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


* checking for file ‘waddR/DESCRIPTION’ ... OK
* preparing ‘waddR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘waddR.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "waddR", and the latter is "The `waddR` package". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘waddR.Rmd’

--- re-building ‘wasserstein_metric.Rmd’ using rmarkdown
Warning: The vignette title specified in \VignetteIndexEntry{} is different from the title in the YAML metadata. The former is "wasserstein_metric", and the latter is "2-Wasserstein distance calculation". If that is intentional, you may set options(rmarkdown.html_vignette.check_title = FALSE) to suppress this check.
--- finished re-building ‘wasserstein_metric.Rmd’

--- re-building ‘wasserstein_singlecell.Rmd’ using rmarkdown

Quitting from wasserstein_singlecell.Rmd:91-94 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
     ▆
  1. ├─waddR::wasserstein.sc(...)
  2. └─waddR::wasserstein.sc(...)
  3.   └─waddR:::.testWass(...)
  4.     ├─base::t(...)
  5.     ├─base::simplify2array(...)
  6.     ├─BiocParallel::bpmapply(onegene, seq(ngenes), seeds)
  7.     └─BiocParallel::bpmapply(onegene, seq(ngenes), seeds)
  8.       ├─BiocParallel::bpmapply(...)
  9.       └─BiocParallel::bpmapply(...)
 10.         ├─BiocParallel::bplapply(...)
 11.         └─BiocParallel::bplapply(...)
 12.           └─BiocParallel:::.bpinit(...)
 13.             ├─BiocParallel::bploop(...)
 14.             └─BiocParallel:::bploop.lapply(...)
 15.               └─BiocParallel:::.bploop_impl(...)
 16.                 └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 17.                   ├─BiocParallel:::.reducer_add(reducer, njob, value)
 18.                   └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘wasserstein_test.Rmd’ using rmarkdown
Warning in file("", "w+b") :
  cannot open file '/tmp/RtmpegpBXJ/Rffc501bf54d7e': No such file or directory

Quitting from wasserstein_test.Rmd:10-15 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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 'wasserstein_test.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wasserstein_test.Rmd’

SUMMARY: processing the following files failed:
  ‘wasserstein_singlecell.Rmd’ ‘wasserstein_test.Rmd’

Error: Vignette re-building failed.
Execution halted