Unable to install ArchR on Mac

[jeanne09jiang]

Hi,

I'm trying to install ArchR but having compilation failed for 'ArchR' error. I'm using a Mac, and have GNU Fortran and Xquartz installed. Below are the error message:

> devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
Downloading GitHub repo GreenleafLab/ArchR@master
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                           
2: CRAN packages only            
3: None                          
4: evaluate (0.19 -> 0.20) [CRAN]
5: formatR  (1.13 -> 1.14) [CRAN]
6: DT       (0.26 -> 0.27) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 
✔  checking for file ‘/private/var/folders/qy/2y67t6zx7q33bjdzb6dvkdr00000gr/T/RtmpUPV9Rj/remotes62c662cb87ee/GreenleafLab-ArchR-79953a9/DESCRIPTION’ ...
─  preparing ‘ArchR’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘ArchR_1.0.2.tar.gz’
   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’
   
* installing *source* package ‘ArchR’ ...
** using staged installation
** libs
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c Correlation.cpp -o Correlation.o
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c Footprinting_utils.cpp -o Footprinting_utils.o
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c General_Utils.cpp -o General_Utils.o
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c KNN_Utils.cpp -o KNN_Utils.o
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c Kmer_Bias.cpp -o Kmer_Bias.o
/usr/local/gfortran/bin/g++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include   -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c RcppExports.cpp -o RcppExports.o
/usr/local/gfortran/bin/g++ -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o ArchR.so Correlation.o Footprinting_utils.o General_Utils.o KNN_Utils.o Kmer_Bias.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
0  0x10be39ffa  __assert_rtn + 139
1  0x10bc6d28d  mach_o::relocatable::Parser<x86_64>::parse(mach_o::relocatable::ParserOptions const&) + 4989
2  0x10bc5df8f  mach_o::relocatable::Parser<x86_64>::parse(unsigned char const*, unsigned long long, char const*, long, ld::File::Ordinal, mach_o::relocatable::ParserOptions const&) + 207
3  0x10bcd49d4  ld::tool::InputFiles::makeFile(Options::FileInfo const&, bool) + 2036
4  0x10bcd7fa0  ___ZN2ld4tool10InputFilesC2ER7Options_block_invoke + 48
5  0x7ff81a1ea34a  _dispatch_client_callout2 + 8
6  0x7ff81a1fb8f5  _dispatch_apply_invoke + 213
7  0x7ff81a1ea317  _dispatch_client_callout + 8
8  0x7ff81a1f9c0c  _dispatch_root_queue_drain + 673
9  0x7ff81a1fa25c  _dispatch_worker_thread2 + 160
10  0x7ff81a39df8a  _pthread_wqthread + 256
A linker snapshot was created at:
	/tmp/ArchR.so-2023-01-18-151744.ld-snapshot
ld: Assertion failed: (_file->_atomsArrayCount == computedAtomCount && "more atoms allocated than expected"), function parse, file macho_relocatable_file.cpp, line 2061.
collect2: error: ld returned 1 exit status
make: *** [ArchR.so] Error 1
ERROR: compilation failed for package ‘ArchR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ArchR’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/qy/2y67t6zx7q33bjdzb6dvkdr00000gr/T//RtmpUPV9Rj/file62c62c59add1/ArchR_1.0.2.tar.gz’ had non-zero exit status

[rcorces]

I dont think this is anything I can help with. A quick google search points to this which might be helpful:
https://github.com/orgs/Homebrew/discussions/3659