############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.14.0’ * 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 ‘wppi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 whether startup messages can be suppressed ... NOTE [2025-01-31 11:50:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 11:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:50:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Contains 1 files. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 11:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:50:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-31 11:50:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-31 11:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:50:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-31 11:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:50:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-31 11:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:50:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-31 11:50:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:50:26] [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 [2025-01-31 11:51:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 11:51:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:51:03] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Contains 1 files. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 11:51:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:51:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-31 11:51:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-31 11:51:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:51:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-31 11:51:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:51:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-31 11:51:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:51:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-31 11:51:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 11:51:03] [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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed wppi 69.911 0.594 71.428 score_candidate_genes_from_PPI 37.130 0.422 39.721 prioritization_genes 35.321 0.467 36.233 random_walk 35.310 0.356 37.054 weighted_adj 27.606 0.281 29.122 count_genes 17.103 1.821 17.289 filter_annot_with_network 15.399 0.297 15.761 common_neighbors 14.972 0.572 17.826 wppi_data 14.254 0.157 14.446 graph_from_op 9.163 0.071 9.282 in_omnipath 9.117 0.052 9.242 subgraph_op 8.960 0.038 9.271 wppi_omnipath_data 7.372 0.041 7.420 wppi_go_data 5.499 0.082 5.588 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log’ for details.