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","29CC:2FB0B0:CA4ECA:E82DD4:697E0649"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 13:40:26 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13940-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769866826.961704,VS0,VE126"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","01bafc7e4ba8534140401ce92713ac7bb1164cfc"),("Expires","Sat, 31 Jan 2026 13:45:26 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 '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","29CC:2FB0B0:CA4ECA:E82DD4:697E0649"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 13:40:29 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13962-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769866830.863181,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","6b213f6756d8275af4b6027b271386fd27a05c13"),("Expires","Sat, 31 Jan 2026 13:45:29 GMT"),("Source-Age","4")], 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","29CC:2FB0B0:CA4ECA:E82DD4:697E0649"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 13:40:41 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13943-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769866841.133125,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","1335b8460d028ce119a1a13acb618a37246ad414"),("Expires","Sat, 31 Jan 2026 13:45:41 GMT"),("Source-Age","15")], 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","29CC:2FB0B0:CA4ECA:E82DD4:697E0649"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 13:41:23 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13933-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769866884.958405,VS0,VE2"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","d47d384ba8c4383d16acb3387e82363df8d0428a"),("Expires","Sat, 31 Jan 2026 13:46:23 GMT"),("Source-Age","58")], 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