Finemap missing dependency in macOS #9
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Hi @tillandlauer, thanks for bringing this up! This is something I've been trying to figure how to best resolve for a while. Installing via brew assumes the user is using a mac and has brew installed, which I could probably write some checks for. Then there's also the issues with root privileges, for installing brew. And of course, we'd need another solution for Linux/Windows users. I've also explored using zstd installed via conda. But from what I recall, FINEMAP wasn't able to find this installation of ztd and doesn't have an argument to specify where zstd is. Ideally, zstandard would be included in FINEMAP itself, but I haven't heard of any plans to do this. So in the end I thought it best to just give user the warning message. But I'll revisit this now and see if I can come up with a better solution. Any suggestions for how to implement this are welcome! |
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I've also noticed that following the instructions from http://www.christianbenner.com/ to install zstd to solve this issue with FINEMAPv1.4 doesn't seem to work on my Mac either (though this does not appear to be an issue on Linux). This is why I have echolocatoR then default to v1.3 upon failing with v1.4. I've reached out to the FINEMAP author to see if he can provide a fix for this. |
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Response from FINEMAP author, Christian Benner, who replied a long time ago but just documenting here now for users:
brew installFollowing these instructions on my Mac: However, the output indicates I already have gcc8 installed: Just in case there are multiple versions of gcc installed on my computer, I checked which version is being defaulted to in the terminal: Not sure why clang is coming up instead of gcc, but this might be related. brew reinstallFull output messages: But this didn't seem to change anything, same issue as before (even when i start a new bash session): Interim solutionSince this issues was first noted, my workaround has been to build in a |
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aha! think i found something regarding the symlinks based on this post: This does indeed seem to be the executable I want. Now i need to find a way to redirect the symlink to this version (preferably from within R). |
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In fact, it seems I have multiple versions of gcc installed on my Mac: Overwrite symlinkAfter starting a new bash session, the right gcc is now being referenced! Now to figure out how to do this within R in a way that communicates with FINEMAP. |
Within REven though I can see the right version of gcc is indeed being referred to.... out <- R.utils::createLink(
link="/usr/local/bin/gcc",
target="/usr/local/bin/gcc-8",
overwrite=TRUE)
system("gcc -v")FINEMAP doesn't' seem to be able to recognize it. Even including the softlink creation within the same command doesn't help: system("/Users/schilder/Library/Caches/org.R-project.R/R/echofinemap/FINEMAP/finemap_v1.4.1_MacOSX/finemap_v1.4.1_MacOSX")
## or
system("ln -sF /usr/local/bin/gcc-8 /usr/local/bin/gcc & /Users/schilder/Library/Caches/org.R-project.R/R/echofinemap/FINEMAP/finemap_v1.4.1_MacOSX/finemap_v1.4.1_MacOSX")Within terminalIt doesn't even seem to be R related, as FINEMAP has this same issue when called from the terminal. Maybe it has something to do with where it's cashed?
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GOT IT!! ProcedureOk, so several things needed to be in place:
Within RI've created an internal function in Because it overwrite any preexisting symlinks, Test runNow FINEMAP v1.4.1 successfully runs all the way through!! Mac specs |
Repository owner
moved this from Todo
to Done
in 🦇🦇 echoverse 🦇🦇
Aug 27, 2022
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apologies for re-opening the issue: I am on a Mac arm64 architecture - and the procedure your have outlined here doesn't seem to be working for me. I was wondering if there is an equivalent for arm64 case? |
Hi @asoroosh, I'll try to look into it Could you send me the specific specs on your Mac? Should be findable via |
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Hi Brian - thanks for your reply. See the spec below: 
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FINEMAP won't run on a Mac unless Zstandard is installed (error message:
dyld: Library not loaded: /usr/local/lib/libzstd.1.dylib), see: http://www.christianbenner.comMac OSX users: If you see dyld: Library not loaded: /usr/local/lib/libzstd.1.dylib, install Zstandard..The Zstandard lib (https://facebook.github.io/zstd/) can be installed in macOS using
brew install zstd. Please consider adding this library to the install routine!The text was updated successfully, but these errors were encountered: