############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:50:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Contains 1 files. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:50:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:50:55] [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 [2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:51:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Contains 1 files. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:51:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-01 00:51:08] [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 76.763 0.142 78.477 omnipath-interactions 41.513 2.018 83.369 curated_ligrec_stats 30.491 1.378 105.566 with_extra_attrs 23.832 0.519 40.698 filter_extra_attrs 15.665 0.087 16.530 nichenet_gr_network_omnipath 13.784 0.225 16.241 omnipath_for_cosmos 13.643 0.366 40.199 pivot_annotations 12.739 0.627 25.339 translate_ids_multi 12.257 0.226 38.545 extra_attr_values 10.696 0.522 14.155 nichenet_signaling_network_omnipath 11.059 0.078 13.810 extra_attrs_to_cols 10.478 0.100 10.579 go_annot_download 9.895 0.489 10.659 static_table 9.825 0.360 19.947 print_interactions 9.662 0.159 17.258 giant_component 8.483 0.168 11.363 signed_ptms 7.351 0.107 9.304 omnipath_query 6.806 0.019 7.881 filter_by_resource 6.400 0.226 8.896 pubmed_open 5.737 0.159 5.907 has_extra_attrs 5.479 0.016 5.496 filter_intercell 4.904 0.279 9.191 extra_attrs 5.046 0.076 5.123 resources_in 4.931 0.058 5.204 curated_ligand_receptor_interactions 4.579 0.377 15.218 print_path_vs 3.789 0.183 6.891 translate_ids 3.377 0.110 21.495 uniprot_full_id_mapping_table 1.548 0.142 23.849 ensembl_id_mapping_table 1.140 0.078 18.274 all_uniprots 0.930 0.066 20.645 biomart_query 0.885 0.107 6.184 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.