############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:MOFA2.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings MOFA2_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MOFA2.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 ‘/home/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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/MOFA2.Rcheck/00check.log’ for details.