############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE [2023-10-15 23:26:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 23:26:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:34] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 23:26:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 23:26:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 23:26:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 23:26:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 23:26:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 23:26:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:34] [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 [2023-10-15 23:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 23:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 23:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 23:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 23:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 23:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 23:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 23:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 23:26:43] [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 92.628 0.712 96.414 dorothea 64.003 1.240 69.669 annotation_categories 65.140 0.072 66.715 curated_ligrec_stats 42.446 2.237 130.656 filter_extra_attrs 35.974 0.128 37.495 nichenet_gr_network_omnipath 21.242 0.755 42.666 pivot_annotations 17.466 1.331 40.047 giant_component 17.718 0.233 31.554 go_annot_download 14.326 1.976 18.580 extra_attrs_to_cols 16.090 0.075 16.614 nichenet_signaling_network_omnipath 15.523 0.287 27.795 extra_attr_values 12.661 0.423 18.438 has_extra_attrs 10.839 0.453 19.333 print_interactions 10.297 0.653 19.885 filter_by_resource 10.259 0.107 15.537 extra_attrs 10.098 0.175 10.281 filter_intercell 9.218 0.231 14.496 find_all_paths 8.666 0.070 9.321 curated_ligand_receptor_interactions 8.125 0.587 25.491 pubmed_open 7.635 0.452 10.225 with_extra_attrs 7.094 0.157 9.420 get_signed_ptms 6.665 0.011 7.371 omnipath 6.224 0.022 9.140 database_summary 2.350 2.065 7.214 import_transcriptional_interactions 2.526 1.783 12.811 intercell_consensus_filter 2.530 0.511 7.406 enzsub_graph 2.976 0.061 6.041 print_path_vs 2.564 0.140 5.963 import_tf_target_interactions 1.269 0.997 19.546 import_omnipath_enzsub 2.123 0.141 7.836 get_complex_genes 1.987 0.031 5.276 import_pathwayextra_interactions 1.764 0.192 7.349 import_mirnatarget_interactions 1.643 0.159 7.162 import_ligrecextra_interactions 1.354 0.115 5.535 omnipath_cache_load 1.352 0.101 6.644 ensembl_id_mapping_table 1.333 0.084 21.344 import_post_translational_interactions 1.108 0.283 6.604 biomart_query 1.197 0.064 10.677 import_omnipath_complexes 1.121 0.061 6.256 kegg_picture 0.343 0.065 6.981 * 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 ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.