install_github issue

[janekim319]

I have followed the instructions to download install ArchR on macOS. I have Big Sur and I'm having trouble even running install_github. I have devtools and biocmanager loaded in R. Below is the error message I get:

Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo GreenleafLab/ArchR@master
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/GreenleafLab/ArchR/tarball/master' failed

Does this error look familiar?

[rcorces]

This looks like it is coming from remotes::install_github() rather than devtools::install_github().
Use
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

[janekim319]

Thank you for the suggestion! I followed everything on the link you provided with a small change from the stack overflow post. I used x86_64-apple-darwin20/11.1.0 instead of x86_64-apple-darwin19/10.2.0 in the Makevars file.

I also ran it after running options(buildtools.check = function(action) TRUE ) to suppress the error "Could not find tools necessary to compile a package". Now I get many errors, mostly dependencies errors, but one stands out. Does "Rhdf5lib" sound familiar to you?

Error: package or namespace load failed for ‘Rhdf5lib’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/Rhdf5lib.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/Rhdf5lib.so, 6): no suitable image found. Did find:
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/Rhdf5lib.so: mach-o, but wrong architecture
/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs/Rhdf5lib.so: mach-o, but wrong architecture
Error: loading failed
Execution halted

[rcorces]

I think you'll need to google around a bit to find your issues since these are not issues with ArchR and my only means of helping you is to google the same things that you could google.

[janekim319]

Thank you so much for your reply. My issue was that I was using the wrong version of R. I had to download R-4.1.0.pkg and not R-4.1.0-arm64.pkg! I hope this help anyone else going through the same issue with a macbook big sur M1 chip!

[mzhibo]

I also have this issue:
"Downloading GitHub repo GreenleafLab/ArchR@master
Error in utils::download.file(url, path, method = method, quiet = quiet, :
download from 'https://api.github.com/repos/GreenleafLab/ArchR/tarball/master' failed"
I have been using ArchR for a while, previously it was fine. Not sure exactly when this error started. I running R in Linux. not on a macbook

[mzhibo]

This seems to be related to secure package download:
https://support.rstudio.com/hc/en-us/articles/206827897-Secure-Package-Downloads-for-R

options(download.file.method = "wget") worked for me (linux)