Bioconductor Single Package Builder - Build History

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 R CMD BUILD

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

quarto render ../inst/

[ 1/38] index.qmd


processing file: index.qmd
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output file: index.knit.md


[ 2/38] pages/bkg-introduction.qmd

[ 3/38] pages/bkg-spatial-omics.qmd

[ 4/38] pages/bkg-infrastructure.qmd


processing file: bkg-infrastructure.qmd
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output file: bkg-infrastructure.knit.md


[ 5/38] pages/bkg-ecosystem.qmd


processing file: bkg-ecosystem.qmd
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output file: bkg-ecosystem.knit.md


[ 6/38] pages/bkg-importing-data.qmd


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output file: bkg-importing-data.knit.md


[ 7/38] pages/bkg-example-datasets.qmd


processing file: bkg-example-datasets.qmd
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output file: bkg-example-datasets.knit.md


[ 8/38] pages/bkg-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
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output file: bkg-python-interoperability.knit.md

Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate

[ 9/38] pages/seq-introduction.qmd


processing file: seq-introduction.qmd
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output file: seq-introduction.knit.md


[10/38] pages/seq-reads-to-counts.qmd

[11/38] pages/seq-quality-control.qmd


processing file: seq-quality-control.qmd
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output file: seq-quality-control.knit.md


[12/38] pages/seq-intermediate-processing.qmd


processing file: seq-intermediate-processing.qmd
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output file: seq-intermediate-processing.knit.md


[13/38] pages/seq-deconvolution.qmd


processing file: seq-deconvolution.qmd
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output file: seq-deconvolution.knit.md


[14/38] pages/seq-workflow-dlpfc.qmd


processing file: seq-workflow-dlpfc.qmd
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output file: seq-workflow-dlpfc.knit.md


[15/38] pages/seq-workflow-visium-crc.qmd


processing file: seq-workflow-visium-crc.qmd
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output file: seq-workflow-visium-crc.knit.md


[16/38] pages/seq-workflow-visium-hd.qmd


processing file: seq-workflow-visium-hd.qmd
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output file: seq-workflow-visium-hd.knit.md


[17/38] pages/img-introduction.qmd


processing file: img-introduction.qmd
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output file: img-introduction.knit.md


[18/38] pages/img-segmentation.qmd


processing file: img-segmentation.qmd
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output file: img-segmentation.knit.md


[19/38] pages/img-quality-control.qmd


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


[20/38] pages/img-intermediate-processing.qmd


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


[21/38] pages/img-neighborhood-analysis.qmd


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


[22/38] pages/img-workflow-xenium.qmd


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


[23/38] pages/ind-normalization.qmd


processing file: ind-normalization.qmd
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output file: ind-normalization.knit.md


[24/38] pages/ind-dimensionality-reduction.qmd


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


[25/38] pages/ind-clustering.qmd


processing file: ind-clustering.qmd
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output file: ind-clustering.knit.md

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘DelayedArray’
Calls: .main ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
WARN: Unable to perform code-link (code-link requires R packages rmarkdown, downlit, and xml2)

[26/38] pages/ind-feature-selection-testing.qmd


processing file: ind-feature-selection-testing.qmd
1/29                    
2/29 [deps]             
Error: package or namespace load failed for 'DESpace' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'DelayedArray'

Quitting from ind-feature-selection-testing.qmd:18-30 [deps]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'DESpace' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'DelayedArray'
---
Backtrace:
    ▆
 1. └─base::library(DESpace)
 2.   └─base::tryCatch(...)
 3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5.         └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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