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This page was generated on 2022-10-19 13:23:18 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 merida1


To the developers/maintainers of the MOFA2 package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1221/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.6.0  (landing page)
Britta Velten
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/MOFA2
git_branch: RELEASE_3_15
git_last_commit: 4f068dd
git_last_commit_date: 2022-04-26 12:09:42 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MOFA2
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOFA2_1.6.0.tar.gz
StartedAt: 2022-10-19 04:58:42 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:04:10 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 328.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MOFA2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOFA2_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/MOFA2.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOFA2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA2’ version ‘1.6.0’
* 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 ‘/Users/biocbuild/bbs-3.15-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 ... NOTE
License components with restrictions not permitted:
  GPL (>= 2) + file LICENSE
* 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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/MOFA2.Rcheck/00check.log’
for details.



Installation output

MOFA2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOFA2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 26 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 18.548   0.815  19.365 

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

nameusersystemelapsed
add_mofa_factors_to_seurat0.0100.0010.009
calculate_contribution_scores0.3600.0260.390
calculate_variance_explained2.8930.1763.074
calculate_variance_explained_per_sample0.8120.0160.829
cluster_samples0.2970.0130.311
compare_elbo0.5770.0250.602
compare_factors0.6840.0260.711
covariates_names0.4020.0180.427
create_mofa1.1140.0581.173
create_mofa_from_df1.4400.0381.480
create_mofa_from_matrix0.0220.0000.022
factors_names0.3030.0130.315
features_metadata0.3370.0350.373
features_names0.3030.0220.325
get_covariates0.3840.0140.399
get_data1.3230.0391.363
get_default_data_options1.5060.0401.549
get_default_mefisto_options0.2120.0050.217
get_default_model_options0.9770.0441.022
get_default_stochastic_options1.0030.0451.049
get_default_training_options1.0150.0391.055
get_dimensions0.2940.0100.305
get_elbo0.3050.0110.318
get_expectations0.2900.0110.301
get_factors0.3140.0120.327
get_imputed_data0.300.010.31
get_lengthscales0.3880.0130.402
get_scales0.3890.0220.412
get_variance_explained0.3080.0170.326
get_weights0.3180.0090.328
groups_names0.3120.0140.326
impute0.3180.0130.332
interpolate_factors0.4490.0210.471
load_model0.2970.0110.308
make_example_data0.0040.0000.005
plot_ascii_data0.3020.0100.312
plot_data_heatmap0.4120.0140.427
plot_data_overview0.5530.0130.567
plot_data_scatter2.6890.0512.745
plot_data_vs_cov1.5070.0361.545
plot_dimred4.6700.0544.706
plot_factor1.9420.0271.973
plot_factor_cor0.3350.0120.348
plot_factors0.9980.0151.016
plot_factors_vs_cov0.8880.0170.906
plot_group_kernel0.6510.0160.668
plot_interpolation_vs_covariate1.0270.0181.046
plot_smoothness0.4190.0130.433
plot_top_weights1.3470.0151.365
plot_variance_explained2.7130.0362.754
plot_variance_explained_by_covariates2.0360.0232.062
plot_variance_explained_per_feature0.6330.0150.649
plot_weights3.5970.0473.651
plot_weights_heatmap0.6420.0180.661
plot_weights_scatter0.6030.0140.617
predict0.3290.0140.343
prepare_mofa1.0820.0291.113
run_mofa0.9840.0241.009
run_tsne0.3110.0140.326
run_umap0.2880.0100.299
samples_metadata0.3070.0290.336
samples_names0.2970.0100.309
set_covariates0.0530.0000.053
subset_factors0.3300.0120.343
subset_groups0.3110.0130.324
subset_samples0.2990.0110.310
subset_views0.3020.0110.312
views_names0.3040.0110.315