* using log directory ‘/Users/ripley/R/packages/tests-devel/myTAI.Rcheck’
* using R Under development (unstable) (2025-11-06 r88990)
* using platform: aarch64-apple-darwin25.1.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.4.4.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.1
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘myTAI/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘myTAI’ version ‘2.3.3’
* 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 ‘myTAI’ can be installed ... [17s/19s] OK
* used C++ compiler: ‘Apple clang version 17.0.0 (clang-1700.4.4.1)’
* used SDK: ‘MacOSX26.1.sdk’
* checking installed package size ... INFO
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
* 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... OK
* 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 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [18s/18s]
 [18s/18s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [57s/65s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘myTAI.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘myTAI.Rmd’

--- re-building ‘other-strata.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘other-strata.Rmd’

--- re-building ‘phylo-expression-object.Rmd’ using rmarkdown
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phylo-expression-object.Rmd’

--- re-building ‘phylostratigraphy.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘phylostratigraphy.Rmd’

--- re-building ‘tai-breaker.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-breaker.Rmd’

--- re-building ‘tai-gallery.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-gallery.Rmd’

--- re-building ‘tai-stats.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-stats.Rmd’

--- re-building ‘tai-transform.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘tai-transform.Rmd’

--- re-building ‘taxonomy.Rmd’ using rmarkdown

Quitting from taxonomy.Rmd:218-222 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Could not connect to server [eutils.ncbi.nlm.nih.gov]:
Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 91 ms: Could not connect to server
---
Backtrace:
     ▆
  1. ├─global taxonomy(organism = "Arabidopsis thaliana", db = "ncbi", output = "taxid")
  2. │ ├─base::as.data.frame(...)
  3. │ ├─taxize::classification(taxize::get_uid(organism), db = "ncbi")
  4. │ └─taxize::get_uid(organism)
  5. │   └─taxize:::repeat_until_it_works(...)
  6. │     └─cli$get(sprintf("entrez/eutils/%s.fcgi", path), query = tc(query))
  7. │       └─private$make_request(rr, mock)
  8. │         └─crul:::crul_fetch(opts)
  9. │           └─curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
 10. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'taxonomy.Rmd' failed with diagnostics:
Could not connect to server [eutils.ncbi.nlm.nih.gov]:
Failed to connect to eutils.ncbi.nlm.nih.gov port 443 after 91 ms: Could not connect to server
--- failed re-building ‘taxonomy.Rmd’

SUMMARY: processing the following file failed:
  ‘taxonomy.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/myTAI.Rcheck/00check.log’
for details.

      147.42 real       122.24 user        14.30 sys