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A neat solution for no access to remote SeuratData repository #80

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mangost opened this issue Dec 10, 2023 · 0 comments
Open

A neat solution for no access to remote SeuratData repository #80

mangost opened this issue Dec 10, 2023 · 0 comments

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@mangost
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mangost commented Dec 10, 2023

Many have run into this error:

Using cached data manifest, last updated at 2021-09-13 15:27:39
Error: No access to remote SeuratData repository, unable to install new datasets

A reason (esp for those in mainland China) can be the wall. A popular solution is a proxy.

How to set up proxy to insall seurat-data?

  1. Set the environment variable http_proxy and https_proxy, by either export (in bash), set (in cmd), or Sys.setenv (in R).
  2. Set options so that install.packages uses curl (which automatically recognizes *_proxy : options(download.file.method = "curl")
  3. Install: install.packages("ifnb.SeuratData", repos= "https://seurat.nygenome.org", type="source")

Hope that an update of this package can bring this solution to trashbin.

Before that day (or any other better solution), I hope to keep the state of this issue being open so that people in need can find it.

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