* using log directory ‘/srv/hornik/tmp/CRAN/taxonomizr.Rcheck’ * using R Under development (unstable) (2023-12-13 r85679) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘taxonomizr/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘taxonomizr’ version ‘0.10.5’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/5s] NOTE Maintainer: ‘Scott Sherrill-Mix ’ New maintainer: Scott Sherrill-Mix Old maintainer(s): Scott Sherrill-Mix * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘taxonomizr’ can be installed ... [2s/2s] OK * used C compiler: ‘Debian clang version 17.0.5 (1)’ * checking package directory ... OK * checking for future file timestamps ... 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 ... [0s/0s] OK * checking whether the package can be loaded with stated dependencies ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK * checking whether the namespace can be unloaded cleanly ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] OK * checking use of S3 registration ... 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 ... [3s/3s] OK * checking Rd files ... [0s/0s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [3s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [16s/16s] ERROR Running ‘testthat.R’ [16s/16s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(taxonomizr) > library(data.table) > library(RSQLite) > test_check("taxonomizr") Download status: 0 done; 1 in progress (0 b/s). Total size: 359 b (100%)... Download status: 1 done; 0 in progress. Total size: 359 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 359 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 359 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 359 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 359 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 4 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 0 b ... done! Download status: 1 done; 0 in progress. Total size: 0 b ... done! Download status: 1 done; 0 in progress. Total size: 359 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 15 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 15 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 15 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 15 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 15 b (100%)... done! Download status: 1 done; 0 in progress. Total size: 0 b ... done! Download status: 1 done; 0 in progress. Total size: 988 b (100%)... done! [ FAIL 2 | WARN 0 | SKIP 0 | PASS 372 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_taxa.R:692:3'): Test getAccession2taxid ────────────────────── `getAccession2taxid(...)` threw an error with unexpected message. Expected match: "missing|[Cc]ould ?n.t open" Actual message: "Download failed with error: \"URL rejected: Bad file:// URL\"." Backtrace: ▆ 1. ├─testthat::expect_error(...) at test_taxa.R:692:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─taxonomizr::getAccession2taxid(...) 7. └─base::mapply(...) 8. └─taxonomizr (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) 9. └─taxonomizr:::resumableDownload(xx, yy, resume = resume) ── Failure ('test_taxa.R:694:3'): Test getAccession2taxid ────────────────────── `getAccession2taxid(...)` threw an error with unexpected message. Expected match: "missing|[Cc]ould ?n.t open" Actual message: "Download failed with error: \"URL rejected: Bad file:// URL\"." Backtrace: ▆ 1. ├─testthat::expect_error(...) at test_taxa.R:694:3 2. │ └─testthat:::quasi_capture(...) 3. │ ├─testthat (local) .capture(...) 4. │ │ └─base::withCallingHandlers(...) 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 6. └─taxonomizr::getAccession2taxid(...) 7. └─base::mapply(...) 8. └─taxonomizr (local) ``(dots[[1L]][[1L]], dots[[2L]][[1L]]) 9. └─taxonomizr:::resumableDownload(xx, yy, resume = resume) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 372 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 1 NOTE