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","C45E:3A2973:81648F:96FE26:697DB665"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 07:59:33 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13975-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769846374.642346,VS0,VE114"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","64433d781ce273e946660ef70ffe5f008e6ff183"),("Expires","Sat, 31 Jan 2026 08:04:33 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","C45E:3A2973:81648F:96FE26:697DB665"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 07:59:38 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13923-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769846379.849416,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","2588675f6cb31ef7faa39f4238a9243b1f15e70f"),("Expires","Sat, 31 Jan 2026 08:04:38 GMT"),("Source-Age","5")], 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","C45E:3A2973:81648F:96FE26:697DB665"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 07:59:54 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13925-MUC"),("X-Cache","HIT"),("X-Cache-Hits","2"),("X-Timer","S1769846395.807552,VS0,VE0"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","a3ff457d66a926c192111ec27cbed1f2a33b0749"),("Expires","Sat, 31 Jan 2026 08:04:54 GMT"),("Source-Age","21")], 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","4668:100BA1:87985E:9D3A4D:697DB6B8"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 08:00:57 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13974-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769846457.195491,VS0,VE113"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","60c6d7d21d00e758e0413f615cf5ce6c0074ab98"),("Expires","Sat, 31 Jan 2026 08:05:57 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