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
nebbiolo1 Linux (Ubuntu 22.04.2 LTS)/x86_64   ERROR     skipped     skipped     skipped  

nebbiolo1 Summary

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Package: SurfR
Version: 0.99.49
RVersion: 4.4
BiocVersion: 3.19
BuildCommand: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SurfR
BuildTime: 0 minutes 35.69 seconds
CheckCommand:
CheckTime:
BuildBinCommand:
BuildBinTime:
PackageFileSize: -1.00 KiB
BuildID:: SurfR_20231213081534
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.

nebbiolo1 BUILD SRC output

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

 R CMD BUILD

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* 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
Error: processing vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
Duplicate chunk label 'metacombine', which has been used for the chunk:
metacomb <- combine_fisher_invnorm(ind_deg = list(TCGA.BRCA =  df.TCGA, 
                                                  GEO.GSE58135 = df.GSE58135),
                                   invnorm = L_invnorm,
                                   fishercomb = L_fishercomb,
                                   adjpval = 0.05)


metacomb_GeneID <- metacomb[metacomb$signFC != 0, "GeneID"]
SP <- Gene2SProtein(genes = metacomb_GeneID, input_type = "gene_name")
Error: tangling vignette 'Intro_to_SurfR.Rmd' failed with diagnostics:
Duplicate chunk label 'metacombine', which has been used for the chunk:
metacomb <- combine_fisher_invnorm(ind_deg = list(TCGA.BRCA =  df.TCGA, 
                                                  GEO.GSE58135 = df.GSE58135),
                                   invnorm = L_invnorm,
                                   fishercomb = L_fishercomb,
                                   adjpval = 0.05)


metacomb_GeneID <- metacomb[metacomb$signFC != 0, "GeneID"]
SP <- Gene2SProtein(genes = metacomb_GeneID, input_type = "gene_name")
--- failed re-building ‘Intro_to_SurfR.Rmd’

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

Error: Vignette re-building failed.
Execution halted

nebbiolo1 CHECK output

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nebbiolo1 BUILD BIN output
 
                    			
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