############################################################################## ############################################################################## ### ### 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 ‘/media/volume/teran2_disk/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 [2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:36] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Contains 1 files. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:36] [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 [2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:46] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Contains 1 files. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-20 06:56:46] [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 74.738 0.039 77.655 curated_ligrec_stats 20.172 0.398 82.500 omnipath-interactions 16.535 0.478 34.338 filter_extra_attrs 12.854 0.008 13.702 nichenet_gr_network_omnipath 7.587 0.105 13.457 extra_attr_values 7.141 0.159 13.200 translate_ids_multi 6.884 0.063 17.282 go_annot_download 6.326 0.578 7.308 extra_attrs_to_cols 6.448 0.006 6.500 pivot_annotations 5.682 0.352 22.004 with_extra_attrs 5.855 0.083 8.283 giant_component 5.851 0.076 7.108 omnipath_for_cosmos 5.230 0.109 14.264 nichenet_signaling_network_omnipath 5.230 0.046 6.374 static_table 3.961 0.124 10.219 filter_intercell 3.273 0.223 5.033 print_interactions 3.399 0.049 6.395 curated_ligand_receptor_interactions 3.152 0.088 11.518 uniprot_full_id_mapping_table 1.653 1.068 155.362 translate_ids 1.381 0.469 399.500 ensembl_id_mapping_table 0.723 0.026 9.855 all_uniprots 0.517 0.055 20.121 biomart_query 0.530 0.040 5.881 * 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 ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.