##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSTA
###
##############################################################################
##############################################################################


* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/43] index.qmd


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[ 2/43] pages/bkg-introduction.qmd


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[ 7/43] pages/bkg-example-datasets.qmd


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[ 8/43] pages/bkg-python-interoperability.qmd


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[ 9/43] pages/seq-introduction.qmd


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[11/43] pages/seq-quality-control.qmd


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[12/43] pages/seq-intermediate-processing.qmd


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[13/43] pages/seq-deconvolution.qmd


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[14/43] pages/seq-workflow-dlpfc.qmd


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[15/43] pages/seq-workflow-visium-crc.qmd


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[16/43] pages/seq-workflow-visium-hd-bin.qmd


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output file: seq-workflow-visium-hd-bin.knit.md

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[17/43] pages/seq-workflow-visium-hd-seg.qmd


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[18/43] pages/img-introduction.qmd


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[20/43] pages/img-quality-control.qmd


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output file: img-quality-control.knit.md

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[21/43] pages/img-intermediate-processing.qmd


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output file: img-intermediate-processing.knit.md

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[22/43] pages/img-neighborhood-analysis.qmd


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output file: img-neighborhood-analysis.knit.md

Warning message:
Duplicated chunk option(s) 'message' in both chunk header and pipe comments of the chunk 'scider-load-package-and-data'. 
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[23/43] pages/img-cell-cell-communication.qmd


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output file: img-cell-cell-communication.knit.md

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[24/43] pages/img-sub-cellular-analysis.qmd


processing file: img-sub-cellular-analysis.qmd
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output file: img-sub-cellular-analysis.knit.md


[25/43] pages/img-workflow-xenium.qmd


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output file: img-workflow-xenium.knit.md

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[26/43] pages/img-workflow-cosmx.qmd


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output file: img-workflow-cosmx.knit.md

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[27/43] pages/ind-normalization.qmd


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output file: ind-normalization.knit.md

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[28/43] pages/ind-dimensionality-reduction.qmd


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output file: ind-dimensionality-reduction.knit.md

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[29/43] pages/ind-clustering.qmd


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output file: ind-clustering.knit.md

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[30/43] pages/ind-feature-selection-testing.qmd


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output file: ind-feature-selection-testing.knit.md

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[31/43] pages/ind-feature-set-signatures.qmd


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output file: ind-feature-set-signatures.knit.md

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[32/43] pages/ind-spatial-statistics.qmd


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output file: ind-spatial-statistics.knit.md

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[33/43] pages/ind-image-analysis.qmd


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[34/43] pages/mult-diff-spatial-patterns.qmd


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output file: mult-diff-spatial-patterns.knit.md

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[35/43] pages/mult-diff-colocalization.qmd


processing file: mult-diff-colocalization.qmd
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Error in `combine_vars()`:
! Faceting variables must have at least one value.
Backtrace:
     ▆
  1. ├─base::withVisible(knit_print(x, ...))
  2. ├─knitr::knit_print(x, ...)
  3. └─knitr:::knit_print.default(x, ...)
  4.   └─knitr::normal_print(x)
  5.     ├─base::print(x)
  6.     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
  7.       ├─ggplot2::ggplot_build(x)
  8.       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
  9.         └─layout$setup(data, plot@data, plot@plot_env)
 10.           └─ggplot2 (local) setup(..., self = self)
 11.             └─self$facet$compute_layout(data, self$facet_params)
 12.               └─ggplot2 (local) compute_layout(..., self = self)
 13.                 └─ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop)
 14.                   └─cli::cli_abort("Faceting variables must have at least one value.")
 15.                     └─rlang::abort(...)

Quitting from mult-diff-colocalization.qmd:278-285 [spatialFDA-bubbleplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `combine_vars()`:
! Faceting variables must have at least one value.
---
Backtrace:
     ▆
  1. ├─base::withVisible(knit_print(x, ...))
  2. ├─knitr::knit_print(x, ...)
  3. └─knitr:::knit_print.default(x, ...)
  4.   └─knitr::normal_print(x)
  5.     ├─base::print(x)
  6.     └─ggplot2 (local) `print.ggplot2::ggplot`(x)
  7.       ├─ggplot2::ggplot_build(x)
  8.       └─ggplot2 (local) `ggplot_build.ggplot2::ggplot`(x)
  9.         └─layout$setup(data, plot@data, plot@plot_env)
 10.           └─ggplot2 (local) setup(..., self = self)
 11.             └─self$facet$compute_layout(data, self$facet_params)
 12.               └─ggplot2 (local) compute_layout(..., self = self)
 13.                 └─ggplot2::combine_vars(data, params$plot_env, vars, drop = params$drop)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
WARN: Error encountered when rendering files
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted