installing ArchR on a mac

Question

[Assa Yeroslaviz]

Can anyone help me installing the library ArchR on a mac book (Intel) with OS Sonoma 14.6.

I have tried to install it but kepp getting the error

> devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())))
Downloading GitHub repo GreenleafLab/ArchR@master
Error: Failed to install 'ArchR' from GitHub:
  Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

When I call the debug command I don't ee any helpful messages.

I have installed the latest version of gfortran and XQuartz. I have installed XCode tools. I even tried to install it all in a conda environment.

But the problem still consists.

Any ideas?

EDIT:

Just to add the output to the debug command:

> devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

Downloading GitHub repo GreenleafLab/ArchR@master
Error: Failed to install 'ArchR' from GitHub:
  Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

> pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
using C compiler: 'clang version 4.0.0 (tags/RELEASE_400/final)'
using SDK: 'MacOSX14.4.sdk'
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
clang-4.0: warning: optimization flag '-falign-functions=64' is not supported [-Wignored-optimization-argument]
/usr/local/clang4/bin/clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/clang4/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
-macosx_version_min has been renamed to -macos_version_min
-macosx_version_min has been renamed to -macos_version_min
dyld[69842]: missing symbol called
clang-4.0: error: unable to execute command: Abort trap: 6
clang-4.0: error: linker command failed due to signal (use -v to see invocation)
make: *** [foo.so] Error 254
Error: Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

[Bastien Hervé]

You already posted your question on the github ArchR : https://github.com/GreenleafLab/ArchR/issues/2206

As they mentioned, they don't have a dedicated person to keep the software up to date, so using the very most up to date version of OS, R and dependencies might be counter productive.

Have you tried what the collaborator advised you to ? On the post you mentioned you have R 4.4.1 (June 14th). Developers need time to adjust their packages to new R version or update of dependencies. So as it was suggested to you before I would try to downgrade your R version to what he suggested, R 4.1

[Assa Yeroslaviz]

Yes I did post it there. And because I got the automated response, I have posted it here to ask for help.

I tried to install R 4.1 in a conda environment. When doing so, I can install BiocManager (installing version 3.14), but I can't install the devtools package.I get all sorts of errors. I also tried in to install earlier versions of devtools, but nothing worked.

So the solution to go back to R 4.1 was not successful.

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS/LAPACK: /Users/yeroslaviz/miniconda3/envs/R4.1/lib/libopenblasp-r0.3.27.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.25

loaded via a namespace (and not attached):
[1] compiler_4.1.3 tools_4.1.3

[Bastien Hervé]

I get all sorts of errors

What are those errors ?

[Assa Yeroslaviz]

They are shown in the question.

[Bastien Hervé]

Try this

[Assa Yeroslaviz]

I will, thanks.