• using R Under development (unstable) (2026-01-28 r89344)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (1+b1)     Debian flang version 21.1.8 (1+b1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘TreeDist/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘TreeDist’ version ‘2.11.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/4s] OK
• 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 ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 21.1.8 (1+b1)’
• checking C++ specification ... INFO   specified C++17
• checking package directory ... OK
• checking for future file timestamps ... 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 ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] 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 ... [17s/23s] OK
• checking Rd files ... [3s/4s] 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 relative paths in package URLs ... NOTE Found the following (possibly) invalid URL:   URL: ../reference/index.html     From: inst/doc/using-distances.html
• checking examples ... [3s/4s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [27s/38s] OK   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [27s/38s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [89s/112s] 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","34C2:2887D:82FA4:9165B:697BBE7E"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 20:09:35 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13928-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769717375.092470,VS0,VE124"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","70d7816fc3b580d8da757b9c47e1e98ffd7f2aec"),("Expires","Thu, 29 Jan 2026 20:14:35 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","34C2:2887D:82FA4:9165B:697BBE7E"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 20:09:40 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13958-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769717381.556719,VS0,VE3"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","1df81510a79949fadab2875787985c7eb8fb1bb5"),("Expires","Thu, 29 Jan 2026 20:14:40 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","34C2:2887D:82FA4:9165B:697BBE7E"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 20:09:55 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13934-MUC"),("X-Cache","HIT"),("X-Cache-Hits","1"),("X-Timer","S1769717396.951393,VS0,VE2"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","1c8177cab64ec9054cf996fe4208a89ee2726974"),("Expires","Thu, 29 Jan 2026 20:14:55 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","5248:2934B4:3D8E4:449DB:697BBECF"),("Accept-Ranges","bytes"),("Date","Thu, 29 Jan 2026 20:10:55 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13945-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1769717456.557722,VS0,VE119"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","00a879646db51de918039841f02c9f608c25adf2"),("Expires","Thu, 29 Jan 2026 20:15:55 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
• checking PDF version of manual ... [8s/11s] OK
• checking HTML version of manual ... [7s/10s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 NOTE