Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 |
Package 1293/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOFA2 1.17.0 (landing page) Ricard Argelaguet
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the MOFA2 package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: MOFA2 |
Version: 1.17.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOFA2_1.17.0.tar.gz |
StartedAt: 2024-12-23 20:15:46 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 20:17:04 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 77.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MOFA2.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOFA2_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MOFA2.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MOFA2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MOFA2’ version ‘1.17.0’ * 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 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-3.21-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 code 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_data_overview: no visible binding for global variable ‘group_label’ 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 group_label 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 ... NOTE checkRd: (-1) calculate_contribution_scores.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) calculate_contribution_scores.Rd:37: Lost braces in \itemize; meant \describe ? checkRd: (-1) calculate_contribution_scores.Rd:38: Lost braces in \itemize; meant \describe ? checkRd: (-1) correlate_factors_with_covariates.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) correlate_factors_with_covariates.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_mofa.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_mofa.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_mofa.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_mofa.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) create_mofa.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_data_options.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_data_options.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_data_options.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_model_options.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_model_options.Rd:26: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_model_options.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_model_options.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_model_options.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_model_options.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_stochastic_options.Rd:25: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_stochastic_options.Rd:27: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_stochastic_options.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_stochastic_options.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:24-25: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:31: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_default_training_options.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) get_expectations.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) get_expectations.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) impute.Rd:24: Lost braces; missing escapes or markup? 24 | \item \strong{response}:{gives mean for gaussian and poisson and probabilities for bernoulli.} | ^ checkRd: (-1) impute.Rd:25: Lost braces; missing escapes or markup? 25 | \item \strong{link}: {gives the linear predictions.} | ^ checkRd: (-1) impute.Rd:26: Lost braces; missing escapes or markup? 26 | \item \strong{inRange}: {rounds the fitted values from "terms" for integer-valued distributions to the next integer (default).} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: compare_elbo.Rd: ggplot load_model.Rd: HDF5Array, DelayedArray plot_data_overview.Rd: ggplot plot_data_scatter.Rd: ggplot plot_enrichment_heatmap.Rd: pheatmap plot_variance_explained.Rd: ggplot plot_variance_explained_by_covariates.Rd: ggplot plot_weights.Rd: ggplot plot_weights_heatmap.Rd: pheatmap run_mofa.Rd: reticulate run_tsne.Rd: Rtsne summarise_factors.Rd: ggplot Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. Package unavailable to check Rd xrefs: ‘PCGSE’ * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from Rd file 'create_mofa_from_Seurat.Rd': create_mofa_from_Seurat Code: function(seurat, groups = NULL, assays = NULL, layer = "data", features = NULL, extract_metadata = FALSE) Docs: function(seurat, groups = NULL, assays = NULL, slot = "scale.data", features = NULL, extract_metadata = FALSE) Argument names in code not in docs: layer Argument names in docs not in code: slot Mismatches in argument names: Position: 4 Code: layer Docs: slot * 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/MOFA2.Rcheck/00check.log’ for details.
