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.