############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.8.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/decoupleR.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘decoupleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘decoupleR’ version ‘2.8.2’ * 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 ... NOTE Found the following hidden files and directories: .bumpversion.cfg These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘decoupleR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... WARNING Output(s) listed in 'build/vignette.rds' but not in package: ‘inst/doc/decoupleR.html’ ‘inst/doc/pw_bk.html’ ‘inst/doc/pw_sc.html’ ‘inst/doc/tf_bk.html’ ‘inst/doc/tf_sc.html’ * 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 dependencies in R code ... WARNING [2024-04-16 01:42:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-16 01:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-16 01:42:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Contains 8 files. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-16 01:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-16 01:42:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-04-16 01:42:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-16 01:42:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-16 01:42:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-16 01:42:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-16 01:42:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-16 01:42:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-16 01:42:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-16 01:42:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-16 01:42:37] [TRACE] [OmnipathR] Cache locked: FALSE '::' or ':::' import not declared from: ‘reshape2’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .ulm_analysis: no visible global function definition for ‘cor’ .ulm_analysis: no visible global function definition for ‘pt’ Undefined global functions or variables: cor pt Consider adding importFrom("stats", "cor", "pt") to your NAMESPACE file. * 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’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘decoupleR.Rmd’ ‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_dorothea 912.036 6.470 986.699 get_collectri 222.036 2.624 247.488 run_fgsea 26.957 0.359 28.447 run_aucell 15.780 1.059 24.036 get_progeny 10.346 0.789 13.321 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’