Last updated on 2026-02-12 12:51:28 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.11.1 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 2.11.1 | 47.52 | 137.35 | 184.87 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.11.1 | 104.00 | 3.35 | 107.35 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 2.11.1 | 97.00 | 3.69 | 100.69 | ERROR | |
| r-devel-macos-arm64 | 2.11.1 | 15.00 | 46.00 | 61.00 | OK | |
| r-devel-windows-x86_64 | 2.11.1 | 84.00 | 230.00 | 314.00 | ERROR | |
| r-patched-linux-x86_64 | 2.11.1 | 68.84 | 186.40 | 255.24 | ERROR | |
| r-release-linux-x86_64 | 2.11.1 | 69.36 | 186.95 | 256.31 | ERROR | |
| 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 | 98.00 | 304.00 | 402.00 | ERROR |
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","4372:5EA59:3734A8F:3D9B7E1:698A4216"),("Accept-Ranges","bytes"),("Date","Mon, 09 Feb 2026 20:22:47 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13935-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770668567.990324,VS0,VE127"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","cc23550db3ba8ee5881e9c677318a8f8a4bdcfcf"),("Expires","Mon, 09 Feb 2026 20:27:47 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","4372:5EA59:3734A8F:3D9B7E1:698A4216"),("Accept-Ranges","bytes"),("Date","Mon, 09 Feb 2026 20:22:52 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13982-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770668573.702157,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","e684ec763b6f0a5365bde12328365f1b345bf6fd"),("Expires","Mon, 09 Feb 2026 20:27:52 GMT"),("Source-Age","6")], 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","4372:5EA59:3734A8F:3D9B7E1:698A4216"),("Accept-Ranges","bytes"),("Date","Mon, 09 Feb 2026 20:23:08 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13946-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770668588.267055,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","8277ac01826889ba5e765d90d785f97adf089e0b"),("Expires","Mon, 09 Feb 2026 20:28:08 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","9E3C:2A4250:3814620:3E7BF88:698A426F"),("Accept-Ranges","bytes"),("Date","Mon, 09 Feb 2026 20:24:15 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13930-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770668656.799447,VS0,VE117"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","8a70577885ce857759ba18cfb87f40efdab47f50"),("Expires","Mon, 09 Feb 2026 20:29:15 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","46A2:13C4:150813B:16E5BBB:698C87A1"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 13:44:02 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13957-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770817443.552377,VS0,VE128"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","5ebab4719fbdb3cff19454b0a9ad457153e12a06"),("Expires","Wed, 11 Feb 2026 13:49:02 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","46A2:13C4:150813B:16E5BBB:698C87A1"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 13:44:06 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13954-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770817446.082824,VS0,VE11"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","8b90c2a109f03895defc47d4c9371e4f8c4097ba"),("Expires","Wed, 11 Feb 2026 13:49:06 GMT"),("Source-Age","3")], 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","46A2:13C4:150813B:16E5BBB:698C87A1"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 13:44:16 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13920-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770817456.434969,VS0,VE2"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","9fab27e6aa00c7340e71f14942b342cdc4af2b5a"),("Expires","Wed, 11 Feb 2026 13:49:16 GMT"),("Source-Age","14")], 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","46A2:13C4:150813B:16E5BBB:698C87A1"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 13:44:52 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13940-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770817493.668500,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","0f0612625a745559c23571b2a7a377008b749599"),("Expires","Wed, 11 Feb 2026 13:49:52 GMT"),("Source-Age","50")], 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: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-linux-x86_64-fedora-clang, 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
--- finished re-building 'Generalized-RF.Rmd'
--- re-building 'Robinson-Foulds.Rmd' using rmarkdown
--- finished re-building 'Robinson-Foulds.Rmd'
--- re-building 'Using-TreeDist.Rmd' using rmarkdown
CiteprocXMLError: 1:1 (0)-1:15 (14): Found content after root element: EventContent (ContentText "404: Not Found")
Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 4
--- failed re-building 'Using-TreeDist.Rmd'
--- re-building 'compare-treesets.Rmd' using rmarkdown
