############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biomaRt.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings biomaRt_2.55.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/biomaRt.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'biomaRt/DESCRIPTION' ... OK * this is package 'biomaRt' version '2.55.0' * 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 whether package 'biomaRt' 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 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 ... NOTE Unexported object imported by a ':::' call: 'AnnotationDbi:::smartKeys' 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 ... NOTE checkRd: (-1) getBM.Rd:16: Escaped LaTeX specials: \_ checkRd: (-1) getGene.Rd:9: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ * 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 * 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: 1. └─biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl") at test_useMart.R:8:2 2. └─biomaRt:::.useMart(...) 3. └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose) 4. └─biomaRt:::.getAttributes(mart, verbose = verbose) 5. └─biomaRt:::.getAttrFilt(mart = mart, verbose = verbose, type = "attributes") 6. └─biomaRt:::bmRequest(...) 7. └─httr::GET(...) 8. └─httr:::request_perform(req, hu$handle$handle) 9. ├─httr:::request_fetch(req$output, req$url, handle) 10. └─httr:::request_fetch.write_memory(req$output, req$url, handle) 11. └─curl::curl_fetch_memory(url, handle = handle) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 147 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... 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-3.17-bioc-rtools43/meat/biomaRt.Rcheck/00check.log' for details.