Last updated on 2026-01-27 02:46:55 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CongreveLamsdell2016 | 13 | ||
| PlotTools | 13 | ||
| Quartet | 13 | ||
| Rogue | 13 | ||
| TBRDist | 13 | ||
| Ternary | 3 | 10 | |
| TotalCopheneticIndex | 2 | 11 | |
| TreeDist | 1 | 4 | 8 |
| 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: 2.3.5
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: 1, NOTE: 4, OK: 8
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","5C8E:19873F:30234D:349A81:69776E93"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 13:39:31 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13921-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769434772.818718,VS0,VE127"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","5b0e9e6cdd075791da461a0b5e59f700b01b16a0"),("Expires","Mon, 26 Jan 2026 13:44:31 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","5C8E:19873F:30234D:349A81:69776E93"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 13:39:35 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13946-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769434775.248685,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","dbfcfe90429c7162ed8f19e6f8dfce2ae239ef3f"),("Expires","Mon, 26 Jan 2026 13:44:35 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","5C8E:19873F:30234D:349A81:69776E93"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 13:39:46 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13927-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769434787.793613,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ee1363d5cd05e36feb041a375f0087ca68eb228e"),("Expires","Mon, 26 Jan 2026 13:44:46 GMT"),("Source-Age","15")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
, responseEarlyHints = []}) "404: Not Found")
Error: processing vignette 'landscapes.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘landscapes.Rmd’
--- re-building ‘treespace.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
HttpExceptionRequest Request {
host = "raw.githubusercontent.com"
port = 443
secure = True
requestHeaders = []
path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
(StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","5C8E:19873F:30234D:349A81:69776E93"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 13:40:29 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13959-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769434829.033039,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","15442027399b752bb0112a618644c4718aaa4f79"),("Expires","Mon, 26 Jan 2026 13:45:29 GMT"),("Source-Age","57")], 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: 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