##############################################################################
##############################################################################
###
### 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
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/RtmpXg9JF3/Rf1610834d25c47': 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/RtmpXg9JF3/Rf161087d3da864': 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$weave(file, quiet = quiet, encoding = enc)
7. └─knitr:::vweave_rmarkdown(...)
8. └─rmarkdown::render(...)
9. └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
10. └─knitr:::process_file(text, output)
11. ├─xfun:::handle_error(...)
12. ├─base::withCallingHandlers(...)
13. └─knitr:::process_group(group)
14. └─knitr:::call_block(x)
15. └─knitr:::block_exec(params)
16. └─knitr:::eng_r(options)
17. ├─knitr:::in_input_dir(...)
18. │ └─knitr:::in_dir(input_dir(), expr)
19. └─knitr (local) evaluate(...)
20. └─evaluate::evaluate(...)
21. └─evaluate:::watchout(...)
22. └─evaluate:::local_persistent_sink_connection(debug, frame)
23. └─base::file("", "w+b")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'CluMSID_lowres-LC-MSMS.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘CluMSID_lowres-LC-MSMS.Rmd’
--- re-building ‘CluMSID_tutorial.Rmd’ using rmarkdown
Warning in file("", "w+b") :
cannot open file '/tmp/RtmpXg9JF3/Rf1610873437ff1': No such file or directory
Quitting from CluMSID_tutorial.Rmd:13-19 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
▆
1. └─tools::buildVignettes(dir = ".", tangle = TRUE)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─engine$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
