• using R Under development (unstable) (2026-01-26 r89334)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)     GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘TreeDist/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘TreeDist’ version ‘2.11.1’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘TreeDistData’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘TreeDist’ can be installed ... [88s/20s] OK See the install log for details.
• used C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
• checking C++ specification ... INFO   specified C++17
• checking package directory ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [14s/14s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [22s/23s] OK   Running ‘spelling.R’   Running ‘testthat.R’ [21s/23s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [85s/86s] 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
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR