############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunotation.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings immunotation_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/immunotation.Rcheck' * using R Under development (unstable) (2025-01-21 r87610 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'immunotation/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'immunotation' 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 'immunotation' can be installed ... OK * checking installed package size ... INFO installed size is 5.5Mb sub-directories of 1Mb or more: R 3.2Mb extdata 2.2Mb * 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_allele_frequency 2.24 0.34 277.55 query_haplotype_frequencies 0.56 0.05 146.61 * 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: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_4_AFND.R:148:5'): query_haplotype_frequencies() returns expected results ── Error in `getURL(url, read_method = "html")`: 'getURL()' failed: URL: http://www.allelefrequencies.net/hla6003a.asp?hla_locus1=A*02:01&hla_locus2=B*&hla_locus3=C*&hla_locus4=DRB1_not&hla_locus5=DPA1_not&hla_locus6=DPB1_not&hla_locus7=DQA1_not&hla_locus8=DQB1_not&hla_population=&hla_country=&hla_dataset=&hla_region=Europe&hla_ethnic=&hla_study=&hla_order=order_1&hla_sample_size_pattern=&hla_sample_size=&hla_sample_year_pattern=equal&hla_sample_year=&hla_loci= error: cannot open the connection Backtrace: ▆ 1. └─immunotation::query_haplotype_frequencies(...) at test_4_AFND.R:148:5 2. └─immunotation:::read_complete_freq_table(queryurl, type = "haplotype") 3. └─immunotation:::getURL(url, read_method = "html") [ FAIL 1 | WARN 5 | SKIP 0 | PASS 144 ] 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 See 'E:/biocbuild/bbs-3.21-bioc/meat/immunotation.Rcheck/00check.log' for details.