Ricard Argelaguet
| Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/MOFA2 |
| git_branch: RELEASE_3_16 |
| git_last_commit: a1ef44d |
| git_last_commit_date: 2022-11-01 11:23:11 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:41 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
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. |
| Package 1243/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MOFA2 1.8.0 (landing page) Ricard Argelaguet
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MOFA2 |
| Version: 1.8.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MOFA2_1.8.0.tar.gz |
| StartedAt: 2023-04-11 03:32:54 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 03:35:58 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 184.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MOFA2.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MOFA2.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings MOFA2_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/MOFA2.Rcheck' * using R version 4.2.3 (2023-03-15 ucrt) * using platform: x86_64-w64-mingw32 (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 '1.8.0' * 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 whether package 'MOFA2' can be installed ... NOTE Found the following notes/warnings: Non-staged installation was used See 'F:/biocbuild/bbs-3.16-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 ... OK * 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: 3 NOTEs See 'F:/biocbuild/bbs-3.16-bioc/meat/MOFA2.Rcheck/00check.log' for details.
MOFA2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL MOFA2 ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.16-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 ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (MOFA2)
MOFA2.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 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 7 | SKIP 0 | PASS 26 ]
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 26 ]
>
> proc.time()
user system elapsed
11.0 0.6 11.6
MOFA2.Rcheck/MOFA2-Ex.timings
| name | user | system | elapsed | |
| add_mofa_factors_to_seurat | 0 | 0 | 0 | |
| calculate_contribution_scores | 0.23 | 0.05 | 0.29 | |
| calculate_variance_explained | 1.92 | 0.13 | 2.05 | |
| calculate_variance_explained_per_sample | 0.64 | 0.00 | 0.64 | |
| cluster_samples | 0.14 | 0.00 | 0.14 | |
| compare_elbo | 0.36 | 0.01 | 0.37 | |
| compare_factors | 0.35 | 0.02 | 0.38 | |
| covariates_names | 0.19 | 0.01 | 0.25 | |
| create_mofa | 0.94 | 0.00 | 0.93 | |
| create_mofa_from_df | 0.43 | 0.03 | 0.47 | |
| create_mofa_from_matrix | 0 | 0 | 0 | |
| factors_names | 0.14 | 0.02 | 0.16 | |
| features_metadata | 0.19 | 0.00 | 0.19 | |
| features_names | 0.15 | 0.02 | 0.17 | |
| get_covariates | 0.14 | 0.06 | 0.20 | |
| get_data | 0.83 | 0.04 | 0.88 | |
| get_default_data_options | 0.89 | 0.02 | 0.90 | |
| get_default_mefisto_options | 0.16 | 0.00 | 0.16 | |
| get_default_model_options | 0.45 | 0.02 | 0.47 | |
| get_default_stochastic_options | 0.44 | 0.04 | 0.48 | |
| get_default_training_options | 0.47 | 0.02 | 0.49 | |
| get_dimensions | 0.14 | 0.00 | 0.14 | |
| get_elbo | 0.15 | 0.00 | 0.15 | |
| get_expectations | 0.15 | 0.01 | 0.16 | |
| get_factors | 0.16 | 0.00 | 0.15 | |
| get_imputed_data | 0.15 | 0.02 | 0.17 | |
| get_lengthscales | 0.27 | 0.03 | 0.30 | |
| get_scales | 0.19 | 0.00 | 0.19 | |
| get_variance_explained | 0.14 | 0.03 | 0.17 | |
| get_weights | 0.22 | 0.02 | 0.23 | |
| groups_names | 0.15 | 0.00 | 0.16 | |
| impute | 0.16 | 0.01 | 0.17 | |
| interpolate_factors | 0.23 | 0.00 | 0.24 | |
| load_model | 0.16 | 0.02 | 0.17 | |
| make_example_data | 0.01 | 0.00 | 0.01 | |
| plot_ascii_data | 0.19 | 0.01 | 0.21 | |
| plot_data_heatmap | 0.25 | 0.05 | 0.29 | |
| plot_data_overview | 0.38 | 0.02 | 0.39 | |
| plot_data_scatter | 1.62 | 0.11 | 1.74 | |
| plot_data_vs_cov | 0.47 | 0.01 | 0.48 | |
| plot_dimred | 3.50 | 0.10 | 3.46 | |
| plot_factor | 1.20 | 0.01 | 1.22 | |
| plot_factor_cor | 0.18 | 0.00 | 0.17 | |
| plot_factors | 0.59 | 0.02 | 0.61 | |
| plot_factors_vs_cov | 0.45 | 0.01 | 0.47 | |
| plot_group_kernel | 0.33 | 0.02 | 0.34 | |
| plot_interpolation_vs_covariate | 0.5 | 0.0 | 0.5 | |
| plot_smoothness | 0.19 | 0.06 | 0.25 | |
| plot_top_weights | 0.80 | 0.02 | 0.81 | |
| plot_variance_explained | 1.36 | 0.03 | 1.39 | |
| plot_variance_explained_by_covariates | 1.09 | 0.04 | 1.14 | |
| plot_variance_explained_per_feature | 0.41 | 0.02 | 0.42 | |
| plot_weights | 2.06 | 0.02 | 2.08 | |
| plot_weights_heatmap | 0.38 | 0.04 | 0.42 | |
| plot_weights_scatter | 0.31 | 0.02 | 0.33 | |
| predict | 0.14 | 0.01 | 0.15 | |
| prepare_mofa | 0.50 | 0.04 | 0.54 | |
| run_mofa | 0.94 | 0.01 | 0.95 | |
| run_tsne | 0.16 | 0.00 | 0.16 | |
| run_umap | 0.16 | 0.02 | 0.17 | |
| samples_metadata | 0.15 | 0.00 | 0.16 | |
| samples_names | 0.14 | 0.00 | 0.14 | |
| set_covariates | 0.03 | 0.00 | 0.03 | |
| subset_factors | 0.17 | 0.01 | 0.18 | |
| subset_groups | 0.14 | 0.02 | 0.16 | |
| subset_samples | 0.14 | 0.01 | 0.16 | |
| subset_views | 0.13 | 0.02 | 0.14 | |
| views_names | 0.14 | 0.00 | 0.14 | |