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This page was generated on 2024-02-21 11:36:12 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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

Package 1297/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.12.1  (landing page)
Ricard Argelaguet
Snapshot Date: 2024-02-20 14:05:06 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/MOFA2
git_branch: RELEASE_3_18
git_last_commit: 6fdef2f
git_last_commit_date: 2024-01-04 04:51:03 -0500 (Thu, 04 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.12.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MOFA2_1.12.1.tar.gz
StartedAt: 2024-02-21 00:16:45 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 00:21:45 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 299.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MOFA2.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings MOFA2_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/MOFA2.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.12.1’
* 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-3.18-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 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
Package unavailable to check Rd xrefs: ‘PCGSE’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'create_mofa_from_Seurat':
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 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/MOFA2.Rcheck/00check.log’
for details.



Installation output

MOFA2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 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 
 13.776   0.728  14.586 

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

nameusersystemelapsed
add_mofa_factors_to_seurat0.0060.0000.005
calculate_contribution_scores0.1770.0120.192
calculate_variance_explained1.4160.1281.544
calculate_variance_explained_per_sample0.1570.0040.161
cluster_samples0.6600.0840.744
compare_elbo0.2680.0040.273
compare_factors0.3070.0080.315
covariates_names0.1680.0090.179
create_mofa1.0360.0241.061
create_mofa_from_df0.5180.0070.527
create_mofa_from_matrix0.010.000.01
factors_names0.1310.0040.135
features_metadata0.1520.0110.164
features_names0.1440.0200.165
get_covariates0.1680.0000.168
get_data0.9570.0521.010
get_default_data_options0.5140.0080.523
get_default_mefisto_options0.1360.0050.141
get_default_model_options0.9880.0551.043
get_default_stochastic_options0.5570.0320.589
get_default_training_options0.6210.0200.641
get_dimensions0.6690.0120.681
get_elbo0.1350.0000.136
get_expectations0.1380.0000.138
get_factors0.1390.0040.143
get_imputed_data0.1630.0000.163
get_lengthscales0.1780.0120.190
get_scales0.1950.0000.195
get_variance_explained0.1410.0040.145
get_weights0.1580.0000.158
groups_names0.1360.0160.152
impute0.1550.0000.155
interpolate_factors0.2150.0040.219
load_model0.1420.0000.142
make_example_data0.0030.0000.002
plot_ascii_data0.1420.0000.142
plot_data_heatmap0.1820.0030.186
plot_data_overview0.2800.0040.284
plot_data_scatter1.1860.0561.242
plot_data_vs_cov0.4560.0040.460
plot_dimred3.3620.0773.403
plot_factor0.9750.0040.978
plot_factor_cor0.1590.0000.159
plot_factors0.4920.0110.504
plot_factors_vs_cov0.4180.0040.422
plot_group_kernel0.2990.0030.303
plot_interpolation_vs_covariate0.4300.0040.434
plot_smoothness0.1730.0070.182
plot_top_weights0.7320.0240.756
plot_variance_explained1.3180.0161.334
plot_variance_explained_by_covariates0.9760.0040.979
plot_variance_explained_per_feature0.3360.0120.347
plot_weights2.6650.0442.709
plot_weights_heatmap0.5260.0360.562
plot_weights_scatter0.4160.0200.436
predict0.1740.0000.174
prepare_mofa0.7050.0200.776
run_mofa0.6990.0000.702
run_tsne0.1840.0040.188
run_umap0.1440.0040.148
samples_metadata0.1330.0040.137
samples_names0.1520.0000.152
set_covariates0.0440.0000.044
subset_factors0.2920.0000.372
subset_groups0.2300.0040.234
subset_samples0.1560.0040.159
subset_views0.9450.0681.015
views_names0.1340.0040.138