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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Installation issues #59

Closed bschilder closed 1 year ago

bschilder commented 1 year ago

Hello, thanks for the great tool! I'm the developer of echofinemap, a fine-mapping pipeline that includes PAINTOR. Unfortunately I don't seem to be able to install PAINTOR_V3.0 on my mac anymore. Do you know what might be going on here? Do you have a conda environment yaml file that might be useful for this (since it seems to be some sort of dependency conflict issue)? @gkichaev @ruthjohnson95

Many thanks in advance, Brian

Reprex

Code

cd /Library/Frameworks/R.framework/Versions/4.2/Resources/library/echofinemap/tools/PAINTOR_V3.0 && bash install.sh

Errors

See attached (too long to include in comment). paintor_install_errors.txt

Potential causes

System

Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4
bschilder commented 1 year ago

Good news, I figured it out!

It was indeed a C compiler issue, but the solution was actually to switch back over to clang (via xcode).

I've written the function setup_gcc for switching back and forth between versions. Running this worked for me:

source("https://github.com/RajLabMSSM/echofinemap/raw/master/R/setup_gcc.R")
setup_gcc(version="clang")
cmd <- "cd /Library/Frameworks/R.framework/Versions/4.2/Resources/library/echofinemap/tools/PAINTOR_V3.0 && bash install.sh"
system(cmd)