Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/scDesign3Workflow
Last Changed Rev:  / Revision: 
Last Changed Date: 

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
lconway macOS 12.6.5 Monterey/x86_64                    
nebbiolo2 Linux (Ubuntu 22.04.2 LTS)/x86_64   ERROR     skipped     skipped     skipped  

lconway Summary

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Package: scDesign3Workflow
Version: 0.99.5
RVersion: 4.3
BiocVersion: 3.18
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data scDesign3Workflow
BuildTime:
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: scDesign3Workflow_20231018150022
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scDesign3Workflow. Starting Build package.
PostProcessing: Finished Git clone. Package type: Workflow. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0.

lconway BUILD SRC output

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lconway CHECK output
 
                    			
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lconway BUILD BIN output
 
                    			
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nebbiolo2 Summary
 
                			
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Package: scDesign3Workflow
 
                					
Version: 0.99.5
 
                					
RVersion: 4.3
                
 
                					
BiocVersion: 3.18
                
 

                					
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data scDesign3Workflow
 
                					
BuildTime: 55 minutes 1.68 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: scDesign3Workflow_20231018150022
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: scDesign3Workflow. Starting Build package. 
 
                					
PostProcessing: Finished Git clone. Package type: Workflow. Installing dependency status: 1. Checking git clone status: 0. Installing package status: 0. Build Package status: 1. 
        				
                				
 
                			
 
                			
 
                			    
                				
nebbiolo2 BUILD SRC output
 
                    			
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===============================

 R CMD BUILD

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* checking for file ‘scDesign3Workflow/DESCRIPTION’ ... OK
* preparing ‘scDesign3Workflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘scDesign3-CITEseq-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-CITEseq-vignette.Rmd’

--- re-building ‘scDesign3-DEanalysis-vignette.Rmd’ using rmarkdown

Quitting from lines 43-61 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'scran' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'edgeR'
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’

--- re-building ‘scDesign3-batchEffect-vignette.Rmd’ using rmarkdown

Quitting from lines 208-218 [unnamed-chunk-17] (scDesign3-batchEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-batchEffect-vignette.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
--- failed re-building ‘scDesign3-batchEffect-vignette.Rmd’

--- re-building ‘scDesign3-clusterGOF-vignette.Rmd’ using rmarkdown

Quitting from lines 45-52 [unnamed-chunk-3] (scDesign3-clusterGOF-vignette.Rmd)
Error: processing vignette 'scDesign3-clusterGOF-vignette.Rmd' failed with diagnostics:
package 'SingleCellExperiment' required by 'scran' could not be found
--- failed re-building ‘scDesign3-clusterGOF-vignette.Rmd’

--- re-building ‘scDesign3-conditionEffect-vignette.Rmd’ using rmarkdown

Quitting from lines 201-202 [unnamed-chunk-16] (scDesign3-conditionEffect-vignette.Rmd)
Error: processing vignette 'scDesign3-conditionEffect-vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘scDesign3-conditionEffect-vignette.Rmd’

--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown

Quitting from lines 64-74 [unnamed-chunk-4] (scDesign3-copulaCompare-vignette.Rmd)
Error: processing vignette 'scDesign3-copulaCompare-vignette.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'bpisup': lazy-load database '/home/biocbuild/bbs-3.18-bioc/R/site-library/BiocParallel/R/BiocParallel.rdb' is corrupt
--- failed re-building ‘scDesign3-copulaCompare-vignette.Rmd’

--- re-building ‘scDesign3-introduction-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-introduction-vignette.Rmd’

--- re-building ‘scDesign3-librarySize-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-librarySize-vignette.Rmd’

--- re-building ‘scDesign3-marginal-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-marginal-vignette.Rmd’

--- re-building ‘scDesign3-multiomics-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-multiomics-vignette.Rmd’

--- re-building ‘scDesign3-multipleLineages-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-multipleLineages-vignette.Rmd’

--- re-building ‘scDesign3-parallelization-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-parallelization-vignette.Rmd’

--- re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-pseudotimeGOF-vignette.Rmd’

--- re-building ‘scDesign3-scATACseq-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-scATACseq-vignette.Rmd’

--- re-building ‘scDesign3-spatial-deconvolution.Rmd’ using rmarkdown

Quitting from lines 38-46 [unnamed-chunk-1] (scDesign3-spatial-deconvolution.Rmd)
Error: processing vignette 'scDesign3-spatial-deconvolution.Rmd' failed with diagnostics:
there is no package called 'IOBR'
--- failed re-building ‘scDesign3-spatial-deconvolution.Rmd’

--- re-building ‘scDesign3-spatial-vignette.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3-spatial-vignette.Rmd’

--- re-building ‘scDesign3.Rmd’ using rmarkdown
--- finished re-building ‘scDesign3.Rmd’

SUMMARY: processing the following files failed:
  ‘scDesign3-DEanalysis-vignette.Rmd’
  ‘scDesign3-batchEffect-vignette.Rmd’
  ‘scDesign3-clusterGOF-vignette.Rmd’
  ‘scDesign3-conditionEffect-vignette.Rmd’
  ‘scDesign3-copulaCompare-vignette.Rmd’
  ‘scDesign3-spatial-deconvolution.Rmd’

Error: Vignette re-building failed.
Execution halted


                				
 

                			
 
                			    
                				
nebbiolo2 CHECK output
 
                    			
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nebbiolo2 BUILD BIN output
 
                    			
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