############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gINTomics_1.3.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gINTomics/DESCRIPTION’ ... OK * this is package ‘gINTomics’ version ‘1.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 40 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 ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘gINTomics’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.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 ... NOTE Warning: program compiled against libxml 212 using older 211 [2025-01-20 07:46:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-20 07:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:46:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Contains 1 files. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-20 07:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:46:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-20 07:46:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-20 07:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:46:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-20 07:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:46:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-20 07:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:46:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-20 07:46:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:46:43] [TRACE] [OmnipathR] Cache locked: FALSE A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 [2025-01-20 07:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-20 07:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:49:50] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Contains 1 files. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-20 07:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:49:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-20 07:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-20 07:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-20 07:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-20 07:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-20 07:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-20 07:49:50] [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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: mmultiassay_ov.Rd: MultiAssayExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. 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 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 15.492 1.347 467.976 extract_model_res 12.714 0.380 13.115 plot_ridge 10.213 0.240 10.470 run_multiomics 5.682 0.311 7.003 * 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: 5 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log’ for details.