Back to Multiple platform build/check report for BioC 3.13 |
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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
############################################################################## ############################################################################## ### ### 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 | |