Last updated on 2026-02-06 11:51:44 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CongreveLamsdell2016 | 13 | ||
| PlotTools | 13 | ||
| Quartet | 13 | ||
| Rogue | 13 | ||
| TBRDist | 13 | ||
| Ternary | 3 | 10 | |
| TotalCopheneticIndex | 2 | 11 | |
| TreeDist | 8 | 2 | 3 |
| TreeSearch | 3 | 10 | |
| TreeTools | 2 | 11 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: NOTE: 3, OK: 10
Version: 2.3.6
Check: installed package size
Result: NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 5.4Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 2, OK: 11
Version: 2.0.1
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Martin R. Smith <martin.smith@durham.ac.uk>’
Package CITATION file contains call(s) to old-style personList() or
as.personList(). Please use c() on person objects instead.
Package CITATION file contains call(s) to old-style citEntry(). Please
use bibentry() instead.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 8, NOTE: 2, OK: 3
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","CB6E:19B084:7B54D:8672D:6984F8C5"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 20:08:37 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13962-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770322118.751370,VS0,VE127"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","e060da48dd26f73f97a8d8ebbd9d937c9eda64a3"),("Expires","Thu, 05 Feb 2026 20:13:37 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","CB6E:19B084:7B54D:8672D:6984F8C5"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 20:08:43 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13923-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770322123.049267,VS0,VE2"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","c73c12dc0e701cbc2f0dd4aabd92406887b68726"),("Expires","Thu, 05 Feb 2026 20:13:43 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","CB6E:19B084:7B54D:8672D:6984F8C5"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 20:08:57 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13974-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770322137.314514,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","851955d2c9854698889feb3df741a29210476320"),("Expires","Thu, 05 Feb 2026 20:13:57 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","BB3A:362C5F:780B9:837D1:6984F90D"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 20:09:51 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13979-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770322191.228486,VS0,VE112"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","2a1910393e1f5bc672387f2b5d43fa8db8597766"),("Expires","Thu, 05 Feb 2026 20:14:51 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-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","6FE4:12B67B:376902:3C086B:69849DC7"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 13:40:26 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13925-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770298826.127879,VS0,VE131"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","82b4977e5bbc0311d9e8844a461095618c76682a"),("Expires","Thu, 05 Feb 2026 13:45:26 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘Using-TreeDist.Rmd’
--- re-building ‘compare-treesets.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
(StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","6FE4:12B67B:376902:3C086B:69849DC7"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 13:40:29 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13925-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770298830.884678,VS0,VE0"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","e09ee0670e132b52116bb2a4b30c08d9b8825bfe"),("Expires","Thu, 05 Feb 2026 13:45:29 GMT"),("Source-Age","4")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'compare-treesets.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘compare-treesets.Rmd’
--- re-building ‘different-leaves.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘different-leaves.Rmd’
--- re-building ‘information.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘information.Rmd’
--- re-building ‘landscapes.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
(StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","6FE4:12B67B:376902:3C086B:69849DC7"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 13:40:42 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13943-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770298843.757965,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","5f8242d8efa83e9195e766bbf352c1ae5ce8e2ce"),("Expires","Thu, 05 Feb 2026 13:45:42 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","6FE4:12B67B:376902:3C086B:69849DC7"),("Accept-Ranges","bytes"),("Date","Thu, 05 Feb 2026 13:41:26 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13965-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770298886.112802,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","86c6a6ee62765798c2a54f1a4621d5b7a6ecdfb8"),("Expires","Thu, 05 Feb 2026 13:46:26 GMT"),("Source-Age","60")], 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","740A:2A0EE:35DC2:5C756:6982066A"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:30:03 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630048-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770129004.847953,VS0,VE104"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","b5d72aabd0be41aeed5360c1834fc8f0c3e61d45"),("Expires","Tue, 03 Feb 2026 14:35:03 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","740A:2A0EE:35DC2:5C756:6982066A"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:30:08 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630026-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770129009.769761,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","3e812cab3fa8f091a0f013a5fed518b7ea18a862"),("Expires","Tue, 03 Feb 2026 14:35:08 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","740A:2A0EE:35DC2:5C756:6982066A"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:30:22 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630072-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770129023.727502,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","584d4c1c61b1d5b7f387b4e9bc9d02643191fd57"),("Expires","Tue, 03 Feb 2026 14:35:22 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","740A:2A0EE:36868:5D835:698206AC"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:31:09 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630056-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770129069.286140,VS0,VE97"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ec612e55ed155086191e84a16ca668bc2e06fe02"),("Expires","Tue, 03 Feb 2026 14:36:09 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","EC7E:411E4:2EB2F:4FB50:698202AF"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:14:17 