##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CluMSID
###
##############################################################################
##############################################################################


* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* preparing ‘CluMSID’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CluMSID_DI-MSMS.Rmd’ using rmarkdown
2025-03-20 20:53:54.959 R[40448:309610460] XType: Using static font registry.
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "CluMSID DI-MS/MS Tutorial", and the latter is "Clustering Spectra from High Resolution DI-MS/MS Data Using CluMSID". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘CluMSID_DI-MSMS.Rmd’

--- re-building ‘CluMSID_GC-EI-MS.Rmd’ using rmarkdown

Quitting from CluMSID_GC-EI-MS.Rmd:126-130 [runCAMERA]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
     ▆
  1. ├─metaMS::runCAMERA(...)
  2. │ └─CAMERA::xsAnnotate(xset, sample = 1)
  3. └─xcms::xcmsSet(pool)
  4.   ├─BiocParallel::bptry(bplapply(argList, findPeaksPar, BPPARAM = BPPARAM))
  5.   │ └─base::tryCatch(expr, ..., bplist_error = bplist_error, bperror = bperror)
  6.   │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  7.   │     ├─base (local) tryCatchOne(...)
  8.   │     │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  9.   │     └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
 10.   │       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.   │         └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 12.   ├─BiocParallel::bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)
 13.   └─BiocParallel::bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)
 14.     └─BiocParallel:::.bpinit(...)
 15.       ├─BiocParallel::bploop(...)
 16.       └─BiocParallel:::bploop.lapply(...)
 17.         └─BiocParallel:::.bploop_impl(...)
 18.           └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 19.             ├─BiocParallel:::.reducer_add(reducer, njob, value)
 20.             └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CluMSID_GC-EI-MS.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘CluMSID_GC-EI-MS.Rmd’

--- re-building ‘CluMSID_MTBLS.Rmd’ using rmarkdown
Warning in file("", "w+b") :
  cannot open file '/tmp/RtmpQeh0AN/Rf9e00146c4061': No such file or directory

Quitting from CluMSID_MTBLS.Rmd:13-20 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
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.     └─knitr:::vweave_rmarkdown(...)
  8.       └─rmarkdown::render(...)
  9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10.           └─knitr:::process_file(text, output)
 11.             ├─xfun:::handle_error(...)
 12.             ├─base::withCallingHandlers(...)
 13.             └─knitr:::process_group(group)
 14.               └─knitr:::call_block(x)
 15.                 └─knitr:::block_exec(params)
 16.                   └─knitr:::eng_r(options)
 17.                     ├─knitr:::in_input_dir(...)
 18.                     │ └─knitr:::in_dir(input_dir(), expr)
 19.                     └─knitr (local) evaluate(...)
 20.                       └─evaluate::evaluate(...)
 21.                         └─evaluate:::watchout(...)
 22.                           └─evaluate:::local_persistent_sink_connection(debug, frame)
 23.                             └─base::file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CluMSID_MTBLS.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CluMSID_MTBLS.Rmd’

--- re-building ‘CluMSID_lowres-LC-MSMS.Rmd’ using rmarkdown
Warning in file("", "w+b") :
  cannot open file '/tmp/RtmpQeh0AN/Rf9e0024444bc0': No such file or directory

Quitting from CluMSID_lowres-LC-MSMS.Rmd:13-20 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
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.     └─knitr:::vweave_rmarkdown(...)
  8.       └─rmarkdown::render(...)
  9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10.           └─knitr:::process_file(text, output)
 11.             ├─xfun:::handle_error(...)
 12.             ├─base::withCallingHandlers(...)
 13.             └─knitr:::process_group(group)
 14.               └─knitr:::call_block(x)
 15.                 └─knitr:::block_exec(params)
 16.                   └─knitr:::eng_r(options)
 17.                     ├─knitr:::in_input_dir(...)
 18.                     │ └─knitr:::in_dir(input_dir(), expr)
 19.                     └─knitr (local) evaluate(...)
 20.                       └─evaluate::evaluate(...)
 21.                         └─evaluate:::watchout(...)
 22.                           └─evaluate:::local_persistent_sink_connection(debug, frame)
 23.                             └─base::file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CluMSID_lowres-LC-MSMS.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CluMSID_lowres-LC-MSMS.Rmd’

--- re-building ‘CluMSID_tutorial.Rmd’ using rmarkdown
Warning in file("", "w+b") :
  cannot open file '/tmp/RtmpQeh0AN/Rf9e0074ba0c19': No such file or directory

Quitting from CluMSID_tutorial.Rmd:13-19 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
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.     └─knitr:::vweave_rmarkdown(...)
  8.       └─rmarkdown::render(...)
  9.         └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
 10.           └─knitr:::process_file(text, output)
 11.             ├─xfun:::handle_error(...)
 12.             ├─base::withCallingHandlers(...)
 13.             └─knitr:::process_group(group)
 14.               └─knitr:::call_block(x)
 15.                 └─knitr:::block_exec(params)
 16.                   └─knitr:::eng_r(options)
 17.                     ├─knitr:::in_input_dir(...)
 18.                     │ └─knitr:::in_dir(input_dir(), expr)
 19.                     └─knitr (local) evaluate(...)
 20.                       └─evaluate::evaluate(...)
 21.                         └─evaluate:::watchout(...)
 22.                           └─evaluate:::local_persistent_sink_connection(debug, frame)
 23.                             └─base::file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'CluMSID_tutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CluMSID_tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘CluMSID_GC-EI-MS.Rmd’ ‘CluMSID_MTBLS.Rmd’
  ‘CluMSID_lowres-LC-MSMS.Rmd’ ‘CluMSID_tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted