Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 22.04.3 LTS)/x86_64   ERROR     skipped     skipped     skipped  
merida1 macOS 12.7.1 Monterey/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo1 Summary

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Package: SpaceMarkers
Version: 0.99.5
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SpaceMarkers
BuildTime: 2 minutes 37.87 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: SpaceMarkers_20240212035416
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SpaceMarkers. Starting Build package.
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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

* checking for file SpaceMarkers/DESCRIPTION ... OK
* preparing SpaceMarkers:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building SpaceMarkers_vignette.Rmd using rmarkdown
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_Human_Breast_Cancer/Visium_Human_Breast_Cancer_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 23942611 bytes (22.8 MB)
==================================================
downloaded 22.8 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_Human_Breast_Cancer/Visium_Human_Breast_Cancer_spatial.tar.gz'
Content type 'application/x-tar' length 5262726 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

--- finished re-building SpaceMarkers_vignette.Rmd

--- re-building vignette.Rmd using rmarkdown
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Breast_Cancer/Visium_FFPE_Human_Breast_Cancer_spatial.tar.gz'
Content type 'application/x-tar' length 8316248 bytes (7.9 MB)
==================================================
downloaded 7.9 MB


Quitting from lines 182-185 [unnamed-chunk-10] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
object 'optParams_breast_cancer' not found
--- failed re-building vignette.Rmd

SUMMARY: processing the following file failed:
  vignette.Rmd

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output
 
                    			
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merida1 Summary
 
                			
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Package: SpaceMarkers
 
                					
Version: 0.99.5
 
                					
RVersion: 4.4
                
 
                					
BiocVersion: 3.19
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SpaceMarkers
 
                					
BuildTime: 3 minutes 39.49 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: SpaceMarkers_20240212035416
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SpaceMarkers. Starting Build package. 
 
                					
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 1. 
        				
                				
 
                			
 
                			
 
                			    
                				
merida1 BUILD SRC output
 
                    			
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===============================

 R CMD BUILD

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

* checking for file SpaceMarkers/DESCRIPTION ... OK
* preparing SpaceMarkers:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building SpaceMarkers_vignette.Rmd using rmarkdown
trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_Human_Breast_Cancer/Visium_Human_Breast_Cancer_filtered_feature_bc_matrix.h5'
Content type 'binary/octet-stream' length 23942611 bytes (22.8 MB)
==================================================
downloaded 22.8 MB

trying URL 'https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_Human_Breast_Cancer/Visium_Human_Breast_Cancer_spatial.tar.gz'
Content type 'application/x-tar' length 5262726 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

2024-02-11 22:59:29.012 R[2205:759295321] XType: com.apple.fonts is not accessible.
2024-02-11 22:59:29.013 R[2205:759295321] XType: XTFontStaticRegistry is enabled.
--- finished re-building SpaceMarkers_vignette.Rmd

--- re-building vignette.Rmd using rmarkdown
sh: wget: command not found

Quitting from lines 83-89 [unnamed-chunk-5] (vignette.Rmd)
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
length(name) == 1 is not TRUE
--- failed re-building vignette.Rmd

SUMMARY: processing the following file failed:
  vignette.Rmd

Error: Vignette re-building failed.
Execution halted


                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
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merida1 BUILD BIN output
 
                    			
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