add details about chromVAR installation issue resolution

intro-sc-atac-seq/ArchR_demo_issues_and_resolutions.txt

@@ -9,6 +9,7 @@ require(devtools)
 install_version("ggplot2", version = "3.4.4", repos = "http://cran.us.r-project.org") 
 
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+ArchR installation
 
 Error: 
 I get the following error message while installing ArchR-> ERROR: dependency ‘chromVAR’ is not available for package ‘ArchR’
@@ -21,7 +22,22 @@ Warning messages:
 
 Resolution:
 1. You would need to install chromVar and then re-run ArchR installation: https://bioconductor.org/packages/release/bioc/html/chromVAR.html
-2. One of the participants had another issue. chromVar isntllation complained about gfortan. If so, please follow the resolution here: I found this issue that might help: https://www.biostars.org/p/9579258/
+
-
+-------------------------------------------------------------------------------------------
+chromVAR installation
+
+Error:
+ld: warning: search path '/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0' not found
+ld: warning: search path '/opt/gfortran/lib' not found
+ld: library 'gfortran' not found
+clang: error: linker command failed with exit code 1 (use -v to see invocation)
+make: *** [chromVAR.so] Error 1
+ERROR: compilation failed for package ‘chromVAR’
+* removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/chromVAR’
+
+Resolution:
+1. chromVAR installation fails on Mac when a fortran compiler is not available.
+2. As of R 4.2 using the homebrew compilers (brew install gcc) is not a stable solution (see the note in the page linked below).
+3. Solution is follow the mandatory tools section on this page: https://mac.r-project.org/tools/
 
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