* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/metacoder.Rcheck’
* using R Under development (unstable) (2026-08-14 r90405)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-14 16:00:17 UTC
* checking for file ‘metacoder/DESCRIPTION’ ... OK
* this is package ‘metacoder’ version ‘0.3.9’
* 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 whether package ‘metacoder’ can be installed ... [26s/26s] OK
* used C++ compiler: ‘g++ (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)’
* 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
Found calls to structure() using deprecated special names:
  metacoder/tests/testthat/test--taxmap_parsers.R (.Names: 1)
'.Names' should be changed to 'names'.
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [21s/21s] OK
* checking examples with --run-donttest ... [220s/274s] ERROR
Running examples in ‘metacoder-Ex.R’ failed
The error most likely occurred in:

> ### Name: ncbi_taxon_sample
> ### Title: Download representative sequences for a taxon
> ### Aliases: ncbi_taxon_sample
> 
> ### ** Examples
> 
> ## No test: 
> if (requireNamespace("traits", quietly = TRUE)) {
+   # Look up 5 ITS sequences from each fungal class
+   data <- ncbi_taxon_sample(name = "Fungi", target_rank = "class", limit = 5, 
+                             entrez_query = '"internal transcribed spacer"[All Fields]')
+   
+   # Look up taxonomic information for sequences
+   obj <- lookup_tax_data(data, type = "seq_id", column = "gi_no")
+   
+   # Plot information
+   metacoder::filter_taxa(obj, taxon_names == "Fungi", subtaxa = TRUE) %>% 
+     heat_tree(node_label = taxon_names, node_color = n_obs, node_size = n_obs)
+ }
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
══  1 queries  ═══════════════

Retrieving data for taxon 'Fungi'

* Reusing existing https: connection with host eutils.ncbi.nlm.nih.gov
> GET /entrez/eutils/esearch.fcgi?db=taxonomy&term=Fungi HTTP/1.1
Host: eutils.ncbi.nlm.nih.gov
Accept-Encoding: gzip, deflate
Accept: application/json, text/xml, application/xml, */*
User-Agent: r-curl/7.1.0 crul/1.6.0 rOpenSci(taxize/0.10.1)
X-USER-AGENT: r-curl/7.1.0 crul/1.6.0 rOpenSci(taxize/0.10.1)

* Request completely sent off
< HTTP/1.1 200 OK
< Date: Fri, 14 Aug 2026 16:06:31 GMT
< Server: Finatra
< Strict-Transport-Security: max-age=31536000; includeSubDomains; preload
< Content-Security-Policy: upgrade-insecure-requests
< Referrer-Policy: origin-when-cross-origin
< Ncbi-Sid: 386722C122D65371_548DSID
< Ncbi-Phid: 1D34FE27E200211500005F04381C9B66.1.1.m_1
< Content-Type: text/xml; charset=UTF-8
< Cache-Control: private
< Content-Encoding: gzip
< X-Ratelimit-Limit: 3
< X-Ratelimit-Remaining: 2
< Access-Control-Allow-Origin: *
< Access-Control-Expose-Headers: X-RateLimit-Limit,X-RateLimit-Remaining
* Added cookie ncbi_sid="386722C122D65371_548DSID" for domain nih.gov, path /, expire 1818259592
< Set-Cookie: ncbi_sid=386722C122D65371_548DSID; domain=.nih.gov; path=/; expires=Sat, 14 Aug 2027 16:06:32 GMT
< X-Ua-Compatible: IE=Edge
< X-Xss-Protection: 1; mode=block
< Via: 1.1 google
< Alt-Svc: clear
< Transfer-Encoding: chunked
< 
* Connection #0 to host eutils.ncbi.nlm.nih.gov:443 left intact
✔  Found:  Fungi
══  Results  ═════════════════

• Total: 1 
• Found: 1 
• Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Processing 'Fungi' (uid: 4751, rank: kingdom)

No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Processing 'Dikarya' (uid: 451864, rank: subkingdom)

No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Processing 'Basidiomycota' (uid: 5204, rank: phylum)

No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Processing 'Wallemiomycotina' (uid: 2204096, rank: subphylum)

No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
Processing 'Geminibasidiomycetes' (uid: 1708517, rank: class)

Getting sequences for Geminibasidiomycetes

using sleep: 0
Working on 1708517...
...retrieving sequence IDs...
...retrieving available genes and their lengths...
Error: Too Many Requests (HTTP 429)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [25s/25s]
 [25s/25s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [10s/11s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/data/localhost/ripley/R/packages/tests-donttest/metacoder.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:27.53, 370.09 + 21.09