Problems with RMark and latest version of MARK

[mspinola]

Dear list members,

I am using the last version of RMark (1.8.6) in 2 computers. One computer has an older version of MARK and the other computer has the latest version of MARK.
When I try to run a simple analysis with of RMark (1.8.6) and the last version of MARK I get the following error:

> data(dipper)
> myexample = mark(dipper)
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In system(paste(dQuote(MarkPath), "Mark.exe BATCH i=", inputfile, :
"c:/Program Files/Mark/"Mark.exe not found
2: In file(con, "r") :
cannot open file 'mark001.out': No such file or directory


********Following model failed to run : Phi(~1)p(~1) **********

The same version of RMark (1.8.6) with an older version of MARK works fine.
Does anybody knows what is causing the problem?
Thank you very much in advance.
Best,

Manuel Spínola

[jlaake]

In the newest version of mark.exe (1 Oct), Gary made some changes to the code that writes out the binary file. RMark will not work with that new mark.exe for some data types with groups (notably occupancy and nest survival). If you copy the old mark.exe over to the machine with the new mark.exe all will be fine. Gary and I will resolve this in the very near future. If you need an old mark.exe email me.

I encourage everyone to read the What's new link on the RMark page. I document changes and problems in that file. This problem is documented there.

regards --jeff

[caique]

Dear all,
I’m still having this problem “Error in file(con, "r")” as it is detailed below.
Sorry for raising this old question again, but I couldn’t solve the problem.
I’m using a RMark version newer than R version. I also followed the recommendation on C.2, C.24, “WhatsNewinRMark.pdf” and “help(mark)”, according to the different location of mark.exe file. But the problem is still going on.
Please, could someone make me clear where my wrong is or if I need to use a different version of mark.exe file.
Thanks,
Carlos

R version 2.12.0 (2010-10-15)
> library(RMark)
This is RMark 2.0.0
Built: R 2.12.1; i386-pc-mingw32; 2011-01-14 17:35:50 UTC;
> MarkPath="C:/Arquivos de programas/MARK"
> data(dipper)
> ls()
[1] "dipper" "MarkPath"
> summary(dipper)
ch sex
Length:294 Female:153
Class :character Male :141
Mode :character
> myexample=mark(dipper)
Error in file(con, "r") : cannot open the connection
Warning message: In file(con, "r") : cannot open file 'mark001.out': No such file or directory
********Following model failed to run : Phi(~1)p(~1) **********
> ls()
[1] "dipper" "MarkPath" "myexample"

[jlaake]

Update your version of MARK and double-check the directory specification where you have Mark.exe in MarkPath.

--jeff

[caique]

Dear Jeff,
Thank you very much.
It is likely the problem was only in MarkPath.
I missed the last slash, sorry.
thanks,
Carlos

[chrissuthy]

Unfortunately I still have the same issue. When executing the following:
data(dipper)
myfirstmodel=mark(dipper)

I get the following error:
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
cannot open file 'mark001.out': No such file or directory

********Following model failed to run : Phi(~1)p(~1) **********

I have followed the instructions Jeff gave, update and check the extension, but am still having the problem. Interestingly, if I do not name/store it (mark(dipper)), I get some output but not the summaries expected (pg 13 RMark Workshop).

Thanks in advance and apologies if this is straight forward BUT, the solutions I have come across appear not to work in this case.

Chris

[bacollier]

Unfortunately I still have the same issue. When executing the following:
data(dipper)
myfirstmodel=mark(dipper)

I get the following error:
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
cannot open file 'mark001.out': No such file or directory

********Following model failed to run : Phi(~1)p(~1) **********

I have followed the instructions Jeff gave, update and check the extension, but am still having the problem. Interestingly, if I do not name/store it (mark(dipper)), I get some output but not the summaries expected (pg 13 RMark Workshop).

Thanks in advance and apologies if this is straight forward BUT, the solutions I have come across appear not to work in this case.

Chris

Chris,
If you post your full session info, or send it to me offline (bret@tamu.edu), I will take a look.

Bret