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R CMD BUILD
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* checking for file ‘phylobar/DESCRIPTION’ ... OK
* preparing ‘phylobar’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘atlas.Rmd’ using rmarkdown
--- finished re-building ‘atlas.Rmd’
--- re-building ‘covid_immunology.Rmd’ using rmarkdown
trying URL 'https://zenodo.org/api/records/17477876/files/su-2020.rds/content'
Content type 'application/octet-stream' length 13463047 bytes (12.8 MB)
==================================================
downloaded 12.8 MB
--- finished re-building ‘covid_immunology.Rmd’
--- re-building ‘customizing_files.Rmd’ using rmarkdown
--- finished re-building ‘customizing_files.Rmd’
--- re-building ‘diet_analysis.Rmd’ using rmarkdown
--- finished re-building ‘diet_analysis.Rmd’
--- re-building ‘exporting.Rmd’ using rmarkdown
--- finished re-building ‘exporting.Rmd’
--- re-building ‘getting_started.Rmd’ using rmarkdown
--- finished re-building ‘getting_started.Rmd’
--- re-building ‘global_patterns.Rmd’ using rmarkdown
--- finished re-building ‘global_patterns.Rmd’
--- re-building ‘hfhs.Rmd’ using rmarkdown
Quitting from hfhs.Rmd:62-68 [data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! lexical error: invalid char in json text.
<html><body><h1>504 Gateway Tim
(right here) ------^
---
Backtrace:
▆
1. └─zen4R::download_zenodo("10.5281/zenodo.18791960", tempdir())
2. └─zen4R::get_zenodo(doi = doi, sandbox = sandbox, logger = logger)
3. └─zenodo$getRecordByDOI(doi)
4. └─self$getRecords(q = query, all_versions = TRUE, exact = TRUE)
5. └─zenReq$execute()
6. └─private$GET(private$url, private$request, private$progress, accept = private$accept)
7. └─httr::content(r, type = "application/json", encoding = "UTF-8")
8. └─httr:::parse_auto(raw, type, encoding, ...)
9. └─httr (local) parser(x = content, type = type, encoding = encoding, ...)
10. └─jsonlite::fromJSON(...)
11. └─jsonlite:::parse_and_simplify(...)
12. └─jsonlite:::parseJSON(txt, bigint_as_char)
13. └─jsonlite:::parse_string(txt, bigint_as_char)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'hfhs.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
<html><body><h1>504 Gateway Tim
(right here) ------^
--- failed re-building ‘hfhs.Rmd’
--- re-building ‘taxonomies.Rmd’ using rmarkdown
trying URL 'https://zenodo.org/api/records/18791960/files/HFHS-data.rds/content'
Content type 'application/octet-stream' length 78041 bytes (76 KB)
==================================================
downloaded 76 KB
--- finished re-building ‘taxonomies.Rmd’
SUMMARY: processing the following file failed:
‘hfhs.Rmd’
Error: Vignette re-building failed.
Execution halted