- using R Under development (unstable) (2024-04-14 r86421)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-13) 13.2.0
GNU Fortran (Debian 13.2.0-13) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- 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 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 ‘RNeXML’ can be installed ... OK
See the install log for details.
- 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 ... [2s/3s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
- checking whether the package can be unloaded cleanly ... [2s/3s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/3s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/4s] OK
- checking loading without being on the library search path ... [2s/4s] 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 ... [16s/29s] OK
- checking Rd files ... [1s/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 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [14s/21s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simmap_to_nexml 3.556 0.05 5.317
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [49s/86s] ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘test-all.R’ [48s/85s]
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
Done simulation(s).
[ FAIL 1 | WARN 1 | SKIP 43 | PASS 300 ]
══ Skipped tests (43) ══════════════════════════════════════════════════════════
• 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'
• 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 ──────────────
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [raw.githubusercontent.com] Resolving timed out after 10001 milliseconds
Backtrace:
▆
1. ├─RNeXML::read.nexml(url) at test_nexml_read.R:14:3
2. └─RNeXML:::nexml_read.character(url)
3. └─httr::GET(x)
4. └─httr:::request_perform(req, hu$handle$handle)
5. ├─httr:::request_fetch(req$output, req$url, handle)
6. └─httr:::request_fetch.write_memory(req$output, req$url, handle)
7. └─curl::curl_fetch_memory(url, handle = handle)
[ FAIL 1 | WARN 1 | SKIP 43 | PASS 300 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [8s/13s] OK
- checking PDF version of manual ... [6s/12s] OK
- checking HTML version of manual ... [1s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE