www.phidot.org

Hello - hopefully someone can help as I hit a dead-end!
Apologies if this is posted in the wrong section!

I have been using RMark to carry out a study of mark/recapture data. I had used the same data and code for a while whilst I played around with the candidate models. However, all of a sudden, inexplicably, RMark gave me an error of:

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Error in run.mark.model(model, invisible = invisible, adjust = adjust,  :
 
Output file does not exist. Unable to find or run mark.exe


I tired a few simple solutions. Reinstalled RMark (now on RMark 3.0.0) to make sure I had a up to date version. Reinstalled R programme (now on R-4.4.2 for Windows), and R Studio (now on 2024.12.0+467). Still the same issue.
I tried using the dipper data, running a simple:

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data(dipper)
mark(dipper)


I get the same thing!
I tired using my work laptop with the dipper data. Exactly the same - even with the dipper data. I tired using an external hard drive as I read in this forum on another post that syncing might be a similar issue - but I get the same thing!

When I run the dipper data an .inp (mark001.inp) file is created. But not the sub-files (mark001.out, mark001.res, mark001.vcv) as expected. Inspecting the .inp file, it looks normal.
When I run my actual real data for my project:

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cand1.1 <- function(){
  Phi.time = list(formula = ~time)
  Phi.habitat = list(formula = ~habitat)
  Phi.landuse = list(formula = ~lu.mean)
  Phi.distance = list(formula = ~dist.mean)
  Phi.null = list(formula = ~1)
  p.time = list(formula = ~time)
  p.null = list(formula = ~1)
  cml = create.model.list("CJS")
  results = mark.wrapper(cml, data = gull.process, ddl = gull.ddl)
  return(results)
}
(gull.results <- cand1.1())


Again, only the single .inp file is created:

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list.files()
[1] "ANALYSIS GULLS SURVIVAL 2024 v3.R" "DATABASE"                         
[3] "GIS"                               "GULL MAP.qgz"                     
[5] "GULLS SURVIVAL 2024 v3.R"          "LINKS.txt"                       
[7] "mark001.inp"                       "OLD"                             
[9] "OUTPUTS"


and I get the error for each of the models (Phi.distance.p.null, Phi.landuse.p.time etc.):

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Error in run.mark.model(model, invisible = invisible, adjust = adjust,  :
 
Output file does not exist. Unable to find or run mark.exe


No mark models found

Error in collect.models() :


As a result, RMark has become unusable for me, and my project has come to a stand-still!
I can't understand why none of it is suddenly not working or what I'm doing wrong.
Any advice or guidance is welcome, but please keep it simple as my coding skills are relatively basic.

Many thanks,
-Luke

It can't find mark.exe. Did the MARK directory get deleted or moved or did your path change? You can test this by opening a command window and typing mark64.exe or mark32.exe.

Thanks for the speedy reply, Jeff.

I can't find the .exe files you've suggested using cmd.

I didn't delete or move anything. Or, well, as I know of! This happened during using the RMark package. However, if I've accidently achieved this - any suggestions as to how to correct it?
I already uninstalled/reinstalled everything already - so I assume its not that simple!

Thanks once again,

Luke worked out that MARK was missing. I'm going to take this opportunity to remind everyone that RMark does absolutely NOTHING without MARK. RMark is simply an interface for building models for MARK to run. I have been seeing some papers in the literature that cite RMark and R but don't cite MARK. Without exception MARK SHOULD BE CITED and RMark should only be described as an interface to MARK. RMark does not contain any models, it just contains a certain set of MARK models that it supports in the interface. Thus you should NEVER refer to these as RMark models! They are MARK models designed and built with the RMark formula interface.

--jeff