############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocPkgTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocPkgTools_1.25.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocPkgTools.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘BiocPkgTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocPkgTools’ version ‘1.25.2’ * 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 ‘BiocPkgTools’ 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 dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocManager:::.repositories’ ‘BiocManager:::.repositories_base’ ‘BiocManager:::.repositories_bioc’ ‘BiocManager:::.repository_container_version’ ‘BiocManager:::.version_bioc’ See the note in ?`:::` about the use of this operator. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed biocBuildReport 13.292 83.242 121.953 get_bioc_data 13.654 1.403 34.864 firstInBioc 13.250 0.957 36.894 biocDownloadStats 12.248 0.765 27.315 pkgCombDependencyGain 10.611 1.349 20.391 class-dependencies 7.082 0.500 18.329 pkgDepMetrics 6.481 0.266 7.277 inducedSubgraphByPkgs 3.899 0.224 5.503 biocRevDepEmail 2.760 0.197 5.586 githubDetails 2.033 0.582 10.693 getBiocVignette 1.378 0.177 15.802 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Error ('test_biocBuildReport.R:18:5'): columns are consistent in report output ── Error in `bfcrpath(bfc, rnames = url, exact = TRUE, download = TRUE, rtype = "web")`: not all 'rnames' found or unique. Backtrace: ▆ 1. └─BiocPkgTools::biocBuildReport("3.14") at test_biocBuildReport.R:18:5 2. └─BiocPkgTools::biocBuildStatusDB(version, pkgType) 3. └─base::lapply(...) 4. └─BiocPkgTools (local) FUN(X[[i]], ...) 5. └─BiocPkgTools:::.cache_url_file(url) 6. ├─BiocFileCache::bfcrpath(...) 7. └─BiocFileCache::bfcrpath(...) [ FAIL 1 | WARN 3 | SKIP 0 | PASS 24 ] Error: Test failures Execution halted * 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, 2 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocPkgTools.Rcheck/00check.log’ for details.