############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SPONGE.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SPONGE_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SPONGE.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 ‘SPONGE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SPONGE’ version ‘1.29.0’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 27 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... WARNING Found the following files with non-portable file names: spongEffects_logo/Endprodukt_Schrift rechts.png spongEffects_logo/Endprodukt_Schrift unten.png spongEffects_logo/SpongEffekt_Endprodukt_Logo alleinstehend.png These are not fully portable file names. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for sufficient/correct file permissions ... OK * checking whether package ‘SPONGE’ can be installed ... WARNING Found the following significant warnings: Note: next used in wrong context: no loop is visible Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’ Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’ Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’ Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’ Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’ Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’ Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’ See ‘/home/biocbuild/bbs-3.21-bioc/meat/SPONGE.Rcheck/00install.out’ for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’. * checking installed package size ... INFO installed size is 8.0Mb sub-directories of 1Mb or more: data 7.7Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Authors@R field gives persons with no role: Fabio Boniolo Azim Dehghani Amirabad Dennis Kostka Marcel H. Schulz * 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 ... WARNING '::' or ':::' imports not declared from: ‘httr’ ‘tibble’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE checkLambda: no visible binding for global variable ‘i’ check_and_convert_expression_data: no visible global function definition for ‘is’ check_and_convert_expression_data: no visible global function definition for ‘attach.big.matrix’ check_and_convert_expression_data: no visible global function definition for ‘mwhich’ compute_p_values: no visible binding for global variable ‘cor_cut’ compute_p_values: no visible binding for global variable ‘df_cut’ compute_p_values: no visible global function definition for ‘J’ compute_p_values: no visible binding for global variable ‘.I’ compute_p_values: no visible binding for global variable ‘.EACHI’ compute_p_values: no visible binding for global variable ‘p.val’ compute_p_values: no visible binding for global variable ‘p.adj’ define_modules: no visible binding for global variable ‘geneA’ define_modules: no visible binding for global variable ‘geneB’ determine_cutoffs_for_null_model_partitioning: no visible binding for global variable ‘cor_cut’ determine_cutoffs_for_null_model_partitioning: no visible binding for global variable ‘df_cut’ enrichment_modules: no visible binding for global variable ‘Module’ filter_ceRNA_network: no visible binding for global variable ‘gene’ fn_discretize_spongeffects: no visible global function definition for ‘quantile’ fn_filter_network: no visible binding for global variable ‘mscor’ fn_filter_network: no visible binding for global variable ‘p.adj’ fn_gene_miRNA_F_test: no visible binding for global variable ‘mirna’ fn_get_model_coef: no visible binding for global variable ‘gene’ get_central_modules: no visible binding for global variable ‘gene’ isplitDT2 : nextEl: no visible global function definition for ‘.’ plot_accuracy_sensitivity_specificity: no visible binding for global variable ‘Accuracy’ plot_accuracy_sensitivity_specificity: no visible binding for global variable ‘Model’ plot_accuracy_sensitivity_specificity: no visible binding for global variable ‘Run’ plot_accuracy_sensitivity_specificity: no visible binding for global variable ‘Class’ plot_accuracy_sensitivity_specificity: no visible binding for global variable ‘Value’ plot_confusion_matrices: no visible global function definition for ‘na.omit’ plot_density_scores: no visible binding for global variable ‘MeanDecreaseGini’ plot_density_scores: no visible binding for global variable ‘Patient’ plot_density_scores: no visible binding for global variable ‘Score’ plot_density_scores: no visible binding for global variable ‘Class’ plot_heatmaps: no visible binding for global variable ‘MeanDecreaseGini’ plot_involved_miRNAs_to_modules: no visible binding for global variable ‘MeanDecreaseGini’ plot_top_modules: no visible binding for global variable ‘trained.model’ plot_top_modules: no visible binding for global variable ‘MeanDecreaseGini’ plot_top_modules: no visible binding for global variable ‘Module’ plot_top_modules: no visible binding for global variable ‘Analysed’ prepare_metabric_for_spongEffects: no visible global function definition for ‘read.delim’ prepare_metabric_for_spongEffects: no visible binding for global variable ‘Entrez_Gene_Id’ prepare_metabric_for_spongEffects: no visible global function definition for ‘fn_convert_gene_names’ prepare_metabric_for_spongEffects: no visible binding for global variable ‘CLAUDIN_SUBTYPE’ prepare_metabric_for_spongEffects: no visible binding for global variable ‘PATIENT_ID’ prepare_tcga_for_spongEffects: no visible binding for global variable ‘sampleID’ prepare_tcga_for_spongEffects: no visible binding for global variable ‘SUBTYPE’ prepare_tcga_for_spongEffects: no visible binding for global variable ‘PATIENT_ID’ prepare_tcga_for_spongEffects: no visible binding for global variable ‘AJCC_PATHOLOGIC_TUMOR_STAGE’ processChunk: no visible binding for global variable ‘geneA_idx’ processChunk: no visible binding for global variable ‘geneB_idx’ processChunk: no visible binding for global variable ‘geneA’ processChunk: no visible binding for global variable ‘geneB’ processChunk: no visible binding for global variable ‘mirna’ sample_zero_mscor_cov: no visible binding for global variable ‘solution’ sample_zero_mscor_cov: no visible global function definition for ‘ginv’ sample_zero_mscor_cov: no visible binding for global variable ‘i’ sample_zero_mscor_data: no visible binding for global variable ‘cov.matrix’ sponge: no visible global function definition for ‘is’ sponge: no visible binding for global variable ‘i’ sponge: no visible global function definition for ‘attach.big.matrix’ sponge: no visible binding for global variable ‘gene_combis’ sponge_build_null_model: no visible binding for global variable ‘precomputed_cov_matrices’ sponge_build_null_model: no visible binding for global variable ‘cov.matrices.m’ sponge_build_null_model: no visible binding for global variable ‘cov.matrices.k’ sponge_build_null_model: no visible binding for global variable ‘m’ sponge_build_null_model: no visible binding for global variable ‘k’ sponge_compute_p_values: no visible binding for global variable ‘dt.m’ sponge_compute_p_values: no visible binding for global variable ‘cor_cut’ sponge_compute_p_values: no visible binding for global variable ‘df_cut’ sponge_gene_miRNA_interaction_filter: no visible global function definition for ‘is’ sponge_gene_miRNA_interaction_filter: no visible binding for global variable ‘chunk’ sponge_gene_miRNA_interaction_filter: no visible binding for global variable ‘g_expr_batch’ sponge_gene_miRNA_interaction_filter : : no visible binding for global variable ‘g_expr_batch’ sponge_gene_miRNA_interaction_filter: no visible binding for global variable ‘gene’ sponge_gene_miRNA_interaction_filter: no visible binding for global variable ‘g_expr’ sponge_network: no visible binding for global variable ‘gene’ sponge_network: no visible binding for global variable ‘mir’ sponge_plot_network_centralities: no visible global function definition for ‘head’ sponge_plot_simulation_results: no visible binding for global variable ‘mscor’ sponge_run_benchmark: no visible binding for global variable ‘precomputed_cov_matrices’ sponge_run_benchmark: no visible binding for global variable ‘elastic.net’ sponge_run_benchmark: no visible binding for global variable ‘each.miRNA’ sponge_subsampling: no visible binding for global variable ‘sub.n’ sponge_subsampling: no visible binding for global variable ‘geneA’ sponge_subsampling: no visible binding for global variable ‘geneB’ Undefined global functions or variables: . .EACHI .I AJCC_PATHOLOGIC_TUMOR_STAGE Accuracy Analysed CLAUDIN_SUBTYPE Class Entrez_Gene_Id J MeanDecreaseGini Model Module PATIENT_ID Patient Run SUBTYPE Score Value attach.big.matrix chunk cor_cut cov.matrices.k cov.matrices.m cov.matrix df_cut dt.m each.miRNA elastic.net fn_convert_gene_names g_expr g_expr_batch gene geneA geneA_idx geneB geneB_idx gene_combis ginv head i is k m mir mirna mscor mwhich na.omit p.adj p.val precomputed_cov_matrices quantile read.delim sampleID solution sub.n trained.model Consider adding importFrom("methods", "is") importFrom("stats", "na.omit", "quantile") importFrom("utils", "head", "read.delim") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: fn_RF_classifier.Rd:30-32: Dropping empty section \value * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘train_genes_miRNA_candidates’ Undocumented data sets: ‘train_genes_miRNA_candidates’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'Random_spongEffects.Rd' ‘min.expression’ Documented arguments not in \usage in Rd file 'Random_spongEffects.Rd': ‘train_gene_expr’ ‘test_gene_expr’ ‘train_meta_data’ ‘test_meta_data’ ‘train_meta_data_type’ ‘test_meta_data_type’ ‘metric’ ‘tunegrid_c’ ‘n.folds’ ‘repetitions’ ‘min.expr’ Documented arguments not in \usage in Rd file 'calibrate_model.Rd': ‘modules’ Undocumented arguments in Rd file 'plot_confusion_matrices.Rd' ‘subtypes.testing.factors’ Documented arguments not in \usage in Rd file 'plot_confusion_matrices.Rd': ‘subtypes_testing_factors’ Documented arguments not in \usage in Rd file 'plot_density_scores.Rd': ‘meta_data_type’ Documented arguments not in \usage in Rd file 'plot_top_modules.Rd': ‘bioMart_gene_symbol_columns’ ‘bioMart_gene_ensembl’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sponge_gene_miRNA_interaction_filter 20.149 0.301 20.450 sponge_build_null_model 12.615 0.140 12.756 sponge_run_benchmark 10.789 0.099 10.887 * 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: 5 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/SPONGE.Rcheck/00check.log’ for details.