Error(s) in re-building vignettes:
--- re-building ‘Generalized-RF.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘Generalized-RF.Rmd’

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

--- re-building ‘Using-TreeDist.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","B5F0:1FEB7E:1260E8:2368D9:697C8E0B"),("Accept-Ranges","bytes"),("Date","Fri, 30 Jan 2026 10:55:07 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630097-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769770508.812365,VS0,VE100"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","3c1484656dd84ea30a98fac15119604f03725b79"),("Expires","Fri, 30 Jan 2026 11:00:07 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘Using-TreeDist.Rmd’

--- re-building ‘compare-treesets.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","B5F0:1FEB7E:1260E8:2368D9:697C8E0B"),("Accept-Ranges","bytes"),("Date","Fri, 30 Jan 2026 10:55:17 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630021-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769770517.443117,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","6ff32f1ee495c0b7c8fbf0a7a40246b21c2cdcfb"),("Expires","Fri, 30 Jan 2026 11:00:17 GMT"),("Source-Age","10")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'compare-treesets.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘compare-treesets.Rmd’

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

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

--- re-building ‘landscapes.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","B5F0:1FEB7E:1260E8:2368D9:697C8E0B"),("Accept-Ranges","bytes"),("Date","Fri, 30 Jan 2026 10:55:47 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630067-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769770547.268280,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","5cccf2a20d2be3089062edb475fa1b7da668f8b9"),("Expires","Fri, 30 Jan 2026 11:00:47 GMT"),("Source-Age","39")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'landscapes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘landscapes.Rmd’

--- re-building ‘treespace.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
 (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","B5F0:1FEB7E:127071:238587:697C8E96"),("Accept-Ranges","bytes"),("Date","Fri, 30 Jan 2026 10:57:26 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630068-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769770647.720505,VS0,VE90"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ef00c3aedb8f22649eb274560c1ec5e57bfb013c"),("Expires","Fri, 30 Jan 2026 11:02:26 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
  proxySecureMode      = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'treespace.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘treespace.Rmd’

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

SUMMARY: processing the following files failed:
  ‘Using-TreeDist.Rmd’ ‘compare-treesets.Rmd’ ‘landscapes.Rmd’
  ‘treespace.Rmd’

Error: Vignette re-building failed.
Execution halted