailed: no visible binding for global variable
  ‘feature.statistic’
plot_factors_vs_cov: no visible binding for global variable ‘E2’
plot_factors_vs_cov: no visible binding for global variable ‘value’
plot_interpolation_vs_covariate: no visible binding for global variable
  ‘variance’
plot_interpolation_vs_covariate: no visible binding for global variable
  ‘group’
plot_interpolation_vs_covariate: no visible binding for global variable
  ‘value.covariate’
plot_interpolation_vs_covariate: no visible binding for global variable
  ‘value.factor’
plot_interpolation_vs_covariate: no visible binding for global variable
  ‘ymin’
plot_interpolation_vs_covariate: no visible binding for global variable
  ‘ymax’
plot_sharedness: no visible binding for global variable ‘sharedness’
plot_sharedness: no visible binding for global variable ‘value’
plot_smoothness: no visible binding for global variable ‘value’
plot_smoothness: no visible binding for global variable ‘smoothness’
plot_top_weights: no visible binding for global variable ‘value’
plot_weights: no visible binding for global variable ‘value’
plot_weights: no visible binding for global variable ‘.’
summarise_factors: no visible binding for global variable ‘value’
summarise_factors: no visible binding for global variable ‘level’
summarise_factors: no visible binding for global variable ‘group’
Undefined global functions or variables:
  . CreateDimReducObject E2 L1 L2 colData covariate covariate_value
  feature.statistic group level ntotal pathway ptotal sample_id
  sharedness smoothness value value.covariate value.factor
  value.unaligned value.warped value_scaled variance view ymax ymin
* 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                |____________|
                 ____________ 
                |            |
  view_1  1000  |    100%    |
                |____________|
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plot.R:18'): plot data scatter ───────────────────────────────
  `p <- plot_data_scatter(test_mofa2, view = 1, factor = 1)` produced warnings.
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MEFISTO_temporal.Rmd’ using ‘UTF-8’... OK
  ‘downstream_analysis.Rmd’ using ‘UTF-8’... OK
  ‘getting_started_R.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘MEFISTO_temporal.Rmd’ using rmarkdown

        #########################################################
        ###           __  __  ____  ______                    ### 
        ###          |  \/  |/ __ \|  ____/\    _             ### 
        ###          | \  / | |  | | |__ /  \ _| |_           ### 
        ###          | |\/| | |  | |  __/ /\ \_   _|          ###
        ###          | |  | | |__| | | / ____ \|_|            ###
        ###          |_|  |_|\____/|_|/_/    \_\              ###
        ###                                                   ### 
        ######################################################### 
       
 
        
use_float32 set to True: replacing float64 arrays by float32 arrays to speed up computations...

Successfully loaded view='view_1' group='group1' with N=200 samples and D=200 features...
Successfully loaded view='view_2' group='group1' with N=200 samples and D=200 features...
Successfully loaded view='view_3' group='group1' with N=200 samples and D=200 features...
Successfully loaded view='view_4' group='group1' with N=200 samples and D=200 features...


Loaded 1 covariate(s) for each sample...


Model options:
- Automatic Relevance Determination prior on the factors: False
- Automatic Relevance Determination prior on the weights: True
- Spike-and-slab prior on the factors: False
- Spike-and-slab prior on the weights: False
Likelihoods:
- View 0 (view_1): gaussian
- View 1 (view_2): gaussian
- View 2 (view_3): gaussian
- View 3 (view_4): gaussian




######################################
## Training the model with seed 42 ##
######################################


