############################################################################## ############################################################################## ### ### 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_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * 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 ‘3.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 33 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 ‘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 [2025-01-31 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 21:59:52] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Contains 1 files. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 21:59:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-31 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-31 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-31 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-31 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-31 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 21:59:52] [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 [2025-01-31 22:00:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 22:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 22:00:09] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Contains 1 files. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 22:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 22:00:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-31 22:00:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-31 22:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 22:00:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-31 22:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 22:00:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-31 22:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 22:00:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-31 22:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 22:00:09] [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 60.154 0.159 61.803 curated_ligrec_stats 29.231 6.179 112.718 omnipath-interactions 26.711 1.257 58.799 filter_extra_attrs 17.369 0.094 18.059 nichenet_gr_network_omnipath 15.616 0.795 22.629 go_annot_download 12.540 1.017 24.211 nichenet_signaling_network_omnipath 12.471 0.568 19.398 extra_attrs_to_cols 11.975 0.233 12.291 with_extra_attrs 10.842 0.318 13.938 giant_component 10.580 0.553 17.362 pivot_annotations 10.126 0.903 19.864 extra_attr_values 10.256 0.218 13.150 omnipath_for_cosmos 7.618 0.362 23.294 filter_intercell 7.010 0.596 16.707 filter_by_resource 7.371 0.222 9.877 static_table 6.384 0.527 7.482 translate_ids_multi 5.891 0.217 23.290 extra_attrs 5.959 0.030 6.000 find_all_paths 5.518 0.249 10.094 print_interactions 5.479 0.225 9.648 has_extra_attrs 5.298 0.136 7.309 signed_ptms 4.791 0.035 5.430 curated_ligand_receptor_interactions 4.490 0.267 13.900 print_path_vs 2.146 0.143 5.054 database_summary 1.375 0.361 5.459 ensembl_id_mapping_table 1.242 0.479 14.639 uniprot_full_id_mapping_table 1.085 0.130 22.099 translate_ids 1.087 0.077 18.473 all_uniprots 0.812 0.092 22.464 * 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-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.