Multiple platform build/check report for BioC 3.20 - CHECK results for MOFA2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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: 1.16.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MOFA2_1.16.0.tar.gz

StartedAt: 2024-12-20 02:54:21 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 03:06:18 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 717.5 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MOFA2.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings MOFA2_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/MOFA2.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.20-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 ... NOTE
checkRd: (-1) calculate_contribution_scores.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_contribution_scores.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_contribution_scores.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correlate_factors_with_covariates.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correlate_factors_with_covariates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_mofa.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_data_options.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_data_options.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_data_options.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_model_options.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_stochastic_options.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_default_training_options.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_expectations.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_expectations.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) impute.Rd:24: Lost braces; missing escapes or markup?
    24 | \item \strong{response}:{gives mean for gaussian and poisson and probabilities for bernoulli.}
       |                         ^
checkRd: (-1) impute.Rd:25: Lost braces; missing escapes or markup?
    25 | \item \strong{link}: {gives the linear predictions.}
       |                      ^
checkRd: (-1) impute.Rd:26: Lost braces; missing escapes or markup?
    26 | \item \strong{inRange}: {rounds the fitted values from "terms" for integer-valued distributions to the next integer (default).}
       |                         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Unknown package ‘PCGSE’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'create_mofa_from_Seurat.Rd':
create_mofa_from_Seurat
  Code: function(seurat, groups = NULL, assays = NULL, layer = "data",
                 features = NULL, extract_metadata = FALSE)
  Docs: function(seurat, groups = NULL, assays = NULL, slot =
                 "scale.data", features = NULL, extract_metadata =
                 FALSE)
  Argument names in code not in docs:
    layer
  Argument names in docs not in code:
    slot
  Mismatches in argument names:
    Position: 4 Code: layer Docs: slot

* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/MOFA2.Rcheck/00check.log’
for details.

Installation output

MOFA2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)

Tests output

MOFA2.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 
 10.224   0.716  10.928

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

name	user	system	elapsed
add_mofa_factors_to_seurat	0.003	0.002	0.005
calculate_contribution_scores	0.181	0.012	0.197
calculate_variance_explained	1.784	0.118	1.901
calculate_variance_explained_per_sample	0.129	0.013	0.141
cluster_samples	0.123	0.011	0.134
compare_elbo	0.255	0.006	0.261
compare_factors	0.288	0.006	0.294
covariates_names	0.188	0.006	0.230
create_mofa	0.563	0.015	0.578
create_mofa_from_df	0.930	0.015	0.945
create_mofa_from_matrix	0.01	0.00	0.01
factors_names	0.124	0.002	0.126
features_metadata	0.144	0.002	0.146
features_names	0.130	0.002	0.132
get_covariates	0.151	0.003	0.154
get_data	0.387	0.002	0.389
get_default_data_options	0.962	0.066	1.028
get_default_mefisto_options	0.133	0.001	0.134
get_default_model_options	0.485	0.000	0.485
get_default_stochastic_options	0.491	0.003	0.494
get_default_training_options	0.487	0.002	0.489
get_dimensions	0.120	0.003	0.123
get_elbo	0.123	0.022	0.145
get_expectations	0.554	0.048	0.601
get_factors	0.124	0.001	0.125
get_imputed_data	0.129	0.002	0.131
get_lengthscales	0.153	0.004	0.157
get_scales	0.161	0.001	0.162
get_variance_explained	0.127	0.006	0.133
get_weights	0.154	0.001	0.155
groups_names	0.123	0.000	0.123
impute	0.133	0.002	0.135
interpolate_factors	0.176	0.004	0.180
load_model	0.134	0.001	0.135
make_example_data	0.003	0.000	0.003
plot_ascii_data	0.126	0.002	0.128
plot_data_heatmap	0.166	0.001	0.167
plot_data_overview	0.267	0.001	0.268
plot_data_scatter	1.154	0.007	1.161
plot_data_vs_cov	0.394	0.004	0.398
plot_dimred	3.292	0.016	3.285
plot_factor	0.972	0.001	0.974
plot_factor_cor	0.133	0.002	0.135
plot_factors	0.461	0.011	0.474
plot_factors_vs_cov	0.376	0.022	0.399
plot_group_kernel	0.282	0.001	0.284
plot_interpolation_vs_covariate	0.420	0.006	0.426
plot_smoothness	0.169	0.001	0.170
plot_top_weights	0.762	0.002	0.764
plot_variance_explained	1.221	0.009	1.230
plot_variance_explained_by_covariates	0.847	0.004	0.850
plot_variance_explained_per_feature	0.277	0.002	0.278
plot_weights	1.965	0.006	1.971
plot_weights_heatmap	0.293	0.006	0.300
plot_weights_scatter	0.347	0.004	0.351
predict	0.132	0.000	0.132
prepare_mofa	0.496	0.021	0.517
run_mofa	0.505	0.003	0.508
run_tsne	0.135	0.002	0.137
run_umap	0.123	0.003	0.127
samples_metadata	0.138	0.002	0.140
samples_names	0.136	0.001	0.136
set_covariates	0.028	0.000	0.027
subset_factors	0.134	0.002	0.136
subset_groups	0.123	0.003	0.126
subset_samples	0.124	0.003	0.128
subset_views	0.137	0.003	0.139
views_names	0.122	0.002	0.124