ELBO before training: -668156.69 

Iteration 1: time=0.09, ELBO=-112628.56, deltaELBO=555528.126 (83.14339043%), Factors=4
Iteration 2: time=0.07, Factors=4
Iteration 3: time=0.07, Factors=4
Iteration 4: time=0.07, Factors=4
Iteration 5: time=0.07, Factors=4
Iteration 6: time=0.09, ELBO=-60038.12, deltaELBO=52590.443 (7.87097448%), Factors=4
Iteration 7: time=0.07, Factors=4
Iteration 8: time=0.07, Factors=4
Iteration 9: time=0.07, Factors=4
Iteration 10: time=0.07, Factors=4
Iteration 11: time=0.09, ELBO=-59874.45, deltaELBO=163.676 (0.02449672%), Factors=4
Iteration 12: time=0.07, Factors=4
Iteration 13: time=0.07, Factors=4
Iteration 14: time=0.07, Factors=4
Iteration 15: time=0.07, Factors=4
Iteration 16: time=0.09, ELBO=-59706.33, deltaELBO=168.117 (0.02516128%), Factors=4
Iteration 17: time=0.07, Factors=4
Iteration 18: time=0.07, Factors=4
Iteration 19: time=0.07, Factors=4
Optimising sigma node...
Iteration 20: time=8.40, Factors=4
Iteration 21: time=0.10, ELBO=-58693.09, deltaELBO=1013.241 (0.15164714%), Factors=4
Iteration 22: time=0.07, Factors=4
Iteration 23: time=0.07, Factors=4
Iteration 24: time=0.07, Factors=4
Iteration 25: time=0.07, Factors=4
Iteration 26: time=0.09, ELBO=-58472.74, deltaELBO=220.352 (0.03297904%), Factors=4
Iteration 27: time=0.07, Factors=4
Iteration 28: time=0.07, Factors=4
Iteration 29: time=0.07, Factors=4
Optimising sigma node...
Iteration 30: time=6.64, Factors=4
Iteration 31: time=0.09, ELBO=-58287.06, deltaELBO=185.678 (0.02778958%), Factors=4
Iteration 32: time=0.07, Factors=4
Iteration 33: time=0.07, Factors=4
Iteration 34: time=0.07, Factors=4
Iteration 35: time=0.07, Factors=4
Iteration 36: time=0.09, ELBO=-58181.29, deltaELBO=105.766 (0.01582952%), Factors=4
Iteration 37: time=0.07, Factors=4
Iteration 38: time=0.07, Factors=4
Iteration 39: time=0.07, Factors=4
Optimising sigma node...
Iteration 40: time=6.29, Factors=4
Iteration 41: time=0.10, ELBO=-58026.91, deltaELBO=154.380 (0.02310532%), Factors=4
Iteration 42: time=0.07, Factors=4
Iteration 43: time=0.07, Factors=4
Iteration 44: time=0.07, Factors=4
Iteration 45: time=0.07, Factors=4
Iteration 46: time=0.09, ELBO=-57938.97, deltaELBO=87.944 (0.01316221%), Factors=4
Iteration 47: time=0.07, Factors=4
Iteration 48: time=0.07, Factors=4
Iteration 49: time=0.07, Factors=4
Optimising sigma node...
Iteration 50: time=6.67, Factors=4
Iteration 51: time=0.09, ELBO=-57831.56, deltaELBO=107.406 (0.01607498%), Factors=4
Iteration 52: time=0.07, Factors=4
Iteration 53: time=0.07, Factors=4
Iteration 54: time=0.07, Factors=4
Iteration 55: time=0.07, Factors=4
Iteration 56: time=0.09, ELBO=-57760.44, deltaELBO=71.125 (0.01064494%), Factors=4
Iteration 57: time=0.07, Factors=4
Iteration 58: time=0.07, Factors=4
Iteration 59: time=0.07, Factors=4
Optimising sigma node...
Iteration 60: time=5.46, Factors=4
Iteration 61: time=0.09, ELBO=-57683.55, deltaELBO=76.889 (0.01150765%), Factors=4
Iteration 62: time=0.07, Factors=4
Iteration 63: time=0.07, Factors=4
Iteration 64: time=0.07, Factors=4
Iteration 65: time=0.07, Factors=4
Iteration 66: time=0.09, ELBO=-57646.15, deltaELBO=37.397 (0.00559706%), Factors=4
Iteration 67: time=0.07, Factors=4
Iteration 68: time=0.07, Factors=4
Iteration 69: time=0.07, Factors=4
Optimising sigma node...
Iteration 70: time=5.98, Factors=4
Iteration 71: time=0.09, ELBO=-57618.65, deltaELBO=27.504 (0.00411637%), Factors=4
Iteration 72: time=0.07, Factors=4
Iteration 73: time=0.08, Factors=4
Iteration 74: time=0.07, Factors=4
Iteration 75: time=0.07, Factors=4
Iteration 76: time=0.09, ELBO=-57601.36, deltaELBO=17.283 (0.00258664%), Factors=4
Iteration 77: time=0.07, Factors=4
Iteration 78: time=0.07, Factors=4
Iteration 79: time=0.07, Factors=4
Optimising sigma node...
Iteration 80: time=7.24, Factors=4
Iteration 81: time=0.09, ELBO=-57581.25, deltaELBO=20.115 (0.00301053%), Factors=4
Iteration 82: time=0.07, Factors=4
Iteration 83: time=0.07, Factors=4
Iteration 84: time=0.07, Factors=4
Iteration 85: time=0.07, Factors=4
Iteration 86: time=0.09, ELBO=-57565.76, deltaELBO=15.492 (0.00231869%), Factors=4
Iteration 87: time=0.07, Factors=4
Iteration 88: time=0.07, Factors=4
Iteration 89: time=0.07, Factors=4
Optimising sigma node...
Iteration 90: time=7.78, Factors=4
Iteration 91: time=0.09, ELBO=-57548.33, deltaELBO=17.423 (0.00260760%), Factors=4
Iteration 92: time=0.07, Factors=4
Iteration 93: time=0.07, Factors=4
Iteration 94: time=0.07, Factors=4
Iteration 95: time=0.07, Factors=4
Iteration 96: time=0.09, ELBO=-57534.18, deltaELBO=14.156 (0.00211860%), Factors=4
Iteration 97: time=0.07, Factors=4
Iteration 98: time=0.07, Factors=4
Iteration 99: time=0.07, Factors=4


#######################
## Training finished ##
#######################


Saving model in /tmp/RtmpsrJFvV/model.hdf5...
--- finished re-building ‘MEFISTO_temporal.Rmd’

--- re-building ‘downstream_analysis.Rmd’ using rmarkdown
--- finished re-building ‘downstream_analysis.Rmd’

--- re-building ‘getting_started_R.Rmd’ using rmarkdown
Quitting from lines 213-215 (getting_started_R.Rmd) 
Error: processing vignette 'getting_started_R.Rmd' failed with diagnostics:
mofapy2_0.7.0 is not detected in the specified python binary, see reticulate::py_config(). Consider setting use_basilisk = TRUE to create a python environment with basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html)
--- failed re-building ‘getting_started_R.Rmd’

SUMMARY: processing the following file failed:
  ‘getting_started_R.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MOFA2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘MOFA2’ ...
** using non-staged installation via StagedInstall field
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘MOFA2’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘MOFA2’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘MOFA2’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘MOFA2’
Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘MOFA2’
Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘MOFA2’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MOFA2)

R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MOFA2)

Attaching package: 'MOFA2'

The following object is masked from 'package:stats':

    predict

> 
> test_check("MOFA2")

               single_group 
                    100     
               ____________ 
              |            |
view_0  1000  |    100%    |
              |____________|
               ____________ 
              |            |
view_1  1000  |    100%    |
              |____________|

[ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:18'): plot data scatter ───────────────────────────────
`p <- plot_data_scatter(test_mofa2, view = 1, factor = 1)` produced warnings.

[ FAIL 1 | WARN 7 | SKIP 0 | PASS 25 ]
Error: Test failures
Execution halted