############################################################################## ############################################################################## ### ### 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_3.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OmnipathR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.8.2’ * 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 startup messages can be suppressed ... NOTE [2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Contains 1 files. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:20] [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 [2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:38] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Contains 1 files. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-18 12:27:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-18 12:27:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-18 12:27:39] [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 126.996 1.633 191.990 dorothea 65.328 0.829 99.681 annotation_categories 55.907 0.429 83.119 curated_ligrec_stats 25.131 2.155 106.646 filter_extra_attrs 18.667 0.173 29.602 nichenet_gr_network_omnipath 13.936 0.354 22.202 giant_component 11.579 0.300 19.537 extra_attr_values 11.073 0.256 18.451 pivot_annotations 10.242 0.782 20.367 extra_attrs_to_cols 10.024 0.084 15.435 go_annot_download 9.031 0.658 23.270 nichenet_signaling_network_omnipath 9.360 0.307 15.626 with_extra_attrs 8.840 0.196 14.814 has_extra_attrs 6.447 0.088 9.458 filter_by_resource 6.026 0.210 10.810 filter_intercell 5.773 0.418 13.784 extra_attrs 5.821 0.055 8.986 print_interactions 5.453 0.272 10.752 find_all_paths 5.489 0.111 8.575 get_signed_ptms 5.044 0.062 8.507 pubmed_open 4.653 0.195 8.365 curated_ligand_receptor_interactions 4.129 0.494 14.280 omnipath 3.838 0.032 5.846 database_summary 1.870 1.087 5.969 import_transcriptional_interactions 2.349 0.125 5.172 print_path_vs 2.086 0.108 5.449 biomart_query 1.391 0.158 6.208 ensembl_id_mapping_table 0.877 0.069 24.333 kegg_picture 0.185 0.089 8.123 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OmnipathR.Rcheck/00check.log’ for details.