Brian M. Schilder

[BUG] pkgdown site build fails within Docker containers

6

[pkgdown site step](https://github.com/lcolladotor/biocthis/blob/341ae80706ecc2950e0a50bc36dc7416f2a5d173/.github/workflows/check-bioc.yml#L279) runs into error when using a Docker container. ## Issue This happens because of the [recent changes to git](https://github.com/actions/checkout/issues/760) regarding security. Supposedly this has been fixed in...

`ggtree::read.tree` crashes RStudio

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Hello, `ggtree::read.tree` aborts RStudio, both on my Desktop Rstudio and within a [Bioconductor Docker container](https://github.com/Bioconductor/bioconductor_docker). ### Reprex ```R tree_path

GitHub Actions checks are randomly failing when trying to build Rmarkdown vignettes with plots. I suspect (but can't be sure) that this might be related to `magick`. GHA output found...

`Response is missing required header Content-Length: for url `

11

**Describe the bug** Unable to import bigwig files stored on a remote server. Originally posted [in the `rtracklayer` GH repo](https://github.com/lawremi/rtracklayer/issues/73) and was directed by `rtracklayer` developer @sanchit-saini to repost here....

`Installation paths not writeable, unable to update packages`

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This only seems to an issue when I try to install MOFA2 within a Docker container (using my local Rstudio installation works fine). Though the Docker container has Bioc v3.16...

Missing fastMNN outputs

1

Looks like some of the output from fastMNN isn't making it into the Seurat object. Could you add these? Thanks! ```R seurat_lvl

Download doesn't work after changing style name and ID

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Hello, Thanks for creating such a useful resource. However, there seems to be some issues with the visual editor: https://editor.citationstyles.org/searchByName/ ## 1. I tried to edit the Human Molecular Genetics...

Request for differential peak analysis. Basically, if you have two groups specified in your design file, you'd run a test of whether they peak overlap is significantly similar (e.g. by...

Reposting here from the [nf-core Slack](https://nf-co.re/join) for posterity. Thanks for @drpatelh for figuring this out! ## Problem nextflow/atacseq pipeline does not recognize the design.csv file, even though it follows the...

phylopic_uid: Error in download_url(path) : Failed to download

3

Originally documented this error in `ggtree`, but realized that many of the internal functions are actually borrowed from `ggimage`. https://github.com/YuLab-SMU/ggtree/issues/482