Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/phylobar

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo1 Summary

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Package: phylobar

Version: 0.99.11

RVersion: 4.6

BiocVersion: 3.23

BuildCommand: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data phylobar

BuildTime: 2 minutes 15.05 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: phylobar_20260505042442

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: phylobar. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* 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

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output

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