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/

[ 1/36] index.qmd


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


[ 2/36] pages/bkg-introduction.qmd

[ 3/36] pages/bkg-spatial-omics.qmd

[ 4/36] pages/bkg-python-interoperability.qmd


processing file: bkg-python-interoperability.qmd
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[ 5/36] pages/bkg-data-infrastructure.qmd


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[ 6/36] pages/bkg-importing-data.qmd


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[ 7/36] pages/bkg-example-datasets.qmd


processing file: bkg-example-datasets.qmd
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[ 8/36] pages/seq-introduction.qmd


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[ 9/36] pages/seq-reads-to-counts.qmd

[10/36] pages/seq-quality-control.qmd


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

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[11/36] pages/seq-intermediate-processing.qmd


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

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[12/36] pages/seq-deconvolution.qmd


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

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[13/36] pages/seq-workflow-dlpfc.qmd


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

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[14/36] 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

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[15/36] 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

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[16/36] pages/img-introduction.qmd


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[17/36] pages/img-segmentation.qmd

[18/36] pages/img-quality-control.qmd


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


[19/36] pages/img-intermediate-processing.qmd


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

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[20/36] pages/img-neighborhood-analysis.qmd


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


[21/36] pages/img-cell-cell-communication.qmd


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[22/36] pages/img-workflow-xenium.qmd


processing file: img-workflow-xenium.qmd
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[23/36] pages/ind-dimensionality-reduction.qmd


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[24/36] pages/ind-clustering.qmd


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[25/36] pages/ind-feature-selection-testing.qmd


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

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[26/36] pages/ind-feature-set-signatures.qmd


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

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[27/36] pages/ind-spatial-statistics.qmd


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


[28/36] pages/crs-spatial-registration.qmd


processing file: crs-spatial-registration.qmd
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12/27 [add-dapi]     
13/27                
14/27 [plt-dapi]     
15/27                
16/27 [mtx]          
17/27                
18/27 [reg]          
19/27                
20/27 [read-save-hne]
21/27                
22/27 [load-hne]     
23/27                
24/27 [add-hne]      
25/27                
26/27 [plt-hne]      
27/27                
output file: crs-spatial-registration.knit.md

Registered S3 method overwritten by 'ggside':
  method from   
  +.gg   ggplot2

[29/36] pages/crs-imputation.qmd


processing file: crs-imputation.qmd
1/27             
2/27 [deps]      
3/27             
4/27 [load-spe]  
5/27             
6/27 [load-sce]  
7/27             
8/27 [obj]       
9/27             
10/27 [int]       
11/27             
12/27 [plt-map]   
13/27             
14/27 [mgs]       
15/27             
16/27 [imp]       
17/27             
18/27 [new-spe]   
19/27             
20/27 [plt-xy-one]
21/27             
22/27 [plt-cor]   
23/27             
24/27 [plt-xy-two]
25/27             
26/27 [bad-gs]    
27/27             
output file: crs-imputation.knit.md

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘Rhdf5lib’
Calls: .main ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
WARN: Unable to perform code-link (code-link requires R packages rmarkdown, downlit, and xml2)

[30/36] pages/crs-workflow-xenvis.qmd


processing file: crs-workflow-xenvis.qmd
1/39            
2/39 [dep]      
Error: package or namespace load failed for 'BayesSpace' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'Rhdf5lib'

Quitting from crs-workflow-xenvis.qmd:7-22 [dep]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! package or namespace load failed for 'BayesSpace' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'Rhdf5lib'
---
Backtrace:
    ▆
 1. └─base::library(BayesSpace)
 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