############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.4.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/OmnipathR.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.4.7’ * 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 ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘rmarkdown’ A package should be listed in only one of these fields. * 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 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 [2022-10-19 05:42:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2022-10-19 05:42:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-10-19 05:42:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2022-10-19 05:42:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2022-10-19 05:42:32] [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 nichenet_lr_network 301.704 2.273 309.849 nichenet_networks 128.502 1.469 133.645 filter_intercell_network 103.226 1.236 140.695 simplify_intercell_network 99.695 0.726 105.774 evex_download 95.155 1.391 114.866 unique_intercell_network 92.271 0.418 92.784 nichenet_gr_network_evex 87.728 1.016 88.469 nichenet_lr_network_omnipath 74.516 0.912 84.628 nichenet_signaling_network 66.513 2.758 73.182 annotation_categories 47.407 0.151 50.827 bioplex_all 43.199 1.504 46.481 curated_ligrec_stats 38.826 1.531 130.088 consensuspathdb_raw_table 34.060 1.932 38.476 pivot_annotations 21.115 1.559 26.596 go_annot_download 19.649 1.534 19.073 filter_extra_attrs 19.730 0.134 24.602 extra_attr_values 16.056 0.277 30.365 ancestors 14.217 1.197 16.287 nichenet_gr_network_pathwaycommons 13.429 0.867 14.932 nichenet_signaling_network_evex 13.356 0.656 13.369 preppi_download 11.783 1.939 22.095 hpo_download 12.742 0.794 14.273 nichenet_gr_network_omnipath 11.562 0.980 14.062 pathwaycommons_download 11.549 0.787 13.060 preppi_filter 10.838 1.167 7.669 with_extra_attrs 11.335 0.200 13.629 nichenet_signaling_network_omnipath 11.082 0.379 11.499 extra_attrs_to_cols 10.723 0.084 10.822 filter_intercell 10.013 0.735 16.458 nichenet_gr_network 10.198 0.483 15.680 extra_attrs 10.032 0.126 15.851 curated_ligand_receptor_interactions 8.723 0.412 21.037 bioplex1 8.114 0.475 9.451 import_intercell_network 8.301 0.267 13.853 has_extra_attrs 8.289 0.025 8.321 giant_component 7.321 0.209 12.561 kegg_info 6.580 0.401 10.191 get_db 6.454 0.384 6.941 ramilowski_download 5.781 0.684 9.449 obo_parser 5.896 0.390 6.357 nichenet_gr_network_harmonizome 5.577 0.403 6.585 bioplex3 4.606 0.348 7.540 kegg_pathway_download 4.368 0.146 17.534 filter_by_resource 4.178 0.168 6.409 print_interactions 3.897 0.212 8.399 guide2pharma_download 3.542 0.220 6.140 htridb_download 3.389 0.186 5.843 pubmed_open 3.239 0.183 5.442 nichenet_gr_network_trrust 3.067 0.071 6.755 print_path_vs 2.695 0.080 5.866 enzsub_graph 2.554 0.096 6.167 all_uniprots 2.247 0.054 236.152 import_dorothea_interactions 2.193 0.103 6.152 import_transcriptional_interactions 2.172 0.096 6.112 uniprot_full_id_mapping_table 2.081 0.101 14.158 import_all_interactions 1.843 0.110 6.933 translate_ids 1.643 0.126 13.408 uniprot_id_mapping_table 0.702 0.017 6.099 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’