* using log directory ‘/Users/ripley/R/packages/tests-devel/rTARDIS.Rcheck’
* using R Under development (unstable) (2026-10-20 r90722)
* using platform: aarch64-apple-darwin27.0.0
* R was compiled by
    Apple clang version 21.0.0 (clang-2100.3.34.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Golden Gate 27.0.1
* using session charset: UTF-8
* current time: 2026-10-21 11:24:51 UTC
* using option ‘--no-stop-on-test-error’
* checking for file ‘rTARDIS/DESCRIPTION’ ... OK
* this is package ‘rTARDIS’ version ‘2.1.1’
* 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 ‘rTARDIS’ can be installed ... [15s/15s] OK
* checking installed package size ... INFO
  installed size is 20.7Mb
  sub-directories of 1Mb or more:
    doc      17.2Mb
    extdata   3.0Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [57s/57s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘building-landscapes.Rmd’ using rmarkdown

Quitting from building-landscapes.Rmd:121-131 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! TopologyException: unable to assign free hole to a shell at -91.414811999999998 -0.031089500000000433
---
Backtrace:
    ▆
 1. └─rTARDIS::domains(rst)
 2.   └─base::lapply(...)
 3.     └─rTARDIS (local) FUN(X[[i]], ...)
 4.       ├─terra::voronoi(x, bnd = x)
 5.       └─terra::voronoi(x, bnd = x)
 6.         └─terra (local) .local(x, ...)
 7.           └─x@pntr$voronoi(bnd@pntr, tolerance, as.lines)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'building-landscapes.Rmd' failed with diagnostics:
TopologyException: unable to assign free hole to a shell at -91.414811999999998 -0.031089500000000433
--- failed re-building ‘building-landscapes.Rmd’

--- re-building ‘geographic-distances-and-re-weighting.Rmd’ using rmarkdown

Quitting from geographic-distances-and-re-weighting.Rmd:92-109 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! TopologyException: unable to assign free hole to a shell at -91.414811999999998 -0.031089500000000433
---
Backtrace:
    ▆
 1. └─rTARDIS::link_islands(rst, klink = 1)
 2.   ├─terra::voronoi(poly, bnd = poly)
 3.   └─terra::voronoi(poly, bnd = poly)
 4.     └─terra (local) .local(x, ...)
 5.       └─x@pntr$voronoi(bnd@pntr, tolerance, as.lines)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'geographic-distances-and-re-weighting.Rmd' failed with diagnostics:
TopologyException: unable to assign free hole to a shell at -91.414811999999998 -0.031089500000000433
--- failed re-building ‘geographic-distances-and-re-weighting.Rmd’

--- re-building ‘package-overview.Rmd’ using rmarkdown

Quitting from package-overview.Rmd:109-113 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! TopologyException: unable to assign free hole to a shell at -89.324812000000009 -0.49108950000000046
---
Backtrace:
    ▆
 1. └─rTARDIS::link_islands(rasts, klink = 1)
 2.   ├─terra::voronoi(poly, bnd = poly)
 3.   └─terra::voronoi(poly, bnd = poly)
 4.     └─terra (local) .local(x, ...)
 5.       └─x@pntr$voronoi(bnd@pntr, tolerance, as.lines)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'package-overview.Rmd' failed with diagnostics:
TopologyException: unable to assign free hole to a shell at -89.324812000000009 -0.49108950000000046
--- failed re-building ‘package-overview.Rmd’

--- re-building ‘palaeogeography-quick-guide.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘palaeogeography-quick-guide.Rmd’

SUMMARY: processing the following files failed:
  ‘building-landscapes.Rmd’ ‘geographic-distances-and-re-weighting.Rmd’
  ‘package-overview.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/rTARDIS.Rcheck/00check.log’
for details.

      172.83 real       158.59 user        13.21 sys