spacexr cannot be installed through devtools::install_github

[yu-tong-wang]

Hello @dmcable , I am using R version 4.1.3 on MacOS (x86_64-apple-darwin17.0 (64-bit)), and below is the error message I got when trying to install the package.

> # install.packages("devtools")
> devtools::install_github("dmcable/spacexr")
Downloading GitHub repo dmcable/spacexr@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  download from 'https://api.github.com/repos/dmcable/spacexr/tarball/HEAD' failed

I am currently using a work-around by first git clone and then

devtools::install("~/Documents/GitHub/spacexr")

which allows me to manually import the spacexr library.

[yu-tong-wang]

I also have a quick question about data accessibility when trying to reproduce the simulation result (Fig 2) in C-SIDE, if you do not mind. What is "../../../spacexr/data/Reference/10xCer/reference.rds" in
https://github.com/dmcable/spacexr/blob/master/AnalysisCSIDE/Figures/figure2.Rmd#L27 ?

I could not find relevant scripts to generate 10xCer-related data from the Visium data provided in ./extdata, maybe ./10xCer is not an intermediate result directory but from some external single cell reference?

Thank you! (Let me know if it is better to create a new issue with a different issue title for this :) )

[dmcable]

Dear Yutong,

Interesting, I haven't been able to reproduce this issue on my computer, and I am not exactly sure what is causing it. The workaround you pursued is good. Here are some potentially relevant webpages I found:

https://stackoverflow.com/questions/65273115/r-devtoolsinstall-githubjzsbioinfo-aprd-error-in-utilsdownload-fileurl
r-lib/devtools#2303
forestgeo/learn#102

Hope this helps.

Best,
Dylan

[dmcable]

The cerebellum 10x reference can be found at the scp portal: https://singlecell.broadinstitute.org/single_cell/study/SCP948/robust-decomposition-of-cell-type-mixtures-in-spatial-transcriptomics

Please note that ./extdata contains toy or downsampled datasets and not the full original data.

Best,
Dylan

[yu-tong-wang]

Thank you for your helpful response, Dylan.

[Jtrachsel]

I think this issue is related to the download from github timing out. Our network is slow and we were having this same issue. When I increased the 'timeout' option the install worked fine.

options(timeout = 600000000)

devtools::install_github("dmcable/spacexr")

[jebard]

I think this issue is related to the download from github timing out. Our network is slow and we were having this same issue. When I increased the 'timeout' option the install worked fine.

options(timeout = 600000000)

devtools::install_github("dmcable/spacexr")

I know this thread is a bit old but I just hit this same error today, and setting the timeout parameter cleared the errors and installed successfully.

[cmiciano]

also was receiving the above error, thank you @Jtrachsel