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rcavalcante / annotatr

Package Homepage: http://bioconductor.org/packages/devel/bioc/html/annotatr.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=annotatr.
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Error in build_annotations() for mm10_cpgs #56

Closed elderelizabeth closed 5 months ago

elderelizabeth commented 1 year ago

Hey there!

I am encountering this error when trying to build annotations for mm10_cpgs. No such error occurs when building other mm10 annotations, and mm10_cpgs worked fine just a few weeks ago. I tried troubleshooting myself but I am at a loss and would really appreciate the help.

Thanks for this great package by the way.

cpgs_annots = build_annotations(genome = "mm10", annotations = "mm10cpgs") Building CpG islands... Error in vroom(file, delim = delim %||% col_types$delim, col_names = col_names, :
bad value

jamesboot commented 1 year ago

I get the same error using the following code:

annots = c('hg38_cpgs', 'hg38_basicgenes')
annotations = build_annotations(genome = 'hg38', annotations = annots)

Any help greatly appreciated!

elderelizabeth commented 1 year ago

Hey! The only way I found to "fix" this error is to re-install (I use the BiocManager package to install and manage packages) and re-load the annotatr package. However, that only seems to temporarily fix it because it eventually bugs again so I have to keep re-installing and reloading the package whenever the error occurs. Not the best fix but at least I got it working. Hopefully this helps.

BiocManager::install("annotatr", update = TRUE, ask = FALSE, force = TRUE)

library(annotatr)

rcavalcante commented 5 months ago

I have not been able to reproduce this issue.