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   ERROR     skipped     skipped     skipped  
nebbiolo2 Linux (Ubuntu 22.04.2 LTS)/x86_64   ERROR     skipped     skipped     skipped  

lconway Summary

[top]

Package: scDesign3Workflow
Version: 0.99.0
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: 35 minutes 2.30 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: scDesign3Workflow_20230906170611
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.

lconway BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* 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

Quitting from lines 78-99 [unnamed-chunk-6] (scDesign3-CITEseq-vignette.Rmd)

Quitting from lines 78-99 [unnamed-chunk-6] (scDesign3-CITEseq-vignette.Rmd)
Error: processing vignette 'scDesign3-CITEseq-vignette.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘scDesign3-CITEseq-vignette.Rmd’

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

Quitting from lines 43-64 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
there is no package called 'monocle3'
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’

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

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

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

--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown
Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 18 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished 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-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-CITEseq-vignette.Rmd’ ‘scDesign3-DEanalysis-vignette.Rmd’
  ‘scDesign3-spatial-deconvolution.Rmd’

Error: Vignette re-building failed.
Execution halted

lconway CHECK output

[top]


                				
 

                            
 
                                
                				
lconway BUILD BIN output
 
                    			
[top]

                				
 
                					

                				
 
                
		    
		        			

                			
                			
nebbiolo2 Summary
 
                			
[top]

                			
 
                				
 
						        
Package: scDesign3Workflow
 
                					
Version: 0.99.0
 
                					
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: 50 minutes 59.61 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: scDesign3Workflow_20230906170611
 
                					
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
 
                    			
[top]

                				
 
                					
===============================

 R CMD BUILD

===============================

* 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 43-64 [unnamed-chunk-3] (scDesign3-DEanalysis-vignette.Rmd)
Error: processing vignette 'scDesign3-DEanalysis-vignette.Rmd' failed with diagnostics:
there is no package called 'monocle3'
--- failed re-building ‘scDesign3-DEanalysis-vignette.Rmd’

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

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

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

--- re-building ‘scDesign3-copulaCompare-vignette.Rmd’ using rmarkdown
Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished 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-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-spatial-deconvolution.Rmd’

Error: Vignette re-building failed.
Execution halted


                				
 

                			
 
                			    
                				
nebbiolo2 CHECK output
 
                    			
[top]

                				
 
                					

                				
 

                            
 
                                
                				
nebbiolo2 BUILD BIN output
 
                    			
[top]