Bioconductor Single Package Builder - Build History

Snapshot Date:

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

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)/x86_64	ERROR	skipped	skipped	skipped

nebbiolo2 Summary

[top]

Package: MetabolomicsPipeline

Version: 0.99.2

RVersion: 4.5

BiocVersion: 3.22

BuildCommand: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MetabolomicsPipeline

BuildTime: 2 minutes 49.88 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: MetabolomicsPipeline_20250929221832

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MetabolomicsPipeline. 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.

nebbiolo2 BUILD SRC output

[top]

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

 R CMD BUILD

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

* checking for file MetabolomicsPipeline/DESCRIPTION ... OK
* preparing MetabolomicsPipeline:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building MetabolomicsPipeline-vignette.Rmd using knitr

Quitting from MetabolomicsPipeline-vignette.Rmd:552-587 [PairwiseAnalysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `path.expand()`:
! invalid 'path' argument
---
Backtrace:
     
  1. tools::buildVignettes(dir = ".", tangle = TRUE)
  2.   base::tryCatch(...)
  3.    base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.      base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5.        base (local) doTryCatch(return(expr), name, parentenv, handler)
  6.   engine$weave(file, quiet = quiet, encoding = enc)
  7.     (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$", ...
  8.       knitr::knit(input, text = text, envir = envir, quiet = quiet)
  9.         knitr:::process_file(text, output)
 10.           xfun:::handle_error(...)
 11.           base::withCallingHandlers(...)
 12.           knitr:::process_group(group)
 13.             knitr:::call_block(x)
 14.               knitr:::block_exec(params)
 15.                 knitr:::eng_r(options)
 16.                   knitr:::in_input_dir(...)
 17.                    knitr:::in_dir(input_dir(), expr)
 18.                   knitr (local) evaluate(...)
 19.                     evaluate::evaluate(...)
 20.                       base::withRestarts(...)
 21.                        base (local) withRestartList(expr, restarts)
 22.                          base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 23.                           base (local) doWithOneRestart(return(expr), restart)
 24.                          base (local) withRestartList(expr, restarts[-nr])
 25.                            base (local) withOneRestart(expr, restarts[[1L]])
 26.                              base (local) doWithOneRestart(return(expr), restart)
 27.                       evaluate:::with_handlers(...)
 28.                        base::eval(call)
 29.                         base::eval(call)
 30.                        base::withCallingHandlers(...)
 31.                       watcher$print_value(ev$value, ev$visible, envir)
 32.                         base::withVisible(handle_value(handler, value, visible, envir))
 33.                         evaluate:::handle_value(handler, value, visible, envir)
 34.                           handler$value(value, visible)
 35.                             knitr (local) fun(x, options = options)
 36.                               base::withVisible(knit_print(x, ...))
 37.                               knitr::knit_print(x, ...)
 38.                                 knitr:::html_screenshot(x)
 39.                                   knitr:::in_dir(...)
 40.                                   base::normalizePath(f3)
 41.                                     base::path.expand(path)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'MetabolomicsPipeline-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building MetabolomicsPipeline-vignette.Rmd

SUMMARY: processing the following file failed:
  MetabolomicsPipeline-vignette.Rmd

Error: Vignette re-building failed.
Execution halted

nebbiolo2 CHECK output

[top]

nebbiolo2 BUILD BIN output

[top]