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630078-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770128057.072722,VS0,VE112"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","20b60b9faa4392f4c8247f015630bc83c8b00b18"),("Expires","Tue, 03 Feb 2026 14:19:17 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","EC7E:411E4:2EB2F:4FB50:698202AF"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:14:22 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630041-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770128062.392160,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","f0b718be75952a4f06d01a0456e57970279a09b6"),("Expires","Tue, 03 Feb 2026 14:19:22 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","EC7E:411E4:2EB2F:4FB50:698202AF"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:14:39 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630042-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770128080.687850,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","0a4abbfcdfdf94eae58bc9f51eb322ed6494dec4"),("Expires","Tue, 03 Feb 2026 14:19:39 GMT"),("Source-Age","23")], 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","3D2E:22BB74:2F6CD:50DD2:698202FD"),("Accept-Ranges","bytes"),("Date","Tue, 03 Feb 2026 14:15:25 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630080-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770128125.447014,VS0,VE95"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","f88140f6353265418556d1dd0a5deccda1a32132"),("Expires","Tue, 03 Feb 2026 14:20:25 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
--- 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","7516:C6B3E:AA6A6A:BCD738:6982FED7"),("Accept-Ranges","bytes"),("Date","Wed, 04 Feb 2026 08:10:00 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13941-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770192600.153367,VS0,VE112"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","d23be51db4880c5b278243b8740b2d92f37f89e1"),("Expires","Wed, 04 Feb 2026 08:15:00 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","7516:C6B3E:AA6A6A:BCD738:6982FED7"),("Accept-Ranges","bytes"),("Date","Wed, 04 Feb 2026 08:10:04 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13934-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770192605.957390,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","7a7074d0ada5e5f6a8671926e0921ce564083979"),("Expires","Wed, 04 Feb 2026 08:15:04 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","7516:C6B3E:AA6A6A:BCD738:6982FED7"),("Accept-Ranges","bytes"),("Date","Wed, 04 Feb 2026 08:10:20 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13971-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1770192621.903726,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","3f070bdc8849af0734117294b2d2a9856f62884e"),("Expires","Wed, 04 Feb 2026 08:15:20 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","9538:CC0C:A74119:B9B5D7:6982FF21"),("Accept-Ranges","bytes"),("Date","Wed, 04 Feb 2026 08:11:17 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13946-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1770192678.859354,VS0,VE107"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","3232b253e8e2cd21047086f4eff93fe75dafee93"),("Expires","Wed, 04 Feb 2026 08:16:17 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 '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","C45E:3A2973:81648F:96FE26:697DB665"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 07:59:33 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13975-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769846374.642346,VS0,VE114"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","64433d781ce273e946660ef70ffe5f008e6ff183"),("Expires","Sat, 31 Jan 2026 08:04:33 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘Using-TreeDist.Rmd’
--- re-building ‘compare-treesets.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
(StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","C45E:3A2973:81648F:96FE26:697DB665"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 07:59:38 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13923-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769846379.849416,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","2588675f6cb31ef7faa39f4238a9243b1f15e70f"),("Expires","Sat, 31 Jan 2026 08:04:38 GMT"),("Source-Age","5")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'compare-treesets.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘compare-treesets.Rmd’
--- re-building ‘different-leaves.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘different-leaves.Rmd’
--- re-building ‘information.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘information.Rmd’
--- re-building ‘landscapes.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
(StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","C45E:3A2973:81648F:96FE26:697DB665"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 07:59:54 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13925-MUC"),("X-Cache","HIT"),("X-Cache-Hits","2"),("X-Timer","S1769846395.807552,VS0,VE0"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","a3ff457d66a926c192111ec27cbed1f2a33b0749"),("Expires","Sat, 31 Jan 2026 08:04:54 GMT"),("Source-Age","21")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'landscapes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘landscapes.Rmd’
--- re-building ‘treespace.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
(StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","4668:100BA1:87985E:9D3A4D:697DB6B8"),("Accept-Ranges","bytes"),("Date","Sat, 31 Jan 2026 08:00:57 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13974-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769846457.195491,VS0,VE113"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","60c6d7d21d00e758e0413f615cf5ce6c0074ab98"),("Expires","Sat, 31 Jan 2026 08:05:57 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'treespace.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘treespace.Rmd’
--- re-building ‘using-distances.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘using-distances.Rmd’
SUMMARY: processing the following files failed:
‘Using-TreeDist.Rmd’ ‘compare-treesets.Rmd’ ‘landscapes.Rmd’
‘treespace.Rmd’
Error: Vignette re-building failed.
Execution halted
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
Current CRAN status: NOTE: 3, OK: 10
Version: 1.7.0
Check: installed package size
Result: NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
datasets 1.6Mb
doc 1.3Mb
libs 1.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 2, OK: 11
Version: 2.0.0
Check: installed package size
Result: NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
R 1.1Mb
libs 4.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.