############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.14.0’ * 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 [2025-02-04 09:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 09:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:31:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Contains 1 files. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 09:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:31:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-02-04 09:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-04 09:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-04 09:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-04 09:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:31:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-04 09:31:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:31:47] [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 [2025-02-04 09:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 09:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:32:06] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Contains 1 files. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-04 09:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:32:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-02-04 09:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-04 09:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-04 09:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-04 09:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:32:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.2/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-04 09:32:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-04 09:32:06] [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 101.003 0.044 109.526 curated_ligrec_stats 33.177 1.026 162.908 omnipath-interactions 30.485 1.314 71.206 filter_extra_attrs 25.511 0.143 53.130 go_annot_download 11.572 7.474 58.630 nichenet_gr_network_omnipath 13.792 0.327 15.861 extra_attr_values 13.623 0.138 17.150 extra_attrs_to_cols 11.784 0.072 12.916 giant_component 11.183 0.231 26.219 nichenet_signaling_network_omnipath 10.062 0.220 12.146 with_extra_attrs 9.739 0.210 11.873 pivot_annotations 9.469 0.238 22.155 omnipath_for_cosmos 8.988 0.110 53.713 extra_attrs 7.527 0.036 7.984 translate_ids_multi 7.349 0.123 29.391 has_extra_attrs 7.397 0.046 8.367 filter_by_resource 6.837 0.071 9.258 print_interactions 6.100 0.174 10.448 static_table 6.125 0.110 13.394 find_all_paths 6.004 0.120 6.429 curated_ligand_receptor_interactions 5.402 0.278 20.973 filter_intercell 5.381 0.123 13.028 signed_ptms 5.292 0.064 6.398 hpo_download 2.375 0.069 19.862 print_path_vs 2.279 0.071 5.783 ensembl_id_mapping_table 1.293 0.052 53.069 translate_ids 1.246 0.008 20.155 all_uniprots 0.851 0.061 23.213 annotated_network 0.856 0.045 5.105 uniprot_full_id_mapping_table 0.853 0.008 22.438 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.