############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:hca.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings hca_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/hca.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 'hca/DESCRIPTION' ... OK * this is package 'hca' 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 'hca' 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 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 ... 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 ... ERROR Running examples in 'hca-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: bundles > ### Title: HCA Bundle Querying > ### Aliases: bundles bundles_facets bundles_default_columns bundles_detail > > ### ** Examples > > title <- paste( + "Tabula Muris: Transcriptomic characterization of 20 organs and", + "tissues from Mus musculus at single cell resolution" + ) > filters <- filters( projectTitle = list(is = title) ) Warning in open.connection(con, "rb") : cannot open URL 'https://service.azul.data.humancellatlas.org/openapi': HTTP status was '403 Forbidden' Error in open.connection(con, "rb") : cannot open the connection to 'https://service.azul.data.humancellatlas.org/openapi' Calls: filters ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection Execution halted * 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: 2. └─hca::filters() 3. └─hca:::.filters_validate(filters_list) 4. └─hca::facet_options() 5. └─hca:::.hca_openapi() 6. └─jsonlite::read_json(api) 7. └─jsonlite::parse_json(...) 8. └─jsonlite:::parse_and_simplify(...) 9. └─jsonlite:::parseJSON(txt, bigint_as_char) 10. └─jsonlite:::parse_con(txt, bigint_as_char) 11. ├─base::open(con, "rb") 12. └─base::open.connection(con, "rb") [ FAIL 12 | WARN 12 | SKIP 1 | PASS 119 ] 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: 2 ERRORs See 'E:/biocbuild/bbs-3.21-bioc/meat/hca.Rcheck/00check.log' for details.