Bioconductor Single Package Builder - Build History

Snapshot Date: 
URL:  https://git.bioconductor.org/packages/SurfR
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   TIMEOUT     skipped     skipped     skipped  

lconway Summary

[top]

Package: SurfR
Version: 0.99.28
RVersion: 4.3
BiocVersion: 3.18
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SurfR
BuildTime: 1 minutes 5.91 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: SurfR_20231021164233
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SurfR. 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.

lconway BUILD SRC output

[top]

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

 R CMD BUILD

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

* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Intro_to_SurfR.Rmd’ using rmarkdown
--2023-10-21 12:44:38--  https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121810/matrix/GSE121810_series_matrix.txt.gz
Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 165.112.9.228, 165.112.9.230
Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|165.112.9.228|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3326 (3.2K) [application/x-gzip]
Saving to: ‘GSE121810_series_matrix.txt.gz’

     0K ...                                                   100%  113M=0s

2023-10-21 12:44:38 (113 MB/s) - ‘GSE121810_series_matrix.txt.gz’ saved [3326/3326]


Quitting from lines 183-211 [GEO input] (Intro_to_SurfR.Rmd)
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
Rhdf5lib was not compiled with support for the S3 VFD

--- failed re-building ‘Intro_to_SurfR.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_to_SurfR.Rmd’

Error: Vignette re-building failed.
Execution halted

lconway CHECK output

[top]


                				
 

                            
 
                                
                				
lconway BUILD BIN output
 
                    			
[top]

                				
 
                					

                				
 
                
		    
		        			

                			
                			
nebbiolo2 Summary
 
                			
[top]

                			
 
                				
 
						        
Package: SurfR
 
                					
Version: 0.99.28
 
                					
RVersion: 4.3
                
 
                					
BiocVersion: 3.18
                
 

                					
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SurfR
 
                					
BuildTime: 15 minutes 0.00 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: SurfR_20231021164233
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: SurfR. 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: -9. 
        				
                				
 
                			
 
                			
 
                			    
                				
nebbiolo2 BUILD SRC output
 
                    			
[top]

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

 R CMD BUILD

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

* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
TIMEOUT: R CMD build exceeded 15 mins




                				
 

                			
 
                			    
                				
nebbiolo2 CHECK output
 
                    			
[top]

                				
 
                					

                				
 

                            
 
                                
                				
nebbiolo2 BUILD BIN output
 
                    			
[top]