Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:55 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 tokay2


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 1190/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOFA2 1.4.0  (landing page)
Britta Velten
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MOFA2
git_branch: RELEASE_3_14
git_last_commit: 2aa2c46
git_last_commit_date: 2021-10-26 13:04:00 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MOFA2
Version: 1.4.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MOFA2_1.4.0.tar.gz
StartedAt: 2022-04-12 23:08:15 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 23:11:35 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 199.3 seconds
RetCode: 0
Status:   OK  
CheckDir: MOFA2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MOFA2_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MOFA2.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MOFA2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MOFA2' version '1.4.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MOFA2' can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See 'C:/Users/biocbuild/bbs-3.14-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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MOFA2.Rcheck/00check.log'
for details.



Installation output

MOFA2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MOFA2
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/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
  converting help for package 'MOFA2'
    finding HTML links ... done
    MOFA                                    html  
    add_mofa_factors_to_seurat              html  
    calculate_contribution_scores           html  
    calculate_variance_explained            html  
    calculate_variance_explained_per_sample
                                            html  
    cluster_samples                         html  
    compare_elbo                            html  
    finding level-2 HTML links ... done

    compare_factors                         html  
    correlate_factors_with_covariates       html  
    covariates_names                        html  
    create_mofa                             html  
    create_mofa_from_MultiAssayExperiment   html  
    create_mofa_from_Seurat                 html  
    create_mofa_from_SingleCellExperiment   html  
    create_mofa_from_df                     html  
    create_mofa_from_matrix                 html  
    factors_names                           html  
    features_metadata                       html  
    features_names                          html  
    get_covariates                          html  
    get_data                                html  
    get_default_data_options                html  
    get_default_mefisto_options             html  
    get_default_model_options               html  
    get_default_stochastic_options          html  
    get_default_training_options            html  
    get_dimensions                          html  
    get_elbo                                html  
    get_expectations                        html  
    get_factors                             html  
    get_group_kernel                        html  
    get_imputed_data                        html  
    get_interpolated_factors                html  
    get_lengthscales                        html  
    get_scales                              html  
    get_variance_explained                  html  
    get_weights                             html  
    groups_names                            html  
    impute                                  html  
    interpolate_factors                     html  
    load_model                              html  
    make_example_data                       html  
    pipe                                    html  
    plot_alignment                          html  
    plot_ascii_data                         html  
    plot_data_heatmap                       html  
    plot_data_overview                      html  
    plot_data_scatter                       html  
    plot_data_vs_cov                        html  
    plot_dimred                             html  
    plot_enrichment                         html  
    plot_enrichment_detailed                html  
    plot_enrichment_heatmap                 html  
    plot_factor                             html  
    plot_factor_cor                         html  
    plot_factors                            html  
    plot_factors_vs_cov                     html  
    plot_group_kernel                       html  
    plot_interpolation_vs_covariate         html  
    plot_sharedness                         html  
    plot_smoothness                         html  
    plot_top_weights                        html  
    plot_variance_explained                 html  
    plot_variance_explained_by_covariates   html  
    plot_variance_explained_per_feature     html  
    plot_weights                            html  
    plot_weights_heatmap                    html  
    plot_weights_scatter                    html  
    predict                                 html  
    prepare_mofa                            html  
    run_enrichment                          html  
    run_mofa                                html  
    run_tsne                                html  
    run_umap                                html  
    samples_metadata                        html  
    samples_names                           html  
    select_model                            html  
    set_covariates                          html  
    subset_factors                          html  
    subset_features                         html  
    subset_groups                           html  
    subset_samples                          html  
    subset_views                            html  
    summarise_factors                       html  
    views_names                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MOFA2)
Making 'packages.html' ... done

Tests output

MOFA2.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  10.07    0.57   10.65 

Example timings

MOFA2.Rcheck/MOFA2-Ex.timings

nameusersystemelapsed
add_mofa_factors_to_seurat0.010.000.02
calculate_contribution_scores0.300.050.64
calculate_variance_explained1.390.141.53
calculate_variance_explained_per_sample0.260.030.30
cluster_samples0.610.050.66
compare_elbo0.330.000.33
compare_factors0.390.050.43
covariates_names0.330.060.57
create_mofa0.940.061.04
create_mofa_from_df0.980.061.05
create_mofa_from_matrix0.020.000.01
factors_names0.150.000.16
features_metadata0.160.050.20
features_names0.150.000.16
get_covariates0.180.020.19
get_data1.040.061.11
get_default_data_options0.720.110.84
get_default_mefisto_options0.190.010.20
get_default_model_options0.560.050.61
get_default_stochastic_options0.550.050.60
get_default_training_options0.500.060.56
get_dimensions0.550.030.58
get_elbo0.140.020.15
get_expectations0.150.000.16
get_factors0.160.000.16
get_imputed_data0.150.010.17
get_lengthscales0.190.000.19
get_scales0.210.000.20
get_variance_explained0.140.030.17
get_weights0.150.030.19
groups_names0.160.000.15
impute0.190.000.19
interpolate_factors0.230.000.24
load_model0.160.000.15
make_example_data0.010.000.02
plot_ascii_data0.160.000.15
plot_data_heatmap0.230.020.25
plot_data_overview0.270.020.29
plot_data_scatter1.300.031.32
plot_data_vs_cov0.500.010.52
plot_dimred3.780.003.78
plot_factor0.950.000.95
plot_factor_cor0.170.020.19
plot_factors0.500.010.52
plot_factors_vs_cov0.420.020.44
plot_group_kernel0.300.030.33
plot_interpolation_vs_covariate0.450.050.50
plot_smoothness0.250.000.25
plot_top_weights0.720.000.72
plot_variance_explained1.280.011.29
plot_variance_explained_by_covariates1.010.021.04
plot_variance_explained_per_feature0.300.010.31
plot_weights1.920.041.95
plot_weights_heatmap0.390.000.39
plot_weights_scatter0.330.000.33
predict0.160.000.16
prepare_mofa0.480.060.54
run_mofa1.030.011.05
run_tsne0.140.020.16
run_umap0.140.010.16
samples_metadata0.130.020.14
samples_names0.140.000.14
set_covariates0.030.000.03
subset_factors0.150.020.17
subset_groups0.140.010.16
subset_samples0.150.000.14
subset_views0.140.030.17
views_names0.150.000.16