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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data CluMSID
###
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* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* preparing ‘CluMSID’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘CluMSID_DI-MSMS.Rmd’ using rmarkdown
2025-12-26 15:55:20.963 R[74879:541897812] 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 '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsrRz3B/Rf1247f77c12777': No such file or directory

Quitting from CluMSID_MTBLS.Rmd:13-20 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from CluMSID_MTBLS.Rmd:13-20 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsrRz3B/Rf1247f7d01b008': No such file or directory

Quitting from CluMSID_lowres-LC-MSMS.Rmd:13-20 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from CluMSID_lowres-LC-MSMS.Rmd:13-20 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 '/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpsrRz3B/Rf1247f4799f5eb': No such file or directory

Quitting from CluMSID_tutorial.Rmd:13-19 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cannot open the connection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from CluMSID_tutorial.Rmd:13-19 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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