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add details about chromVAR installation issue resolution

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Natalie Elphick 2024-11-18 11:22:15 -08:00
parent 5399e89871
commit ed21334348
1 changed files with 17 additions and 1 deletions
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20
intro-sc-atac-seq/ArchR_demo_issues_and_resolutions.txt
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@ -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/
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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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