############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * 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 ‘3.14.0’ * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2025-01-21 00:32:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-21 00:32:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-21 00:32:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-21 00:32:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-21 00:32:28] [TRACE] [OmnipathR] Contains 1 files. [2025-01-21 00:32:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-21 00:32:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-21 00:32:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-21 00:32:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-21 00:32:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-21 00:32:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-21 00:32:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-21 00:32:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-21 00:32:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:29] [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 [2025-01-21 00:32:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-21 00:32:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:41] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-21 00:32:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-21 00:32:41] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-21 00:32:41] [TRACE] [OmnipathR] Contains 1 files. [2025-01-21 00:32:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-21 00:32:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-21 00:32:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-21 00:32:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-21 00:32:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-21 00:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-21 00:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-21 00:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-21 00:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-21 00:32:42] [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 128.549 0.142 199.919 curated_ligrec_stats 40.326 1.458 124.183 omnipath-interactions 20.979 0.693 67.002 filter_extra_attrs 15.345 0.099 16.219 go_annot_download 9.736 0.554 10.442 nichenet_gr_network_omnipath 10.080 0.147 12.396 pivot_annotations 9.197 0.715 32.460 extra_attr_values 9.246 0.183 15.017 giant_component 8.056 0.228 14.778 extra_attrs_to_cols 8.181 0.040 8.222 nichenet_signaling_network_omnipath 7.230 0.096 13.312 with_extra_attrs 7.059 0.208 9.885 omnipath_for_cosmos 6.805 0.374 25.882 translate_ids_multi 5.279 0.167 27.552 static_table 5.105 0.293 8.238 extra_attrs 5.177 0.097 5.274 filter_intercell 4.870 0.297 8.888 has_extra_attrs 5.060 0.034 5.095 print_interactions 4.798 0.142 11.092 curated_ligand_receptor_interactions 4.467 0.325 17.984 filter_by_resource 4.622 0.096 6.755 database_summary 2.444 0.032 5.596 ensembl_id_mapping_table 1.446 0.079 17.557 translate_ids 1.154 0.030 133.803 all_uniprots 1.000 0.106 469.732 uniprot_full_id_mapping_table 0.807 0.080 169.353 * 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 ...