MOFA2.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOFA2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 25 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 25 ] > > # setwd("/Users/rargelaguet/mofa/MOFA2/tests/testthat") > > proc.time() user system elapsed 4.385 0.214 4.604
MOFA2.Rcheck/MOFA2-Ex.timings
name | user | system | elapsed | |
add_mofa_factors_to_seurat | 0.009 | 0.001 | 0.010 | |
calculate_contribution_scores | 0.052 | 0.006 | 0.059 | |
calculate_variance_explained | 0.680 | 0.029 | 0.714 | |
calculate_variance_explained_per_sample | 0.045 | 0.004 | 0.049 | |
cluster_samples | 0.046 | 0.004 | 0.049 | |
compare_elbo | 0.083 | 0.008 | 0.093 | |
compare_factors | 0.099 | 0.009 | 0.109 | |
covariates_names | 0.053 | 0.006 | 0.067 | |
create_mofa | 0.439 | 0.021 | 0.464 | |
create_mofa_from_df | 0.193 | 0.012 | 0.207 | |
create_mofa_from_matrix | 0.003 | 0.001 | 0.004 | |
factors_names | 0.042 | 0.002 | 0.044 | |
features_metadata | 0.052 | 0.010 | 0.063 | |
features_names | 0.049 | 0.007 | 0.056 | |
get_covariates | 0.044 | 0.003 | 0.048 | |
get_data | 0.362 | 0.009 | 0.378 | |
get_default_data_options | 0.184 | 0.007 | 0.193 | |
get_default_mefisto_options | 0.060 | 0.002 | 0.062 | |
get_default_model_options | 0.39 | 0.01 | 0.40 | |
get_default_stochastic_options | 0.182 | 0.005 | 0.187 | |
get_default_training_options | 0.186 | 0.002 | 0.188 | |
get_dimensions | 0.040 | 0.004 | 0.043 | |
get_elbo | 0.041 | 0.006 | 0.050 | |
get_expectations | 0.045 | 0.005 | 0.051 | |
get_factors | 0.042 | 0.007 | 0.051 | |
get_imputed_data | 0.045 | 0.004 | 0.049 | |
get_lengthscales | 0.048 | 0.006 | 0.053 | |
get_scales | 0.045 | 0.004 | 0.049 | |
get_variance_explained | 0.043 | 0.003 | 0.048 | |
get_weights | 0.051 | 0.006 | 0.057 | |
groups_names | 0.044 | 0.004 | 0.049 | |
impute | 0.045 | 0.005 | 0.050 | |
interpolate_factors | 0.059 | 0.004 | 0.063 | |
load_model | 0.040 | 0.003 | 0.044 | |
make_example_data | 0.001 | 0.000 | 0.001 | |
plot_ascii_data | 0.041 | 0.004 | 0.045 | |
plot_data_heatmap | 0.059 | 0.004 | 0.064 | |
plot_data_overview | 0.089 | 0.004 | 0.093 | |
plot_data_scatter | 0.379 | 0.015 | 0.394 | |
plot_data_vs_cov | 0.123 | 0.005 | 0.128 | |
plot_dimred | 1.403 | 0.022 | 1.412 | |
plot_factor | 0.334 | 0.012 | 0.346 | |
plot_factor_cor | 0.048 | 0.006 | 0.053 | |
plot_factors | 0.159 | 0.008 | 0.167 | |
plot_factors_vs_cov | 0.118 | 0.005 | 0.122 | |
plot_group_kernel | 0.096 | 0.006 | 0.101 | |
plot_interpolation_vs_covariate | 0.138 | 0.006 | 0.144 | |
plot_smoothness | 0.052 | 0.004 | 0.056 | |
plot_top_weights | 0.223 | 0.007 | 0.231 | |
plot_variance_explained | 0.399 | 0.014 | 0.417 | |
plot_variance_explained_by_covariates | 0.283 | 0.007 | 0.290 | |
plot_variance_explained_per_feature | 0.096 | 0.006 | 0.102 | |
plot_weights | 0.663 | 0.039 | 0.708 | |
plot_weights_heatmap | 0.104 | 0.007 | 0.112 | |
plot_weights_scatter | 0.106 | 0.005 | 0.112 | |
predict | 0.043 | 0.004 | 0.047 | |
prepare_mofa | 0.198 | 0.012 | 0.210 | |
run_mofa | 0.209 | 0.007 | 0.216 | |
run_tsne | 0.043 | 0.004 | 0.047 | |
run_umap | 0.042 | 0.004 | 0.046 | |
samples_metadata | 0.307 | 0.010 | 0.316 | |
samples_names | 0.042 | 0.003 | 0.044 | |
set_covariates | 0.010 | 0.001 | 0.011 | |
subset_factors | 0.046 | 0.004 | 0.050 | |
subset_groups | 0.041 | 0.003 | 0.044 | |
subset_samples | 0.045 | 0.005 | 0.051 | |
subset_views | 0.041 | 0.004 | 0.046 | |
views_names | 0.041 | 0.003 | 0.045 | |