############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SPONGE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SPONGE_1.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/SPONGE.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SPONGE/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SPONGE’ version ‘1.16.1’ * 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 ‘SPONGE’ can be installed ... OK * checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: data 8.0Mb * 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 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 global function definition for ‘:=’ compute_p_values: no visible binding for global variable ‘p.adj’ determine_cutoffs_for_null_model_partitioning: no visible global function definition for ‘:=’ 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’ fn_elasticnet: no visible binding for global variable ‘alpha’ fn_gene_miRNA_F_test: no visible binding for global variable ‘mirna’ fn_get_model_coef: no visible binding for global variable ‘gene’ isplitDT2 : nextEl: no visible global function definition for ‘.’ 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 global function definition for ‘:=’ 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 := J alpha attach.big.matrix chunk cor_cut cov.matrices.k cov.matrices.m cov.matrix df_cut dt.m each.miRNA elastic.net g_expr g_expr_batch gene geneA geneA_idx geneB geneB_idx gene_combis ginv head i is k m mir mirna mscor mwhich p.adj p.val precomputed_cov_matrices solution sub.n Consider adding importFrom("methods", "is") importFrom("utils", "head") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... WARNING LazyData DB of 8.0 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * 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 24.554 0.288 24.842 sponge_build_null_model 13.337 0.216 13.554 sponge_run_benchmark 10.389 0.000 10.389 * 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: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/SPONGE.Rcheck/00check.log’ for details.