############################################################################## ############################################################################## ### ### 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_3.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.8.2’ * 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 R 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 startup messages can be suppressed ... NOTE [2023-10-16 04:48:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-16 04:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:48:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Contains 1 files. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-16 04:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:48:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-16 04:48:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-16 04:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:48:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-16 04:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:48:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-16 04:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:48:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-16 04:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:48:48] [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 [2023-10-16 04:49:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-16 04:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:49:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Contains 1 files. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-16 04:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:49:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-16 04:49:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-16 04:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:49:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-16 04:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:49:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-16 04:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:49:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-16 04:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-16 04:49:13] [TRACE] [OmnipathR] Cache locked: FALSE uniprot_idmapping_id_types: no visible binding for global variable ‘groups’ uniprot_idmapping_id_types: no visible binding for global variable ‘items’ Undefined global functions or variables: groups items * 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 224.589 3.008 296.566 dorothea 122.260 1.060 174.247 annotation_categories 101.585 0.482 129.382 curated_ligrec_stats 51.344 2.797 118.537 filter_extra_attrs 46.865 0.227 58.975 extra_attr_values 26.517 0.569 65.928 nichenet_gr_network_omnipath 24.735 0.686 33.098 extra_attrs_to_cols 23.543 0.266 44.411 giant_component 21.369 0.489 27.354 with_extra_attrs 20.435 0.361 28.916 pivot_annotations 17.120 1.478 25.369 nichenet_signaling_network_omnipath 17.914 0.537 23.880 extra_attrs 15.182 0.142 42.426 has_extra_attrs 15.198 0.102 19.779 go_annot_download 13.863 1.056 22.820 filter_by_resource 12.510 0.359 16.486 print_interactions 12.257 0.435 17.517 find_all_paths 12.123 0.190 15.007 get_signed_ptms 11.251 0.072 14.722 pubmed_open 9.798 0.340 13.112 filter_intercell 8.866 0.900 12.078 curated_ligand_receptor_interactions 8.318 0.651 17.236 omnipath 8.561 0.039 11.360 database_summary 3.744 3.103 9.492 import_transcriptional_interactions 4.922 0.186 7.344 print_path_vs 4.453 0.152 7.382 enzsub_graph 3.758 0.159 19.548 hpo_download 3.459 0.378 5.035 biomart_query 2.232 0.233 31.213 ensembl_id_mapping_table 1.461 0.127 25.262 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.