CiteprocXMLError: 1:1 (0)-1:15 (14): Found content after root element: EventContent (ContentText "404: Not Found")
Error: processing vignette 'compare-treesets.Rmd' failed with diagnostics:
pandoc document conversion failed with error 4
--- failed re-building 'compare-treesets.Rmd'
--- re-building 'different-leaves.Rmd' using rmarkdown
--- finished re-building 'different-leaves.Rmd'
--- re-building 'information.Rmd' using rmarkdown
--- finished re-building 'information.Rmd'
--- re-building 'landscapes.Rmd' using rmarkdown
CiteprocXMLError: 1:1 (0)-1:15 (14): Found content after root element: EventContent (ContentText "404: Not Found")
Error: processing vignette 'landscapes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 4
--- failed re-building 'landscapes.Rmd'
--- re-building 'treespace.Rmd' using rmarkdown
CiteprocXMLError: 1:1 (0)-1:15 (14): Found content after root element: EventContent (ContentText "404: Not Found")
Error: processing vignette 'treespace.Rmd' failed with diagnostics:
pandoc document conversion failed with error 4
--- failed re-building 'treespace.Rmd'
--- re-building 'using-distances.Rmd' using rmarkdown
--- 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
Flavors: r-devel-windows-x86_64, r-oldrel-windows-x86_64
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","3BE0:30899F:1CC1B6A:1F8B377:698C39EF"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 08:12:32 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13926-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770797552.305021,VS0,VE133"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ad975acefe5181fccdb8e102ac21930385a41881"),("Expires","Wed, 11 Feb 2026 08:17:32 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","3BE0:30899F:1CC1B6A:1F8B377:698C39EF"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 08:12:36 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13925-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770797556.187518,VS0,VE0"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","0c6c6fd4249add827404b2fee79712c870d76ba2"),("Expires","Wed, 11 Feb 2026 08:17:36 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","3BE0:30899F:1CC1B6A:1F8B377:698C39EF"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 08:12:51 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13948-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770797571.316399,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","a00360951585fa41d1ff0bd38b74d3c3f916c90a"),("Expires","Wed, 11 Feb 2026 08:17:51 GMT"),("Source-Age","19")], 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","5218:1E442E:1D05B79:1FCF90C:698C3A39"),("Accept-Ranges","bytes"),("Date","Wed, 11 Feb 2026 08:13:45 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13944-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770797626.695095,VS0,VE113"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","b6803171ba5cde4693fc67edbbfa966298c1f7fc"),("Expires","Wed, 11 Feb 2026 08:18:45 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: 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","F3FC:982AD:5ED8EB:6DC6DC:6986F18B"),("Accept-Ranges","bytes"),("Date","Sat, 07 Feb 2026 08:02:19 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13937-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770451340.760304,VS0,VE117"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","213384d30a2bab0777ba51dc92e93d8093c5d940"),("Expires","Sat, 07 Feb 2026 08:07:19 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","F3FC:982AD:5ED8EB:6DC6DC:6986F18B"),("Accept-Ranges","bytes"),("Date","Sat, 07 Feb 2026 08:02:25 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13935-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770451345.381521,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","d2dfb108dca9580a693214f5c713f3874b9e063e"),("Expires","Sat, 07 Feb 2026 08:07:25 GMT"),("Source-Age","6")], 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","F3FC:982AD:5ED8EB:6DC6DC:6986F18B"),("Accept-Ranges","bytes"),("Date","Sat, 07 Feb 2026 08:02:39 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13979-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770451359.452008,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ff009cac885ee88eba8d871c7190ea33fea8055d"),("Expires","Sat, 07 Feb 2026 08:07:39 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","7766:1BEBC8:5BF88D:6AB1A4:6986F1E1"),("Accept-Ranges","bytes"),("Date","Sat, 07 Feb 2026 08:03:45 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13945-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770451426.760625,VS0,VE115"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","31eb7a4465ee3b383b6dba9b7824489a6b7ae187"),("Expires","Sat, 07 Feb 2026 08:08:45 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-release-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