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This page was generated on 2021-10-15 15:06:43 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MOFA2_1.2.2.tar.gz |
StartedAt: 2021-10-14 21:20:17 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 21:24:09 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 231.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MOFA2.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MOFA2_1.2.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MOFA2.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.2.2’ * 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 .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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-3.13-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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/MOFA2.Rcheck/00check.log’ for details.
MOFA2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MOFA2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
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-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 4 | SKIP 0 | PASS 26 ] > > proc.time() user system elapsed 11.145 0.573 11.707
MOFA2.Rcheck/MOFA2-Ex.timings
name | user | system | elapsed | |
add_mofa_factors_to_seurat | 0.008 | 0.000 | 0.008 | |
calculate_contribution_scores | 0.245 | 0.018 | 0.267 | |
calculate_variance_explained | 2.057 | 0.042 | 2.100 | |
calculate_variance_explained_per_sample | 0.220 | 0.013 | 0.233 | |
cluster_samples | 0.553 | 0.011 | 0.563 | |
compare_elbo | 0.401 | 0.021 | 0.421 | |
compare_factors | 0.494 | 0.025 | 0.519 | |
covariates_names | 0.298 | 0.026 | 0.331 | |
create_mofa | 1.192 | 0.043 | 1.235 | |
create_mofa_from_df | 0.899 | 0.030 | 0.930 | |
create_mofa_from_matrix | 0.019 | 0.000 | 0.020 | |
factors_names | 0.564 | 0.019 | 0.584 | |
features_metadata | 0.291 | 0.070 | 0.362 | |
features_names | 0.219 | 0.027 | 0.247 | |
get_covariates | 0.289 | 0.020 | 0.309 | |
get_data | 0.555 | 0.048 | 0.604 | |
get_default_data_options | 1.045 | 0.044 | 1.089 | |
get_default_mefisto_options | 0.199 | 0.005 | 0.204 | |
get_default_model_options | 0.712 | 0.034 | 0.746 | |
get_default_stochastic_options | 0.860 | 0.027 | 0.886 | |
get_default_training_options | 1.061 | 0.030 | 1.091 | |
get_dimensions | 0.212 | 0.010 | 0.222 | |
get_elbo | 0.173 | 0.007 | 0.181 | |
get_expectations | 0.233 | 0.011 | 0.244 | |
get_factors | 0.241 | 0.015 | 0.255 | |
get_imputed_data | 0.218 | 0.013 | 0.231 | |
get_lengthscales | 0.284 | 0.014 | 0.298 | |
get_scales | 0.282 | 0.012 | 0.294 | |
get_variance_explained | 0.213 | 0.023 | 0.237 | |
get_weights | 0.189 | 0.009 | 0.198 | |
groups_names | 0.157 | 0.007 | 0.164 | |
impute | 0.276 | 0.018 | 0.294 | |
interpolate_factors | 0.315 | 0.017 | 0.332 | |
load_model | 0.176 | 0.008 | 0.184 | |
make_example_data | 0.003 | 0.000 | 0.003 | |
plot_ascii_data | 0.204 | 0.007 | 0.212 | |
plot_data_heatmap | 0.286 | 0.012 | 0.298 | |
plot_data_overview | 0.403 | 0.013 | 0.416 | |
plot_data_scatter | 2.217 | 0.080 | 2.301 | |
plot_data_vs_cov | 0.561 | 0.015 | 0.576 | |
plot_dimred | 3.634 | 0.067 | 3.681 | |
plot_factor | 1.205 | 0.035 | 1.244 | |
plot_factor_cor | 0.179 | 0.008 | 0.188 | |
plot_factors | 0.573 | 0.014 | 0.589 | |
plot_factors_vs_cov | 0.577 | 0.015 | 0.593 | |
plot_group_kernel | 0.376 | 0.011 | 0.388 | |
plot_interpolation_vs_covariate | 0.617 | 0.014 | 0.631 | |
plot_smoothness | 0.323 | 0.015 | 0.338 | |
plot_top_weights | 0.997 | 0.015 | 1.013 | |
plot_variance_explained | 1.605 | 0.037 | 1.646 | |
plot_variance_explained_by_covariates | 1.342 | 0.028 | 1.378 | |
plot_variance_explained_per_feature | 0.389 | 0.008 | 0.398 | |
plot_weights | 2.430 | 0.042 | 2.475 | |
plot_weights_heatmap | 0.490 | 0.015 | 0.506 | |
plot_weights_scatter | 0.418 | 0.015 | 0.434 | |
predict | 0.221 | 0.010 | 0.231 | |
prepare_mofa | 0.905 | 0.023 | 0.928 | |
run_mofa | 0.776 | 0.026 | 0.802 | |
run_tsne | 0.211 | 0.010 | 0.220 | |
run_umap | 0.190 | 0.010 | 0.199 | |
samples_metadata | 0.163 | 0.009 | 0.172 | |
samples_names | 0.198 | 0.010 | 0.208 | |
set_covariates | 0.039 | 0.001 | 0.039 | |
subset_factors | 0.229 | 0.014 | 0.242 | |
subset_groups | 0.173 | 0.007 | 0.181 | |
subset_samples | 0.192 | 0.010 | 0.202 | |
subset_views | 0.231 | 0.010 | 0.242 | |
views_names | 0.226 | 0.011 | 0.236 | |