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biocbuild@kunpeng1 ~/git> R CMD build --keep-empty-dirs --no-resave-data ELMER * checking for file ‘ELMER/DESCRIPTION’ ... OK * preparing ‘ELMER’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘analysis_data_input.Rmd’ using rmarkdown --- finished re-building ‘analysis_data_input.Rmd’ --- re-building ‘analysis_diff_meth.Rmd’ using rmarkdown --- finished re-building ‘analysis_diff_meth.Rmd’ --- re-building ‘analysis_get_pair.Rmd’ using rmarkdown --- finished re-building ‘analysis_get_pair.Rmd’ --- re-building ‘analysis_gui.Rmd’ using rmarkdown --- finished re-building ‘analysis_gui.Rmd’ --- re-building ‘analysis_motif_enrichment.Rmd’ using rmarkdown --- finished re-building ‘analysis_motif_enrichment.Rmd’ --- re-building ‘analysis_regulatory_tf.Rmd’ using rmarkdown Quitting from lines 93-103 (analysis_regulatory_tf.Rmd) Quitting from lines 93-103 (analysis_regulatory_tf.Rmd) Error: processing vignette 'analysis_regulatory_tf.Rmd' failed with diagnostics: argument is of length zero --- failed re-building ‘analysis_regulatory_tf.Rmd’ --- re-building ‘index.Rmd’ using rmarkdown --- finished re-building ‘index.Rmd’ --- re-building ‘input.Rmd’ using rmarkdown --- finished re-building ‘input.Rmd’ --- re-building ‘pipe.Rmd’ using rmarkdown --- finished re-building ‘pipe.Rmd’ --- re-building ‘plots_TF.Rmd’ using rmarkdown Quitting from lines 41-46 (plots_TF.Rmd) Error: processing vignette 'plots_TF.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘plots_TF.Rmd’ --- re-building ‘plots_heatmap.Rmd’ using rmarkdown --- finished re-building ‘plots_heatmap.Rmd’ --- re-building ‘plots_motif_enrichment.Rmd’ using rmarkdown --- finished re-building ‘plots_motif_enrichment.Rmd’ --- re-building ‘plots_scatter.Rmd’ using rmarkdown --- finished re-building ‘plots_scatter.Rmd’ --- re-building ‘plots_schematic.Rmd’ using rmarkdown --- finished re-building ‘plots_schematic.Rmd’ --- re-building ‘usecase.Rmd’ using rmarkdown --- finished re-building ‘usecase.Rmd’ SUMMARY: processing the following files failed: ‘analysis_regulatory_tf.Rmd’ ‘plots_TF.Rmd’ Error: Vignette re-building failed. Execution halted
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I wasn't able to find a Github repo for ELMER.
The best place to report the issue would be https://support.bioconductor.org/ https://bioconductor.org/packages/release/bioc/html/ELMER.html says Maintainer: Tiago Chedraoui Silva <tiagochst at usp.br> We could do this for 3.18.
Maintainer: Tiago Chedraoui Silva <tiagochst at usp.br>
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