############################################################################## ############################################################################## ### ### 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_3.12.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘3.12.4’ * 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 ... NOTE License stub is invalid DCF. * 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 [2024-10-17 10:17:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 10:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:17:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-17 10:17:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 10:17:59] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-17 10:17:59] [TRACE] [OmnipathR] Contains 1 files. [2024-10-17 10:17:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 10:17:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 10:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:17:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-17 10:18:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:00] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 10:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:00] [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 [2024-10-17 10:18:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 10:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:27] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-17 10:18:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 10:18:27] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-17 10:18:27] [TRACE] [OmnipathR] Contains 1 files. [2024-10-17 10:18:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 10:18:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 10:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-17 10:18:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 10:18:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 10:18:28] [TRACE] [OmnipathR] Cache locked: FALSE oma_organisms: no visible binding for global variable ‘ncbi_tax_id’ Undefined global functions or variables: ncbi_tax_id * 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 collectri 299.545 2.708 342.552 dorothea 160.893 1.748 209.019 annotation_categories 100.634 0.631 116.365 curated_ligrec_stats 55.831 2.207 122.655 filter_extra_attrs 52.115 0.308 62.238 extra_attr_values 29.808 0.540 59.486 nichenet_gr_network_omnipath 25.826 0.754 30.076 extra_attrs_to_cols 25.173 0.267 29.032 giant_component 21.428 0.604 42.179 with_extra_attrs 21.450 0.367 25.673 nichenet_signaling_network_omnipath 19.905 0.500 22.729 go_annot_download 16.806 1.403 25.119 pivot_annotations 16.121 1.447 22.039 extra_attrs 16.828 0.320 36.298 has_extra_attrs 16.026 0.195 18.667 filter_by_resource 13.542 0.305 16.008 print_interactions 12.791 0.399 16.702 find_all_paths 12.533 0.188 17.988 get_signed_ptms 12.315 0.155 22.636 pubmed_open 10.188 0.307 12.630 filter_intercell 9.523 0.889 20.234 omnipath 10.120 0.126 11.550 static_table 9.486 0.746 11.942 curated_ligand_receptor_interactions 9.540 0.453 18.401 resources_in 8.993 0.058 10.674 import_transcriptional_interactions 5.281 0.158 7.275 import_all_interactions 4.479 0.229 7.123 print_path_vs 4.405 0.109 7.136 enzsub_graph 4.109 0.142 10.530 annotated_network 2.890 0.254 6.904 get_complex_genes 2.198 0.128 5.661 ensembl_id_mapping_table 1.774 0.147 17.680 biomart_query 1.510 0.155 9.938 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.