############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:fenr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings fenr_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/fenr.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘fenr/DESCRIPTION’ ... OK * this is package ‘fenr’ version ‘1.8.0’ * 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 ‘fenr’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 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 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 ... OK * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘fenr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: fetch_reactome > ### Title: Get functional term data from Reactome > ### Aliases: fetch_reactome > > ### ** Examples > > reactome_data <- fetch_reactome("Saccharomyces cerevisiae", on_error = "warn") Warning: download failed web resource path: ‘https://reactome.org/download/current/Ensembl2Reactome_PE_Pathway.txt’ local file path: ‘/Users/biocbuild/Library/Caches/org.R-project.R/R/fenr/10a0d671b8ae_Ensembl2Reactome_PE_Pathway.txt’ reason: Failed to perform HTTP request. Caused by error in `curl::curl_fetch_disk()`: ! Transferred a partial file [reactome.org]: transfer closed with outstanding read data remaining Warning: bfcadd() failed; resource removed rid: BFC8 fpath: ‘https://reactome.org/download/current/Ensembl2Reactome_PE_Pathway.txt’ reason: download failed Error in .util_download(x, rid[i], proxy, progress, config, "bfcadd()", : bfcadd() failed; see warnings() Calls: fetch_reactome ... cache_path -> -> -> .util_download Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed fetch_go 23.438 3.595 42.319 fetch_kegg 0.770 0.032 20.333 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * 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: 1 ERROR See ‘/Users/biocbuild/bbs-3.22-bioc/meat/fenr.Rcheck/00check.log’ for details.