############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.14.0’ * 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 ‘OmnipathR’ can be installed ... OK * checking installed package size ... OK * checking package 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 whether startup messages can be suppressed ... NOTE [2025-01-28 07:41:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-28 07:41:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:41:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-28 07:41:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-28 07:41:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-28 07:41:48] [TRACE] [OmnipathR] Contains 1 files. [2025-01-28 07:41:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-28 07:41:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-28 07:41:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:41:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-28 07:41:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-28 07:41:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-28 07:41:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:41:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-28 07:41:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:41:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-28 07:41:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:41:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-28 07:41:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:41:49] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 [2025-01-28 07:42:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-28 07:42:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:42:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Contains 1 files. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-28 07:42:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:42:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-28 07:42:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-28 07:42:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:42:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-28 07:42:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:42:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-28 07:42:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:42:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-28 07:42:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-28 07:42:19] [TRACE] [OmnipathR] Cache locked: FALSE * 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 101.604 0.340 106.576 curated_ligrec_stats 58.023 1.688 119.890 omnipath-interactions 54.853 1.940 116.311 filter_extra_attrs 51.592 0.242 55.765 extra_attr_values 28.041 0.428 29.481 nichenet_gr_network_omnipath 26.055 1.208 31.167 extra_attrs_to_cols 25.067 0.174 26.060 giant_component 21.139 0.440 23.050 with_extra_attrs 20.961 0.335 22.854 nichenet_signaling_network_omnipath 19.188 1.515 44.395 go_annot_download 16.940 1.812 18.596 pivot_annotations 16.432 1.558 20.293 omnipath_for_cosmos 17.009 0.398 40.345 has_extra_attrs 15.796 0.116 16.705 extra_attrs 15.718 0.091 16.882 filter_by_resource 13.858 0.279 15.466 translate_ids_multi 13.574 0.279 52.189 find_all_paths 12.798 0.159 13.587 print_interactions 12.515 0.345 15.127 signed_ptms 11.382 0.073 19.934 static_table 9.806 0.760 17.365 curated_ligand_receptor_interactions 9.373 0.394 19.973 filter_intercell 8.827 0.750 9.880 omnipath_query 9.160 0.062 9.464 pubmed_open 9.129 0.083 12.417 resources_in 8.655 0.051 12.584 enzsub_graph 4.525 0.134 6.030 print_path_vs 4.391 0.123 6.233 hpo_download 3.534 0.337 10.320 ensembl_id_mapping_table 1.795 0.156 16.901 translate_ids 1.677 0.143 20.676 all_uniprots 1.509 0.162 60.516 uniprot_full_id_mapping_table 1.448 0.192 158.386 obo_parser 0.183 0.013 6.403 relations_list_to_table 0.157 0.009 6.124 * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.