• using R Under development (unstable) (2026-08-15 r90413)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 22.1.8 (1+b2)     Debian flang version 22.1.8 (1+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-08-17 16:06:54 UTC
• checking for file ‘EpiNow2/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘EpiNow2’ version ‘1.9.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [5s/11s] OK
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘cmdstanr’
• 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 ‘EpiNow2’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 22.1.8 (1+b2)’
• 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 ... [6s/9s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/9s] OK
• checking whether the package can be unloaded cleanly ... [5s/11s] OK
• checking whether the namespace can be loaded with stated dependencies ... [6s/11s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/10s] OK
• checking loading without being on the library search path ... [8s/16s] 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 ... [46s/65s] OK
• checking Rd files ... [2s/2s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... INFO Package unavailable to check Rd xrefs: ‘cmdstanr’
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... INFO Exported functions without usage information:   collapse discretise fix_parameters is_constrained
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking line endings in shell scripts ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements.
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 ... [31s/38s] OK Examples with CPU (user + system) or elapsed time > 5s                   user system elapsed report_plots 5.788 0.048 7.179 regional_summary 4.386 0.046 6.325
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [18s/23s] OK   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [18s/22s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [19s/77s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘EpiNow2.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","85CC:1AD73D:3C33C8:3DD903:6A833308"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:00 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13955-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983177.919462,VS0,VE3226"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","924d6050ce880ca11d3e76c8c7efff2f26bb89c0"),("Expires","Mon, 17 Aug 2026 16:18:00 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'EpiNow2.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘EpiNow2.Rmd’ --- re-building ‘case-studies.Rmd’ using rmarkdown --- finished re-building ‘case-studies.Rmd’ --- re-building ‘delays.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","8618:23D671:3C2747:3DD047:6A83330E"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:05 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13961-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983183.820453,VS0,VE3127"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","fa4ce7460bce7ce20b3bc22e1fcf9364af26377b"),("Expires","Mon, 17 Aug 2026 16:18:05 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'delays.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘delays.Rmd’ --- re-building ‘epinow.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","A1EA:23D671:3C39A7:3DE3F7:6A833313"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:10 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13921-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983187.414638,VS0,VE3178"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","aedfd1b5ce13ab344998ea1cbbf02d6c00308be2"),("Expires","Mon, 17 Aug 2026 16:18:10 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'epinow.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘epinow.Rmd’ --- re-building ‘estimate_dist.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","A1DA:290645:3B9490:3D3F4F:6A833318"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:15 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13974-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983192.402112,VS0,VE3364"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","d7351b8af3234e0a07d36f2a8a3cd01f8160d8c3"),("Expires","Mon, 17 Aug 2026 16:18:15 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_dist.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_dist.Rmd’ --- re-building ‘estimate_dist_workflow.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","F514:357E9F:3D0436:3EAFE9:6A83331D"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:20 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13963-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983197.179156,VS0,VE3359"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","0a280378f4bb3531854b7c53658cb182aa999ffd"),("Expires","Mon, 17 Aug 2026 16:18:20 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_dist_workflow.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_dist_workflow.Rmd’ --- re-building ‘estimate_infections.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","F52A:2C07BA:3B94DF:3D3FFA:6A833322"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:25 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13934-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983202.344833,VS0,VE3413"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","c4d0f958e6f66a66f5291dbbd00a0f2aac05e776"),("Expires","Mon, 17 Aug 2026 16:18:25 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_infections.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_infections.Rmd’ --- re-building ‘estimate_infections_options.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","B088:2C83CE:3C9BB1:3E44B6:6A833327"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:30 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13972-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983207.303188,VS0,VE3371"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","a6ec5f1be3a8020022565dccba6db72995abfd6d"),("Expires","Mon, 17 Aug 2026 16:18:30 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_infections_options.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_infections_options.Rmd’ --- re-building ‘estimate_infections_workflow.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","F52A:2C07BA:3BC0EA:3D6BAE:6A83332C"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:35 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13975-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983212.295158,VS0,VE3122"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","ef4da27810cc2fb522268248fdfa28f1efb1b113"),("Expires","Mon, 17 Aug 2026 16:18:35 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_infections_workflow.