############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbUniprot_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbUniprot.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'biodbUniprot/DESCRIPTION' ... OK * this is package 'biodbUniprot' version '1.15.0' * 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 'biodbUniprot' can be installed ... OK * checking installed package size ... OK * checking package 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 ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... OK * checking tests in 'longtests' ... Running 'testthat.R' ERROR Running the tests in 'longtests/testthat.R' failed. Last 13 lines of output: 2. └─biodbUniprot (local) ``(conn = ``) 3. └─conn$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:28:5 4. └─self$wsSearch(query, retfmt = "ids", size = limit) ── Error ('test_long_200_conversions.R:102:1'): We can convert gene symbols to UniProt IDs. ── Error in `self$wsSearch(query, retfmt = "ids", size = limit)`: object 'BiodbUrl' not found Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodbUniprot (local) ``(conn = ``) 3. └─conn$geneSymbolToUniprotIds(names(expected_ids), ignore.nonalphanum = TRUE) at test_long_200_conversions.R:42:5 4. └─self$wsSearch(query, retfmt = "ids", size = limit) [ FAIL 15 | WARN 0 | SKIP 0 | PASS 429 ] Error: Test failures Execution halted * DONE Status: 1 ERROR See 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbUniprot.Rcheck/00check.log' for details.