* using log directory 'd:/Rcompile/CRANpkg/local/4.5/RNeXML.Rcheck'
* using R version 4.5.3 (2026-03-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'RNeXML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNeXML' version '2.4.11'
* 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 'RNeXML' 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 ... [2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s] OK
* checking loading without being on the library search path ... [2s] 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 ... [13s] OK
* checking Rd files ... [1s] NOTE
checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [21s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [63s] ERROR
  Running 'spelling.R' [0s]
  Running 'test-all.R' [63s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  Saving _problems/test_nexml_read-14.R
  Done simulation(s).
  [ FAIL 1 | WARN 1 | SKIP 46 | PASS 300 ]
  
  ══ Skipped tests (46) ══════════════════════════════════════════════════════════
  • On CRAN (42): 'test_02_summary.R:6:3', 'test_ape.R:7:3', 'test_ape.R:15:3',
    'test_ape.R:30:3', 'test_ape.R:49:3', 'test_ape.R:65:3', 'test_ape.R:83:3',
    'test_ape.R:95:3', 'test_ape.R:108:3', 'test_ape.R:119:3',
    'test_comp_analysis.R:7:3', 'test_comp_analysis.R:20:3',
    'test_global_ids.R:4:3', 'test_meta.R:9:3', 'test_meta.R:32:3',
    'test_meta.R:48:3', 'test_meta.R:59:3', 'test_meta.R:75:3',
    'test_meta.R:100:3', 'test_meta.R:121:3', 'test_meta.R:152:3',
    'test_meta.R:220:3', 'test_meta.R:246:3', 'test_meta.R:273:3',
    'test_meta.R:282:3', 'test_parsing.R:8:3', 'test_parsing.R:21:3',
    'test_parsing.R:54:3', 'test_parsing.R:74:3', 'test_serializing.R:9:3',
    'test_serializing.R:44:3', 'test_serializing.R:61:3', 'test_taxonomy.R:21:3',
    'test_taxonomy.R:50:3', 'test_taxonomy.R:61:3', 'test_toplevel_api.R:7:3',
    'test_toplevel_api.R:17:3', 'test_toplevel_api.R:33:3',
    'test_toplevel_api.R:57:3', 'test_validate.R:5:3', 'test_validate.R:12:3',
    'test_validate.R:30:3'
  • empty test (3): , ,
  • rootedge is not valid by XSD schema? (1): 'test_serializing.R:86:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_nexml_read.R:14:3'): we can read nexml from a url ──────────────
  <http_429/http_400/http_error/error/condition>
  Error in `nexml_read.character(url)`: Too Many Requests (RFC 6585) (HTTP 429).
  Backtrace:
      ▆
   1. ├─RNeXML::read.nexml(url) at test_nexml_read.R:14:3
   2. └─RNeXML:::nexml_read.character(url)
   3.   └─httr::stop_for_status(tmp)
  
  [ FAIL 1 | WARN 1 | SKIP 46 | PASS 300 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [13s] OK
* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [9s] OK
* DONE
Status: 1 ERROR, 1 NOTE