mark giving "missing symbol" error

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mark giving "missing symbol" error

Postby ghaines » Wed May 03, 2023 10:41 am

Hi all,

I am receiving an error with mark that I can't find a fix to anywhere, and would appreciate some help finding a fix.

I have been following the instructions here: https://oliviergimenez.github.io/popdyn-workshop/tutorials/rmark-mac.html on downloading the RMark package.

Everything went well until the last step, when I ran into the permission error with the 'mark' exe file addressed by Dāvis Ūlands's note at the bottom of the page of the linked instructions. Unfortunately, after running his fix in the terminal [
Code: Select all
sudo chmod 755 /usr/local/bin/mark
], I get the following error (I am running macOS Monterey 12.6, and have installed v 12.1 of gcc and gfortran):

Code: Select all
$ mark
dyld[6792]: missing symbol called

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0  0x10bb0c29d
#1  0x10bb0b6cd
#2  0x7ff81321cdfc
Abort trap: 6


I am okay with R but don't normally do any work in the terminal, so any suggestions you have here to get RMark running would be greatly appreciated.

thanks very much
ghaines
 
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Re: mark giving "missing symbol" error

Postby egc » Wed May 03, 2023 11:01 am

Two quick questions:

1\ Intel or M1/M2-based Mac?

2\ did you try the older version of MARK that is included in the .zip archive? It contains 'version 10' and the older 'version 9'.

Beyond that, hard to provide much help. Each iteration of OS/X tweaks enough things this way or that it is increasingly likely that a binary the runs on one flavor doesn't work as intended on another. [Whereas basic system structures for Windows and Linux tend not change much, which is why supporting those OS is much easier...] Neither Gary or I have access to a Mac, so we'll need to reach out to colleagues...
egc
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Re: mark giving "missing symbol" error

Postby ghaines » Thu May 04, 2023 5:35 am

Thanks, it's an intel-based Mac, and I used the file in the mark.osx.zip folder that is named mark.64.osx (I assume this is the version 9 file, since the other one is called mark64.10.osx). Should I try the mark64.10.osx file instead?

There is a minor OS update I need to install, so maybe that will sort things out.

thanks again
ghaines
 
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Joined: Wed May 03, 2023 9:40 am

Re: mark giving "missing symbol" error

Postby cooch » Thu May 04, 2023 6:38 am

No harm in trying version 10. Alas, I doubt minor OS update will fix the problem, but - fingers crossed.

The main limit to providing help is that neither Gary or I have a Mac to suss out the issues at our end. Colleagues (most recently Brett McClintock at NOAA) have in past kindly compiled the executable, but only as a favour. Asking them to trouble-shoot is a step too far, and much of the time involves getting further down in the weeds with various things than is fair to ask. [In contrast, compilation under Windows and Linux is straightforward, and nary an issue with people getting things to run - although there were a few minor issues when Windows 10 first rolled out having to do with 'compatibility mode' settings'. But on balance...using a Windows- or Linux-based machine eliminates your hassles using MARK]

Good luck!
cooch
 
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Re: mark giving "missing symbol" error

Postby sbonner » Thu May 04, 2023 11:06 pm

Have you tried installing Mark through homebrew following the instructions here http://www.phidot.org/forum/viewtopic.php?f=21&t=3233&p=10916&hilit=brew#p10916. I've just update the tap to the latest version of the Mark binary for Mac available from the phidot pages and it works for me.

The important thing about this approach is that it will keep your versions of GCC inline because everything is handled through homebrew.
sbonner
 
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Re: mark giving "missing symbol" error

Postby ghaines » Sun May 07, 2023 9:54 am

Thanks very much to you both. I will give v. 10 a shot and then try MARK installation through homebrew if that doesn't work.

cheers
ghaines
 
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Re: mark giving "missing symbol" error

Postby cooch » Sun May 07, 2023 2:29 pm

Fair enough - keep us posted.
cooch
 
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