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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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Error in utils:download.file when installing SingleR #18

Open hfberg opened 5 years ago

hfberg commented 5 years ago

I have tried to install Single R in all the following ways in different combinations:

devtools::install_github('dviraran/SingleR')

devtools::install_github("dviraran/SingleR")

library(curl)
library(devtools)
install_github('dviraran/SingleR')

I have also re-installed curl, re-installed devtools with dependencies, restarted R (3.4.4) updated everything, installed libcurl4-gnutls-dev instead of libcurl4-openssl-dev (they always replace each other) but after a loooooong wait I always get the following error:

Downloading GitHub repo dviraran/SingleR@master
Error in utils::download.file(url, path, method = download_method(), quiet = quiet,  : 
  download from 'https://api.github.com/repos/dviraran/SingleR/tarball/master' failed

And at one point I got an error in curl (sorry, i did not save the full curl error message!)

Error in curl::curl_fetch_memory(url, handle = h) : 
  Timeout was reached:

I also tried with and without proxy. Same problem.

This might be unrelated to Single R, but in fact i used devtools:install_github earlier today and it worked. I already have a working version of Seurat installed, could this cause issues? If possible, can I install Single R without Seurat? OR is there any other way to install Single R?

dviraran commented 5 years ago

Thanks for the input. Because of the reference datasets, the package is pretty big and takes a while to download.

I am having issues with downloading from Github as well now. I am guessing that they are experiencing some issues with their servers.

Anyhow, you can try downloading SingleR is a zip file and install it directly using install.package. Please let me know if the problem still persists.

Best, Dvir

hfberg commented 5 years ago

This issue was something with the github server as you said, this monday it was installed as it should. Thank you for you help!

simon2073 commented 5 years ago

Thanks for the input. Because of the reference datasets, the package is pretty big and takes a while to download.

I am having issues with downloading from Github as well now. I am guessing that they are experiencing some issues with their servers.

Anyhow, you can try downloading SingleR is a zip file and install it directly using install.package. Please let me know if the problem still persists.

Best, Dvir

dear dvir I came across the same same problem and I have try downloading SingleR zip file,but I can't install it directly using install.package. Library(singR) shows can't find this package.And singleR-master was in Library file . Quite confused.