Bioconductor Single Package Builder - Build History

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

Hostname OS /Arch BUILD CHECK BUILD BIN POST-PROCESSING
nebbiolo1 Linux (Ubuntu 20.04.4 LTS)/x86_64   ERROR     skipped     skipped     skipped  
merida1 macOS 10.14.6 Mojave/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo1 Summary

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Package: borealis
Version: 0.99.2
RVersion: 4.2
BiocVersion: 3.15
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data borealis
BuildTime: 0 minutes 54.10 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: borealis_20220419221628
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: borealis. 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 ‘borealis/DESCRIPTION’ ... OK
* preparing ‘borealis’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘borealis.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
loading in Bismark data.
Looping over 274 positions in model building. It will take some time.
modeling complete. Storing results.
Writing results for each sample to file.
Quitting from lines 139-140 (borealis.Rmd) 
Error: processing vignette 'borealis.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘borealis.Rmd’

SUMMARY: processing the following file failed:
  ‘borealis.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: borealis
 
                					
Version: 0.99.2
 
                					
RVersion: 4.2
                
 
                					
BiocVersion: 3.15
                
 

                					
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data borealis
 
                					
BuildTime: 1 minutes 45.68 seconds
 
                					
CheckCommand: 

   							
CheckTime: 

                 					
BuildBinCommand: 

 							
BuildBinTime: 

                					
PackageFileSize: -1.00 KiB
 
                					
BuildID:: borealis_20220419221628
 
                					
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: borealis. 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 ‘borealis/DESCRIPTION’ ... OK
* preparing ‘borealis’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘borealis.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Warning: replacing previous import 'matrixStats::rowMedians' by 'Biobase::rowMedians' when loading 'DSS'
Warning: replacing previous import 'matrixStats::anyMissing' by 'Biobase::anyMissing' when loading 'DSS'
loading in Bismark data.
Looping over 274 positions in model building. It will take some time.
modeling complete. Storing results.
Writing results for each sample to file.
Quitting from lines 139-140 (borealis.Rmd) 
Error: processing vignette 'borealis.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘borealis.Rmd’

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

Error: Vignette re-building failed.
Execution halted


                				
 

                			
 
                			    
                				
merida1 CHECK output
 
                    			
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merida1 BUILD BIN output
 
                    			
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