############################################################################## ############################################################################## ### ### 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_3.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/OmnipathR.Rcheck’ * using R version 4.3.2 (2023-10-31) * 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 Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.10.1’ * 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 [2024-03-06 21:45:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 21:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:17] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Contains 1 files. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 21:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-03-06 21:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-06 21:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-06 21:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-06 21:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-06 21:45:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:17] [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 [2024-03-06 21:45:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 21:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Contains 1 files. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 21:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-03-06 21:45:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-06 21:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-06 21:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-06 21:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-06 21:45:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 21:45:30] [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 105.094 0.172 105.715 collectri 81.322 0.626 82.015 dorothea 44.108 0.327 47.738 curated_ligrec_stats 26.135 1.188 42.526 filter_extra_attrs 18.361 0.082 18.573 nichenet_gr_network_omnipath 13.095 0.626 13.966 pivot_annotations 12.242 0.690 20.548 go_annot_download 10.202 0.474 10.392 giant_component 10.372 0.258 13.148 extra_attr_values 9.912 0.128 10.035 extra_attrs_to_cols 9.606 0.027 9.639 nichenet_signaling_network_omnipath 8.456 0.468 10.691 with_extra_attrs 8.427 0.126 8.667 static_table 6.695 0.291 6.946 extra_attrs 6.384 0.031 6.430 has_extra_attrs 5.949 0.092 6.041 filter_by_resource 5.819 0.109 6.017 filter_intercell 5.283 0.316 5.636 pubmed_open 4.777 0.161 5.013 curated_ligand_receptor_interactions 4.074 0.239 6.925 ensembl_id_mapping_table 0.925 0.077 13.818 * 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-3.18-bioc-mac-arm64/meat/OmnipathR.Rcheck/00check.log’ for details.