CRAN Package Check Results for Maintainer ‘Martin R. Smith <martin.smith at durham.ac.uk>’

Last updated on 2026-01-27 15:49:09 CET.

Package ERROR NOTE OK
CongreveLamsdell2016 13
PlotTools 13
Quartet 13
Rogue 13
TBRDist 13
Ternary 3 10
TotalCopheneticIndex 2 11
TreeDist 4 3 6
TreeSearch 3 10
TreeTools 2 11

Package CongreveLamsdell2016

Current CRAN status: OK: 13

Package PlotTools

Current CRAN status: OK: 13

Package Quartet

Current CRAN status: OK: 13

Package Rogue

Current CRAN status: OK: 13

Package TBRDist

Current CRAN status: OK: 13

Package Ternary

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

Package TotalCopheneticIndex

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

Package TreeDist

Current CRAN status: ERROR: 4, NOTE: 3, OK: 6

Additional issues

M1mac

Version: 2.11.1
Check: relative paths in package URLs
Result: NOTE Found the following (possibly) invalid URL: URL: ../reference/index.html From: inst/doc/using-distances.html Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Generalized-RF.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Generalized-RF.Rmd’ --- re-building ‘Robinson-Foulds.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Robinson-Foulds.Rmd’ --- re-building ‘Using-TreeDist.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","9A04:FB156:89FE83:97C6F1:6977C952"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:06:42 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13975-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769458003.806477,VS0,VE127"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","9156e767509f7d3ea73832a90937b57cee31384b"),("Expires","Mon, 26 Jan 2026 20:11:42 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "404: Not Found") Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘Using-TreeDist.Rmd’ --- re-building ‘compare-treesets.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","9A04:FB156:89FE83:97C6F1:6977C952"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:06:47 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13972-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769458008.809060,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","5b7945d36c08e375ea1c73731588a76e167225ea"),("Expires","Mon, 26 Jan 2026 20:11:47 GMT"),("Source-Age","5")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "404: Not Found") Error: processing vignette 'compare-treesets.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘compare-treesets.Rmd’ --- re-building ‘different-leaves.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘different-leaves.Rmd’ --- re-building ‘information.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘information.Rmd’ --- re-building ‘landscapes.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","9A04:FB156:89FE83:97C6F1:6977C952"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:07:02 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13953-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769458022.481910,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","6e58ebfdc7a451c5ef6f4fc802ebd668b70ffb08"),("Expires","Mon, 26 Jan 2026 20:12:02 GMT"),("Source-Age","20")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "404: Not Found") Error: processing vignette 'landscapes.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘landscapes.Rmd’ --- re-building ‘treespace.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","CD80:1D80A5:8C78E1:9A4CAA:6977C9A4"),("Accept-Ranges","bytes"),("Date","Mon, 26 Jan 2026 20:08:04 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13982-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769458085.710527,VS0,VE114"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","83f66b2c27f68e1e77c6f50e2f803f4f493c218c"),("Expires","Mon, 26 Jan 2026 20:13:04 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "404: Not Found") Error: processing vignette 'treespace.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘treespace.Rmd’ --- re-building ‘using-distances.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘using-distances.Rmd’ SUMMARY: processing the following files failed: ‘Using-TreeDist.Rmd’ ‘compare-treesets.Rmd’ ‘landscapes.Rmd’ ‘treespace.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.11.1
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘Generalized-RF.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Generalized-RF.Rmd’ --- re-building ‘Robinson-Foulds.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Robinson-Foulds.Rmd’ --- re-building ‘Using-TreeDist.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","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: 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","0C72:3C2CD6:107CC:1AFC9:697887B1"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 09:38:58 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630092-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769506738.932210,VS0,VE124"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","6b97c51d3a68cb49391e9cf94c0c73fbacb38993"),("Expires","Tue, 27 Jan 2026 09:43:58 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "404: Not Found") Error: processing vignette 'Using-TreeDist.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘Using-TreeDist.Rmd’ --- re-building ‘compare-treesets.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl HttpExceptionRequest Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } (StatusCodeException (Response {responseStatus = Status {statusCode = 404, statusMessage = "Not Found"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","14"),("Content-Security-Policy","default-src 'none'; style-src 'unsafe-inline'; sandbox"),("Strict-Transport-Security","max-age=31536000"),("X-Content-Type-Options","nosniff"),("X-Frame-Options","deny"),("X-XSS-Protection","1; mode=block"),("Content-Type","text/plain; charset=utf-8"),("X-GitHub-Request-Id","0C72:3C2CD6:107CC:1AFC9:697887B1"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 09:39:01 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630065-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769506742.904710,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","f15cfe0c4c301ee1cac821ad967d5726d70dee2d"),("Expires","Tue, 27 Jan 2026 09:44:01 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","0C72:3C2CD6:107CC:1AFC9:697887B1"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 09:39:13 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630042-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769506753.274250,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","7ce9b04584362ba856bc9051de619bed47c7b3b4"),("Expires","Tue, 27 Jan 2026 09:44:13 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","AD93:208F95:125D5:1D3A5:697887EC"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 09:39:58 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630053-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769506798.163816,VS0,VE112"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","50e39bc28793f2dc595d522f3b73850d6f40f397"),("Expires","Tue, 27 Jan 2026 09:44:58 GMT"),("Source-Age","0")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request { host = "raw.githubusercontent.com" port = 443 secure = True requestHeaders = [] path = "/citation-style-language/styles/master/apa-old-doi-prefix.csl" queryString = "" method = "GET" proxy = Nothing rawBody = False redirectCount = 10 responseTimeout = ResponseTimeoutDefault requestVersion = HTTP/1.1 proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "404: Not Found") Error: processing vignette '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","80A6:3C2CD6:41E6C:6E55C:69789E23"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 11:14:45 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630064-LCY"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769512485.449531,VS0,VE89"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","f65afdb57f74c3f4b91bc1c20a4150de4ffc58c6"),("Expires","Tue, 27 Jan 2026 11:19:45 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 '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","80A6:3C2CD6:41E6C:6E55C:69789E23"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 11:14:49 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630076-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769512489.121997,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","d6de976e0b86163af3f9d4952344dc6f6f708055"),("Expires","Tue, 27 Jan 2026 11:19:49 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","80A6:3C2CD6:41E6C:6E55C:69789E23"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 11:14:59 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630025-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769512500.852131,VS0,VE1"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","f70c074501ee8ac2028816445c527d527951f92a"),("Expires","Tue, 27 Jan 2026 11:19:59 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","80A6:3C2CD6:41E6C:6E55C:69789E23"),("Accept-Ranges","bytes"),("Date","Tue, 27 Jan 2026 11:15:41 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-lcy-egml8630098-LCY"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769512541.382433,VS0,VE4"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","475b9fadf94c74f807e0e82fca9d6d28da01137d"),("Expires","Tue, 27 Jan 2026 11:20:41 GMT"),("Source-Age","56")], 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: 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

Package TreeSearch

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

Package TreeTools

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