Last updated on 2026-01-30 07:49:01 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.11.1 | 68.33 | 203.10 | 271.43 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.11.1 | 46.70 | 143.36 | 190.06 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.11.1 | 152.00 | 342.55 | 494.55 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 2.11.1 | 144.00 | 348.82 | 492.82 | ERROR | |
| r-devel-windows-x86_64 | 2.11.1 | 82.00 | 240.00 | 322.00 | OK | |
| r-patched-linux-x86_64 | 2.11.1 | 69.35 | 188.08 | 257.43 | ERROR | |
| r-release-linux-x86_64 | 2.11.1 | 65.47 | 192.11 | 257.58 | OK | |
| r-release-macos-arm64 | 2.11.1 | OK | ||||
| r-release-macos-x86_64 | 2.11.1 | 42.00 | 244.00 | 286.00 | OK | |
| r-release-windows-x86_64 | 2.11.1 | 81.00 | 231.00 | 312.00 | OK | |
| r-oldrel-macos-arm64 | 2.11.1 | NOTE | ||||
| r-oldrel-macos-x86_64 | 2.11.1 | 41.00 | 241.00 | 282.00 | NOTE | |
| r-oldrel-windows-x86_64 | 2.11.1 | 99.00 | 304.00 | 403.00 | NOTE |
Version: 2.11.1
Check: relative paths in package URLs
Result: NOTE
Found the following (possibly) invalid URL:
URL: ../reference/index.html
From: inst/doc/using-distances.html
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
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","9A04:FB156:89FE83:97C6F1:6977C952"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:06:42 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13975-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769458003.806477,VS0,VE127"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","9156e767509f7d3ea73832a90937b57cee31384b"),("Expires","Mon, 26 Jan 2026 20:11:42 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","9A04:FB156:89FE83:97C6F1:6977C952"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:06:47 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13972-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769458008.809060,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","5b7945d36c08e375ea1c73731588a76e167225ea"),("Expires","Mon, 26 Jan 2026 20:11:47 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","9A04:FB156:89FE83:97C6F1:6977C952"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:07:02 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13953-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769458022.481910,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","6e58ebfdc7a451c5ef6f4fc802ebd668b70ffb08"),("Expires","Mon, 26 Jan 2026 20:12:02 GMT"),("Source-Age","20")], 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","CD80:1D80A5:8C78E1:9A4CAA:6977C9A4"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:08:04 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13982-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769458085.710527,VS0,VE114"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","83f66b2c27f68e1e77c6f50e2f803f4f493c218c"),("Expires","Mon, 26 Jan 2026 20:13:04 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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
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","56FE:2F8C5C:29403D:2D65D6:697B62F1"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 13:38:58 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13924-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769693938.906829,VS0,VE125"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","60abafdedb5c1b9e4703cf3f2978d812955352aa"),("Expires","Thu, 29 Jan 2026 13:43:58 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","56FE:2F8C5C:29403D:2D65D6:697B62F1"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 13:39:02 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13941-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769693942.439281,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","55711a358e85a879697a8732d657fc61888b2552"),("Expires","Thu, 29 Jan 2026 13:44:02 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","56FE:2F8C5C:29403D:2D65D6:697B62F1"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 13:39:13 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13946-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769693954.822543,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","4d1ce69dd4d6d70218eae1ea447ee065d03216cb"),("Expires","Thu, 29 Jan 2026 13:44:13 GMT"),("Source-Age","16")], 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","56FE:2F8C5C:29403D:2D65D6:697B62F1"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 13:39:55 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13952-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769693996.788652,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","53eb2777eec5652bf88f90466dc7ee423b40c86e"),("Expires","Thu, 29 Jan 2026 13:44:55 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
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
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","2957:20DD02:740B0:C6B92:697B9D9B"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:49:17 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630096-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769708958.705838,VS0,VE91"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","62ac878e885f75d427fb023703597364b1a20c3e"),("Expires","Thu, 29 Jan 2026 17:54:17 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","2957:20DD02:740B0:C6B92:697B9D9B"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:49:43 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630026-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769708983.048498,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","99b8c1e0cf9650e9bc44cc4673b7c7f7774dec2b"),("Expires","Thu, 29 Jan 2026 17:54:43 GMT"),("Source-Age","25")], 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","2957:20DD02:74CAA:C8099:697B9DFC"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:50:53 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630033-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769709053.973155,VS0,VE97"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","8cc6dcdb86562e1e5bd2f9fbe6fd4a54478f67d9"),("Expires","Thu, 29 Jan 2026 17:55:53 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 '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","E5EA:159863:7A099:CF856:697B9F62"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:56:51 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630037-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769709411.966698,VS0,VE92"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","797c676184809351e8e910568feba6531fe42c74"),("Expires","Thu, 29 Jan 2026 18:01:51 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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
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","70EE:D5822:75021:C2C3D:697B9A45"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:35:01 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630095-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769708102.846850,VS0,VE109"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","c205f77639c2aece0347af9cd26b3388559c9df1"),("Expires","Thu, 29 Jan 2026 17:40:01 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","70EE:D5822:75021:C2C3D:697B9A45"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:35:28 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630025-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769708128.074450,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","b1331d4fdb1e65c81cdaebb17c7d56d476f9fc80"),("Expires","Thu, 29 Jan 2026 17:40:28 GMT"),("Source-Age","26")], 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","B1B4:217638:729BA:C0F7A:697B9AAF"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:36:48 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630067-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769708208.443911,VS0,VE93"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","7f5ea60bfaea35657907e1de97cec9f7f2659f21"),("Expires","Thu, 29 Jan 2026 17:41:48 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 '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","2957:20DD02:70DB6:C1315:697B9C11"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 17:42:41 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630051-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769708562.525920,VS0,VE104"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","11327acb8da81642e06254201bfb6bc9f0eea317"),("Expires","Thu, 29 Jan 2026 17:47:41 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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR
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","376A:24FD08:4F1DAC:5D5412:6979C47A"),("Accept-Ranges","bytes"),("Date","Wed, 28 Jan 2026 08:10:34 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13978-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769587835.529382,VS0,VE117"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","16900780ece33bd503d6d4658151e44d929a7c83"),("Expires","Wed, 28 Jan 2026 08:15:34 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","376A:24FD08:4F1DAC:5D5412:6979C47A"),("Accept-Ranges","bytes"),("Date","Wed, 28 Jan 2026 08:10:39 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13958-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769587839.098343,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ab19be1a22a6e6fb3030738f6c12820c3665d8a2"),("Expires","Wed, 28 Jan 2026 08:15:39 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","376A:24FD08:4F1DAC:5D5412:6979C47A"),("Accept-Ranges","bytes"),("Date","Wed, 28 Jan 2026 08:10:54 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13968-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769587855.677849,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","81754f5ba1b473cbfd03d093810ce0893ea53c8a"),("Expires","Wed, 28 Jan 2026 08:15:54 GMT"),("Source-Age","20")], 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","CA6A:364B60:4F5DF6:5D9BD9:6979C4C5"),("Accept-Ranges","bytes"),("Date","Wed, 28 Jan 2026 08:11:51 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13927-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769587911.321315,VS0,VE134"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","937d23a38db9509826665f4a151c866788adc322"),("Expires","Wed, 28 Jan 2026 08:16:51 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
Flavor: r-patched-linux-x86_64
Version: 2.11.1
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘TreeDistData’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 2.11.1
Check: installed package size
Result: NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
doc 1.2Mb
libs 4.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64