Failed to install ArchR_1.0.3 to Rstudio verison 4.4.1

[ryao-mdanderson]

Dear author,

I used the commands in RStudion 4.4.1

library(devtools)
devtools::install_github("GreenleafLab/ArchR", ref="dev", repos = BiocManager::repositories())

It installed over hundred dependency packaged but hit an error message at the end:
...
Installing package into ‘/home/ryao/R/ubuntu/4.4.1’
(as ‘lib’ is unspecified)

• installing source package ‘ArchR’ ...
  ** using staged installation
  ERROR: configuration failed for package ‘ArchR’
• removing ‘/home/ryao/R/ubuntu/4.4.1/ArchR’
  Warning message:
  In i.p(...) :
  installation of package ‘/tmp/RtmpqN38wl/file1c590358323294/ArchR_1.0.3.tar.gz’ had non-zero exit status

I tried the above command with ref="master", hit the same error.

Would you please advise any pointer for the root cause? any suggestion for the fix?

Thank you very much for your help.
Rong

[immanuelazn]

Hi Rong,
Happy to help. It is pretty hard to diagnose without the rest of the call, since the output is only showing me that there was a failure. Could you give me the rest of the output from the installation function call?

[ryao-mdanderson]

ArchR-1.0.3.txt
Hi Immanuel, thanks for your quick response. I attached the installation full terminal output.

Best,
Rong

[ryao-mdanderson]

BTW, for ref=dev and for ref=master, every time I started with a clean empty library.

[ryao-mdanderson]

Hello Immanuel, @immanuelazn, have you got a chance to review the installation note? Any suggestion? Thank you for your help.

[immanuelazn]

Hi Rong,

Not entirely sure but my best guess is you're missing some ubuntu header files. Unfortunately I can't see which ones are missing, but I can give you a comprehensive list of all the requirements. Unfortunately devtools, remotes, and base install package doesn't handle this for you.

Here is everthing that's normally required:

sudo apt-get install -y curl libz-dev \
    libhdf5-dev libpoppler-cpp-dev libgit2-dev libproj-dev libgdal-dev \
    libbz2-dev liblzma-dev libgsl-dev libtesseract-dev libudunits2-dev \
    libxml2 libcairo2-dev libxt-dev libglpk-dev python3-dev python3-pip

But you can also just try installing via pak instead, or using one of the docker images provided

[ryao-mdanderson]

Hello Immanuel, I appreciate the suggestion! I will give a try and update this solution.

[ryao-mdanderson]

Hi Immaneul, @immanuelazn

With all the above suggested header files packages installed inside the container, unfortunate, no luck to install ArchR successfully, at the end seeing the following message, same as before.
...
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘ArchR/.github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/ryao/R/ubuntu/4.4.1’
(as ‘lib’ is unspecified)

• installing source package ‘ArchR’ ...
  ** using staged installation
  ERROR: configuration failed for package ‘ArchR’

Well, this appears hard to troubleshooting. Thank you for your helps as this far.

Rong