Multiple platform build/check report for BioC 3.19 - CHECK results for MOFA2 on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4709
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4483
merida1	macOS 12.7.4 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4512
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4461
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 nebbiolo1

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: 1.14.0

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MOFA2_1.14.0.tar.gz

StartedAt: 2024-07-08 01:19:05 -0400 (Mon, 08 Jul 2024)

EndedAt: 2024-07-08 01:24:03 -0400 (Mon, 08 Jul 2024)

EllapsedTime: 298.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: MOFA2.Rcheck

Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MOFA2_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MOFA2.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.14.0’
* 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-3.19-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
Package unavailable to check Rd xrefs: ‘PCGSE’
* 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-3.19-bioc/meat/MOFA2.Rcheck/00check.log’
for details.

Installation output

MOFA2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 15.196   0.875  16.427

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

name	user	system	elapsed
add_mofa_factors_to_seurat	0.002	0.003	0.005
calculate_contribution_scores	0.178	0.019	0.200
calculate_variance_explained	1.427	0.108	1.534
calculate_variance_explained_per_sample	0.570	0.056	0.626
cluster_samples	0.129	0.004	0.133
compare_elbo	0.262	0.008	0.270
compare_factors	0.292	0.012	0.304
covariates_names	0.170	0.020	0.191
create_mofa	0.980	0.052	1.033
create_mofa_from_df	0.500	0.000	0.499
create_mofa_from_matrix	0.01	0.00	0.01
factors_names	0.122	0.004	0.126
features_metadata	0.145	0.028	0.172
features_names	0.13	0.02	0.15
get_covariates	0.150	0.016	0.166
get_data	0.917	0.015	0.932
get_default_data_options	0.501	0.012	0.513
get_default_mefisto_options	0.130	0.000	0.131
get_default_model_options	0.491	0.008	0.500
get_default_stochastic_options	0.490	0.012	0.503
get_default_training_options	0.494	0.005	0.500
get_dimensions	0.124	0.006	0.130
get_elbo	0.123	0.008	0.130
get_expectations	0.132	0.008	0.141
get_factors	0.131	0.000	0.130
get_imputed_data	0.144	0.000	0.144
get_lengthscales	0.160	0.000	0.161
get_scales	0.163	0.000	0.163
get_variance_explained	0.138	0.008	0.146
get_weights	0.644	0.032	0.675
groups_names	0.127	0.004	0.131
impute	0.144	0.020	0.165
interpolate_factors	0.185	0.015	0.200
load_model	0.150	0.004	0.153
make_example_data	0.003	0.000	0.003
plot_ascii_data	0.118	0.024	0.143
plot_data_heatmap	0.172	0.008	0.181
plot_data_overview	0.266	0.008	0.274
plot_data_scatter	1.179	0.016	1.194
plot_data_vs_cov	0.399	0.004	0.402
plot_dimred	3.248	0.082	3.295
plot_factor	1.031	0.028	1.059
plot_factor_cor	0.134	0.015	0.149
plot_factors	0.480	0.020	0.501
plot_factors_vs_cov	0.389	0.008	0.397
plot_group_kernel	0.296	0.008	0.304
plot_interpolation_vs_covariate	0.467	0.008	0.475
plot_smoothness	0.208	0.000	0.208
plot_top_weights	0.77	0.02	0.79
plot_variance_explained	1.272	0.028	1.300
plot_variance_explained_by_covariates	0.883	0.008	0.891
plot_variance_explained_per_feature	0.293	0.004	0.297
plot_weights	2.112	0.052	2.165
plot_weights_heatmap	0.310	0.012	0.322
plot_weights_scatter	0.292	0.012	0.303
predict	0.142	0.004	0.145
prepare_mofa	0.512	0.018	0.531
run_mofa	0.512	0.001	0.513
run_tsne	0.133	0.004	0.137
run_umap	0.162	0.004	0.166
samples_metadata	0.156	0.003	0.159
samples_names	0.130	0.005	0.136
set_covariates	0.790	0.054	0.851
subset_factors	0.136	0.008	0.144
subset_groups	0.131	0.004	0.135
subset_samples	0.182	0.008	0.190
subset_views	0.253	0.016	0.269
views_names	0.225	0.008	0.233