Configuration failed, installtion of dev branch on no-network-machine

[ZeroLi-Bio]

Hello,

I tried to install dev branch ArchR on a network-restricted machine (only specific sites allowd to access, such as github, CRAN, etc.) and got errors as below:

* installing *source* package ‘ArchR’ ...
** using staged installation
ERROR: configuration failed for package ‘ArchR’
* removing ‘/00.software/miniconda3/envs/r421/lib/R/library/ArchR’
* restoring previous ‘/00.software/miniconda3/envs/r421/lib/R/library/ArchR’
Warning message:
In i.p(...) :
  installation of package ‘/software/tmp_cache/R/RtmpTkROn1/file41a9665f4af7/ArchR_1.0.3.tar.gz’ had non-zero exit status

I tried in two ways as install.packages from local and devtools::install_github with ref="dev" and got the same results above. Then I found that in dev branch, the file "configure" seems to need network access. While in the master branch, there's no such file. I don't know its usage but I deleted this file from the tar.gz, retried to install from tar.gz and it worked.

I think this explains this similar issue #1750. I wonder will it affect usage? If not I suggest considering delete this for easier intalltion or give a hint on this.

Thanks.

[rcorces]

Hi @ZeroLi-Bio! Thanks for using ArchR! Lately, it has been very challenging for me to keep up with maintenance of this package and all of my other responsibilities as a PI. I have not been responding to issue posts and I have not been pushing updates to the software. We are actively searching to hire a computational biologist to continue to develop and maintain ArchR and related tools. If you know someone who might be a good fit, please let us know! In the meantime, your issue will likely go without a reply. Most issues with ArchR right not relate to compatibility. Try reverting to R 4.1 and Bioconductor 3.15. Newer versions of Seurat and Matrix also are causing issues. Sorry for not being able to provide active support for this package at this time.

[LAMaglan]

It would be great if it could be explicitly mentioned that the installation also runs the "configure" file, as this implications for how to deal with any required software proxy (e.g. for servers that have restricted access due to company policy).

Either mention this in the README.md and/or https://www.archrproject.com/