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_infections_workflow.Rmd’ --- re-building ‘estimate_secondary.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","B0AA:305F60:3CE511:3E9073:6A833330"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:40 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13967-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983217.272294,VS0,VE3367"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","bcf3d9f4843362a934c6b31bb50c205b5100a350"),("Expires","Mon, 17 Aug 2026 16:18:40 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_secondary.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_secondary.Rmd’ --- re-building ‘estimate_truncation.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","B042:23D671:3CD832:3E8399:6A833336"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:45 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13923-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983223.557417,VS0,VE3417"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","28c2245ea9cfa4d887cc89a1ca86136c49d40ba0"),("Expires","Mon, 17 Aug 2026 16:18:45 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'estimate_truncation.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘estimate_truncation.Rmd’ --- re-building ‘forecasting_multiple_data_streams.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","DCDA:34BB73:3DA610:3F524B:6A83333B"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:51 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13969-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983228.827130,VS0,VE3436"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","e421f1362428cc833a57186ba44931b39987cad4"),("Expires","Mon, 17 Aug 2026 16:18:51 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'forecasting_multiple_data_streams.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘forecasting_multiple_data_streams.Rmd’ --- re-building ‘gaussian_process_implementation_details.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","DD46:2C83CE:3D0AAA:3EB750:6A833340"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:13:56 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13946-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983233.820570,VS0,VE3455"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","fda854976a4ef42f29e651b6235ef12e565140a2"),("Expires","Mon, 17 Aug 2026 16:18:56 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'gaussian_process_implementation_details.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘gaussian_process_implementation_details.Rmd’ --- re-building ‘model_features.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","DD2A:34BB73:3DCD58:3F7CC8:6A833346"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:14:01 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13925-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983238.031148,VS0,VE3158"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","2cf3a28af9fdc995e137d8a3a0970f9dd801bf72"),("Expires","Mon, 17 Aug 2026 16:19:01 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'model_features.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘model_features.Rmd’ --- re-building ‘model_overview.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","DD16:357E9F:3DCA97:3F7BA5:6A83334A"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:14:05 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13949-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983243.850661,VS0,VE3132"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","6bf3d952b9af804b6f72de18fcef3dcba8ed5916"),("Expires","Mon, 17 Aug 2026 16:19:05 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'model_overview.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘model_overview.Rmd’ --- re-building ‘prior_choice_guide.Rmd’ using rmarkdown Could not fetch https://raw.githubusercontent.com/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl HttpExceptionRequest Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect }  (StatusCodeException (Response {responseStatus = Status {statusCode = 429, statusMessage = "Too Many Requests"}, responseVersion = HTTP/1.1, responseHeaders = [("Connection","keep-alive"),("Content-Length","199"),("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","2B6A:357E9F:3DDD57:3F9008:6A83334F"),("x-github-edge-region","fra"),("Accept-Ranges","bytes"),("Date","Mon, 17 Aug 2026 16:14:11 GMT"),("Via","1.1 varnish"),("X-Served-By","cache-muc13947-MUC"),("X-Cache","MISS"),("X-Cache-Hits","0"),("X-Timer","S1786983248.610305,VS0,VE3420"),("Vary","Authorization,Accept-Encoding"),("Access-Control-Allow-Origin","*"),("Cross-Origin-Resource-Policy","cross-origin"),("X-Fastly-Request-ID","3b63a7e2a364d4f5eb122d3e3c047e123df5f2c7"),("Expires","Mon, 17 Aug 2026 16:19:11 GMT")], responseBody = (), responseCookieJar = CJ {expose = []}, responseClose' = ResponseClose, responseOriginalRequest = Request {   host = "raw.githubusercontent.com"   port = 443   secure = True   requestHeaders = [("User-Agent","pandoc/3.10.2")]   path = "/citation-style-language/styles/master/apa-numeric-superscript-brackets.csl"   queryString = ""   method = "GET"   proxy = Nothing   rawBody = False   redirectCount = 10   responseTimeout = ResponseTimeoutDefault   requestVersion = HTTP/1.1   proxySecureMode = ProxySecureWithConnect } , responseEarlyHints = []}) "429: Too Many Requests\nFor more on scraping GitHub and how it may affect your rights, please review our Terms of Service (https://docs.github.com/en/site-policy/github-terms/github-terms-of-service).") Error: processing vignette 'prior_choice_guide.Rmd' failed with diagnostics: pandoc document conversion failed with error 61 --- failed re-building ‘prior_choice_guide.Rmd’ SUMMARY: processing the following files failed:   ‘EpiNow2.Rmd’ ‘delays.Rmd’ ‘epinow.Rmd’ ‘estimate_dist.Rmd’   ‘estimate_dist_workflow.Rmd’ ‘estimate_infections.Rmd’   ‘estimate_infections_options.Rmd’ ‘estimate_infections_workflow.Rmd’   ‘estimate_secondary.Rmd’ ‘estimate_truncation.Rmd’   ‘forecasting_multiple_data_streams.Rmd’   ‘gaussian_process_implementation_details.Rmd’ ‘model_features.Rmd’   ‘model_overview.Rmd’ ‘prior_choice_guide.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [13s/17s] OK
• checking HTML version of manual ... [7s/9s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR