Build/check report for BioC 3.24 - CHECK results for MOFA2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4894
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for MOFA2 on nebbiolo2

To the developers/maintainers of the MOFA2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOFA2.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: MOFA2

Version: 1.23.0

Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings MOFA2_1.23.0.tar.gz

StartedAt: 2026-05-15 02:03:37 -0400 (Fri, 15 May 2026)

EndedAt: 2026-05-15 02:08:49 -0400 (Fri, 15 May 2026)

EllapsedTime: 312.3 seconds

RetCode: 0

Status: OK

CheckDir: MOFA2.Rcheck

Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings MOFA2_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/MOFA2.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-15 06:03:38 UTC
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.23.0’
* 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 ... 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-3.24-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 code 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 loading without being on the library search path ... 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_data_overview: no visible binding for global variable
  ‘group_label’
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 group_label 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
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare_elbo.Rd: ggplot
  load_model.Rd: HDF5Array, DelayedArray
  plot_data_overview.Rd: ggplot
  plot_data_scatter.Rd: ggplot
  plot_enrichment_heatmap.Rd: pheatmap
  plot_variance_explained.Rd: ggplot
  plot_variance_explained_by_covariates.Rd: ggplot
  plot_weights.Rd: ggplot
  plot_weights_heatmap.Rd: pheatmap
  run_mofa.Rd: reticulate
  run_tsne.Rd: Rtsne
  summarise_factors.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/MOFA2.Rcheck/00check.log’
for details.

Installation output

MOFA2.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘MOFA2’ ...
** this is package ‘MOFA2’ version ‘1.23.0’
** 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)

Tests output

MOFA2.Rcheck/tests/testthat.Rout


R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 0 | WARN 2 | SKIP 0 | PASS 25 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 25 ]
> 
> # setwd("/Users/rargelaguet/mofa/MOFA2/tests/testthat")
> 
> proc.time()
   user  system elapsed 
 12.215   0.739  12.945

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

name	user	system	elapsed
add_mofa_factors_to_seurat	0.004	0.002	0.006
calculate_contribution_scores	0.243	0.012	0.260
calculate_variance_explained	2.389	0.173	2.563
calculate_variance_explained_per_sample	0.140	0.009	0.150
cluster_samples	0.141	0.015	0.156
compare_elbo	0.280	0.015	0.295
compare_factors	0.323	0.009	0.332
covariates_names	0.168	0.003	0.173
create_mofa	1.062	0.061	1.124
create_mofa_from_df	1.038	0.055	1.094
create_mofa_from_matrix	0.009	0.000	0.010
factors_names	0.124	0.003	0.128
features_metadata	0.140	0.008	0.148
features_names	0.126	0.010	0.137
get_covariates	0.154	0.004	0.159
get_data	0.364	0.016	0.380
get_default_data_options	1.075	0.004	1.079
get_default_mefisto_options	0.131	0.004	0.135
get_default_model_options	0.519	0.001	0.520
get_default_stochastic_options	0.51	0.00	0.51
get_default_training_options	0.997	0.002	1.000
get_dimensions	0.132	0.004	0.137
get_elbo	0.124	0.003	0.128
get_expectations	0.124	0.003	0.127
get_factors	0.133	0.000	0.133
get_imputed_data	0.151	0.002	0.152
get_lengthscales	0.155	0.006	0.161
get_scales	0.157	0.002	0.159
get_variance_explained	0.130	0.003	0.133
get_weights	0.153	0.000	0.153
groups_names	0.140	0.001	0.141
impute	0.140	0.002	0.142
interpolate_factors	0.178	0.003	0.181
load_model	0.136	0.004	0.141
make_example_data	0.003	0.000	0.003
plot_ascii_data	0.134	0.001	0.135
plot_data_heatmap	0.169	0.011	0.180
plot_data_overview	0.341	0.020	0.361
plot_data_scatter	1.608	0.006	1.614
plot_data_vs_cov	0.596	0.018	0.614
plot_dimred	4.038	0.143	4.149
plot_factor	1.566	0.008	1.574
plot_factor_cor	0.147	0.004	0.151
plot_factors	0.775	0.002	0.777
plot_factors_vs_cov	0.533	0.005	0.539
plot_group_kernel	0.346	0.004	0.350
plot_interpolation_vs_covariate	0.591	0.002	0.592
plot_smoothness	0.188	0.003	0.191
plot_top_weights	1.026	0.019	1.045
plot_variance_explained	1.649	0.019	1.668
plot_variance_explained_by_covariates	1.162	0.010	1.173
plot_variance_explained_per_feature	0.395	0.032	0.428
plot_weights	2.528	0.004	2.533
plot_weights_heatmap	0.301	0.036	0.338
plot_weights_scatter	0.419	0.034	0.454
predict	0.134	0.005	0.140
prepare_mofa	0.513	0.022	0.534
run_mofa	0.559	0.008	0.567
run_tsne	0.130	0.002	0.132
run_umap	0.145	0.000	0.144
samples_metadata	0.135	0.001	0.135
samples_names	0.128	0.001	0.129
set_covariates	0.027	0.002	0.029
subset_factors	0.711	0.066	0.777
subset_groups	0.127	0.001	0.129
subset_samples	0.126	0.000	0.126
subset_views	0.123	0.005	0.128
views_names	0.127	0.002	0.129