Installing RMark on Mac OS X Yosemite or El Capitan

posts related to the RMark library, which may not be of general interest to users of 'classic' MARK

Re: Installing RMark on Mac OS X Yosemite or El Capitan

Postby tiffanygoh » Tue Aug 11, 2020 2:01 am

I downloaded the zip file for OS/X and it works. Got RMark running now! Thanks :)
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Re: Installing RMark on Mac OS X Yosemite or El Capitan

Postby cooch » Tue Aug 11, 2020 9:52 am

tiffanygoh wrote:I downloaded the zip file for OS/X and it works. Got RMark running now! Thanks :)


That's good. I made an error in pointing you at mark.64.zip. That applies to Linux users. For Mac users, the correct file is mac.osx.zip, which you found. I suspect that the OS/X binary is a bit out of date, but as long as you're not using a very new data type, that shouldn't be a problem.
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Re: Installing RMark on Mac OS X Yosemite or El Capitan

Postby tiffanygoh » Tue Aug 11, 2020 11:54 am

I suspect that the OS/X binary is a bit out of date, but as long as you're not using a very new data type, that shouldn't be a problem.


What do you mean by a very new data type? :?
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Re: Installing RMark on Mac OS X Yosemite or El Capitan

Postby cooch » Wed Aug 12, 2020 9:35 am

At the moment, MARK has 182 different data types. The full list can be found under the 'Help' menu. The newest data types are those at the bottom - generally, these are very new data types that have just been described in the literature (and are of specialized, but often not general, interest). Here are the first ~20 lines of that list:

Available data types in Program MARK (# indicates allowed with median chat,
$ indicates simulation possible,
_ indicates dots are allowed in encounter histories, and
* indicates also available with RMark):

1. #$_*Live: Live Recaptures (CJS)
2. #$*Dead: Dead Recoveries (Seber)
3. #$*Both: Joint Live and Dead Encounters (Burnham)
4. #$_*Known: Known Fate
5. $*Closed: Full Likelihood p and c
6. #$BTO: BTO Dead Recoveries and Unknown Ringings
7. $*Robust: Robust Design with Full Likelihood p and c
8. #$*Barker: Joint Live and Dead Encounters (Barker)
9. #$_*Multistrata: Multi-state with Live Recaptures
10. #$*Brownie: Dead Recoveries (Brownie et al.)
11. $*Jolly: Jolly-Seber Lambda (Burnham)
12. #$_*Huggins: Huggins' p and c
13. $_*RDHuggins: Robust Design with Huggins' p and c
14. *Pradel: Pradel Recruitment Only
15. $*PradSen: Pradel Survival and Seniority
16. $*PradLambda: Pradel Survival and Lambda
17. $*PradRec: Pradel Survival and Recruitment
18. $_*RDBarker: Barker Live and Dead with Robust Design Full Likelihood p and c
19. $_*POPAN: POPAN
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Re: Installing RMark on Mac OS X Yosemite or El Capitan

Postby luke.eberhart » Mon Feb 14, 2022 12:10 pm

to anyone out there struggling to get RMark to run on macOS Monterey (12.1)...

I followed david.koons@usu.edu steps at the start of this thread and all worked well until step 8.

When I typed "mark" in the command line (without quotes), Terminal responded with:
"zsh: permission denied: mark"

To get around this permission issue I typed the following into terminal, which gives access to the current user:
Code: Select all
chmod u+x /usr/local/bin/mark


this also subsequently successfully made the "/usr/local/bin/mark" file an executable (the icon should turn from white to black with green "exec" labelled within).

The next issue was that Apple saw the "/usr/local/bin/mark" file as an 'unidentified third-party application' and killed my attempt to try step 8 again. To get around this, I typed the following into Terminal, which forced mark to open regardless of if the developer was from a third-party:
Code: Select all
xattr -dr com.apple.quarantine "/usr/local/bin/mark"


This resulted in Terminal printing the following, which confirms that the Mark was successfully installed:
"No input file was specified, so MARK job is done.
STOP No input file"

To confirm in R that RMark can find the mark executable you can run the following after installing and loading the RMark package (i.e., "require(RMark)")
Code: Select all
data(dipper)
dipper_Phidot_pdot <- mark(dipper, threads = 1)

if it worked, the model should run and the output should be displayed in your R console.
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Re: Installing RMark on Mac OS X Yosemite or El Capitan

Postby quinn.c » Thu May 05, 2022 9:22 am

Hello,

I had a lot of trouble installing mark on my mac (2014 macbook pro running Big Sur) and finally got it to work, so thought I’d post here in case it helps someone in the future. I Frankenstein-ed a few solutions together from this blog post.

1. I already had XCode installed. I then installed the command-line tools for xcode (link to find the correct version: https://developer.apple.com/download/all/?q=xcode)

2. Test in terminal that the command-line tools were successfully installed by typing: xcode-select -p

3. The following output indicates this was installed successfully: /Library/Developer/CommandLineTools

4. Install gfortran using homebrew (install homebrew first if needed). Type: brew install gcc

Note: I opted to install via homebrew because, although I was able to install and gunzip gcc/gfortran from http://hpc.sourceforge.net/, I encountered errors when trying to use sudo tar.

5. After installing gcc using homebrew, download mark for mac osx. Double-click to unzip, rename this file ‘mark’. Drag the file to usr/local/bin using the earlier suggestion (open -a Finder /usr/local/bin)

6. Make the mark file executable using the earlier suggestion (chmod +x mark). You can check this worked by viewing the permissions for ‘mark’ by typing: ls -l (if you are in the /usr/local/bin directory)

7. Type: mark

8. The correct display message should now show up: “No input file was specified, so MARK job is done”

9. RMark should now work when installed

Good luck!
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