############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomeInfoDb.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GenomeInfoDb_1.41.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GenomeInfoDb.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GenomeInfoDb/DESCRIPTION' ... OK * this is package 'GenomeInfoDb' version '1.41.1' * 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 whether package 'GenomeInfoDb' can be installed ... OK * checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: extdata 3.6Mb * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: 'utils:::.roman2numeric' 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed loadTaxonomyDb 12.22 0.11 12.36 GenomeDescription-class 9.02 0.50 9.58 seqinfo 4.99 0.36 5.42 seqlevels-wrappers 4.09 0.75 5.94 seqlevelsStyle 4.12 0.67 7.43 getChromInfoFromUCSC 2.75 1.87 6.16 getChromInfoFromEnsembl 0.73 0.19 31.29 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'run_unitTests.R' ERROR Running the tests in 'tests/run_unitTests.R' failed. Last 13 lines of output: 1 Test Suite : GenomeInfoDb RUnit Tests - 21 test functions, 1 error, 0 failures ERROR in test_seqlevelsStyle_Seqinfo: Error in download.file(url, destfile, quiet = TRUE) : download from 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/002/255/GCA_000002255.2_Mmul_051212/GCA_000002255.2_Mmul_051212_assembly_report.txt' failed Test files with failing tests test_seqlevelsStyle.R test_seqlevelsStyle_Seqinfo Error in BiocGenerics:::testPackage("GenomeInfoDb") : unit tests failed for package GenomeInfoDb Calls: -> 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 'F:/biocbuild/bbs-3.20-bioc/meat/GenomeInfoDb.Rcheck/00check.log' for details.