* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/taxonomizr.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc-14 (Debian 14.2.0-16) 14.2.0
GNU Fortran (Debian 14.2.0-16) 14.2.0
* 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 ‘0.10.8’
* 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 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 ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/taxonomizr-00install.html' for details.
* used C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’
* 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 code 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 ... [4s/6s] 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 ... [26s/44s] ERROR
Running ‘testthat.R’ [26s/43s]
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: 0 done; 1 in progress (0 b/s). Total size: 0 b (??%)...
Download status: 1 done; 0 in progress. Total size: 0 b ... done!
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 378 ]
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Failure ('test_taxa.R:987:3'): Test resumableDownload ───────────────────────
`resumableDownload(...)` threw an error with unexpected message.
Expected match: "404"
Actual message: "Download failed with error: \"Timeout was reached [ftp.ncbi.nih.gov]: Resolving timed out after 10000 milliseconds\"."
Backtrace:
â–†
1. ├─testthat::expect_error(...) at test_taxa.R:987:3
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:::resumableDownload(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 378 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/4s] OK
* checking PDF version of manual ... [4s/6s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR