From ed21334348a52a3de4f2c872998ffda73adde49a Mon Sep 17 00:00:00 2001 From: Natalie Elphick Date: Mon, 18 Nov 2024 11:22:15 -0800 Subject: [PATCH] add details about chromVAR installation issue resolution --- .../ArchR_demo_issues_and_resolutions.txt | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/intro-sc-atac-seq/ArchR_demo_issues_and_resolutions.txt b/intro-sc-atac-seq/ArchR_demo_issues_and_resolutions.txt index 706a80c..66284c2 100644 --- a/intro-sc-atac-seq/ArchR_demo_issues_and_resolutions.txt +++ b/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") ------------------------------------------------------------------------------------------- +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/ ------------------------------------------------------------------------------------------- \ No newline at end of file