Britta Velten
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MOFA2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: 98a2d44 |
| git_last_commit_date: 2021-08-23 11:25:24 -0400 (Mon, 23 Aug 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1173/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MOFA2 1.2.2 (landing page) Britta Velten
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MOFA2 |
| Version: 1.2.2 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MOFA2_1.2.2.tar.gz |
| StartedAt: 2021-10-15 02:10:48 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:13:59 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 190.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MOFA2.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MOFA2_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MOFA2.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.2.2' * 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-3.13-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-3.13-bioc/meat/MOFA2.Rcheck/00check.log' for details.
MOFA2.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MOFA2
###
##############################################################################
##############################################################################
* installing to library 'C:/Users/biocbuild/bbs-3.13-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
MOFA2.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 4 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
9.67 0.50 10.18
MOFA2.Rcheck/MOFA2-Ex.timings
| name | user | system | elapsed | |
| add_mofa_factors_to_seurat | 0 | 0 | 0 | |
| calculate_contribution_scores | 0.85 | 0.04 | 1.22 | |
| calculate_variance_explained | 1.60 | 0.14 | 1.74 | |
| calculate_variance_explained_per_sample | 0.14 | 0.05 | 0.18 | |
| cluster_samples | 0.53 | 0.01 | 0.55 | |
| compare_elbo | 0.26 | 0.00 | 0.27 | |
| compare_factors | 0.69 | 0.03 | 0.72 | |
| covariates_names | 0.34 | 0.02 | 0.50 | |
| create_mofa | 0.86 | 0.09 | 1.07 | |
| create_mofa_from_df | 0.99 | 0.06 | 1.05 | |
| create_mofa_from_matrix | 0 | 0 | 0 | |
| factors_names | 0.14 | 0.02 | 0.15 | |
| features_metadata | 0.14 | 0.03 | 0.17 | |
| features_names | 0.15 | 0.01 | 0.16 | |
| get_covariates | 0.15 | 0.02 | 0.17 | |
| get_data | 0.45 | 0.03 | 0.49 | |
| get_default_data_options | 0.47 | 0.05 | 0.51 | |
| get_default_mefisto_options | 0.12 | 0.01 | 0.14 | |
| get_default_model_options | 0.83 | 0.06 | 0.90 | |
| get_default_stochastic_options | 0.48 | 0.04 | 0.52 | |
| get_default_training_options | 0.81 | 0.07 | 0.89 | |
| get_dimensions | 0.13 | 0.02 | 0.14 | |
| get_elbo | 0.14 | 0.00 | 0.14 | |
| get_expectations | 0.15 | 0.00 | 0.16 | |
| get_factors | 0.14 | 0.00 | 0.14 | |
| get_imputed_data | 0.16 | 0.01 | 0.17 | |
| get_lengthscales | 0.19 | 0.00 | 0.19 | |
| get_scales | 0.17 | 0.00 | 0.17 | |
| get_variance_explained | 0.12 | 0.05 | 0.17 | |
| get_weights | 0.16 | 0.02 | 0.18 | |
| groups_names | 0.12 | 0.01 | 0.14 | |
| impute | 0.16 | 0.05 | 0.20 | |
| interpolate_factors | 0.24 | 0.00 | 0.23 | |
| load_model | 0.15 | 0.00 | 0.16 | |
| make_example_data | 0 | 0 | 0 | |
| plot_ascii_data | 0.14 | 0.02 | 0.16 | |
| plot_data_heatmap | 0.22 | 0.01 | 0.23 | |
| plot_data_overview | 0.27 | 0.02 | 0.28 | |
| plot_data_scatter | 1.50 | 0.01 | 1.52 | |
| plot_data_vs_cov | 0.43 | 0.03 | 0.47 | |
| plot_dimred | 3.41 | 0.02 | 3.28 | |
| plot_factor | 0.86 | 0.01 | 0.87 | |
| plot_factor_cor | 0.16 | 0.00 | 0.16 | |
| plot_factors | 0.45 | 0.02 | 0.47 | |
| plot_factors_vs_cov | 0.42 | 0.02 | 0.44 | |
| plot_group_kernel | 0.30 | 0.03 | 0.32 | |
| plot_interpolation_vs_covariate | 0.44 | 0.01 | 0.46 | |
| plot_smoothness | 0.2 | 0.0 | 0.2 | |
| plot_top_weights | 0.62 | 0.08 | 0.70 | |
| plot_variance_explained | 1.18 | 0.00 | 1.17 | |
| plot_variance_explained_by_covariates | 0.84 | 0.02 | 0.86 | |
| plot_variance_explained_per_feature | 0.3 | 0.0 | 0.3 | |
| plot_weights | 1.76 | 0.00 | 1.77 | |
| plot_weights_heatmap | 0.35 | 0.00 | 0.34 | |
| plot_weights_scatter | 0.25 | 0.01 | 0.27 | |
| predict | 0.14 | 0.00 | 0.14 | |
| prepare_mofa | 0.5 | 0.0 | 0.5 | |
| run_mofa | 1.00 | 0.03 | 1.03 | |
| run_tsne | 0.14 | 0.00 | 0.14 | |
| run_umap | 0.14 | 0.00 | 0.14 | |
| samples_metadata | 0.15 | 0.00 | 0.16 | |
| samples_names | 0.14 | 0.00 | 0.14 | |
| set_covariates | 0.04 | 0.00 | 0.03 | |
| subset_factors | 0.15 | 0.01 | 0.17 | |
| subset_groups | 0.14 | 0.00 | 0.15 | |
| subset_samples | 0.14 | 0.02 | 0.15 | |
| subset_views | 0.13 | 0.02 | 0.14 | |
| views_names | 0.14 | 0.00 | 0.14 | |