############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings gINTomics_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/gINTomics.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘gINTomics/DESCRIPTION’ ... OK * this is package ‘gINTomics’ version ‘1.0.0’ * 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 ‘gINTomics’ can be installed ... OK * 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 [2024-06-23 23:48:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-23 23:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-23 23:48:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Contains 1 files. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-23 23:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-23 23:48:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-23 23:48:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-23 23:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-23 23:48:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-23 23:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-23 23:48:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-23 23:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-23 23:48:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-23 23:48:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-23 23:48:43] [TRACE] [OmnipathR] Cache locked: FALSE .build_histo: no visible binding for global variable ‘chr_cov’ .build_histo: no visible binding for global variable ‘significance’ .build_ridge: no visible binding for global variable ‘coef’ .build_ridge: no visible binding for global variable ‘significance’ .circos_preprocess: no visible binding for global variable ‘cnv_met’ .prepare_cnv_heatmap: no visible binding for global variable ‘cnv’ .prepare_gen_heatmap: no visible binding for global variable ‘met’ .prepare_gen_heatmap: no visible binding for global variable ‘cnv’ .prepare_met_heatmap: no visible binding for global variable ‘met’ .prepare_mirna_heatmap: no visible binding for global variable ‘mirna_cnv’ .prepare_network: no visible binding for global variable ‘omics’ .prepare_reactive_histo_tf: no visible binding for global variable ‘Freq’ .prepare_reactive_venn: no visible binding for global variable ‘cnv_met’ .prepare_reactive_venn: no visible binding for global variable ‘pval’ .shiny_preprocess: no visible binding for global variable ‘cov’ plot_tf_distribution: no visible binding for global variable ‘Freq’ Undefined global functions or variables: Freq chr_cov cnv cnv_met coef cov met mirna_cnv omics pval significance Consider adding importFrom("stats", "coef", "cov") to your NAMESPACE file. * 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 data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_volcano 12.280 1.421 21.126 extract_model_res 10.693 0.676 11.369 plot_ridge 7.779 0.504 8.283 * 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 NOTE See ‘/home/biocbuild/bbs-3.19-bioc/meat/gINTomics.Rcheck/00check.log’ for details.