[ADMB Users] new version of R2admb on R-forge

Motoki Wu tokestermw at gmail.com
Wed Aug 18 21:51:33 PDT 2010

Hi Ben, thanks a lot for this.

I am checking the code for the simple.tpl example in the original ADMB installation, and I am getting an error when I do do_admb(). When I follow the error message, it leads to the following portion of the code:

    cred <- coutfile[!substr(coutfile, 1, 85) %in% c("cat: xxalloc4.tmp: No such file or directory", 
        "cat: xxalloc5.tmp: No such file or directory", "Error executing command cat xxglobal.tmp   xxhtop.tmp   header.tmp   xxalloc1.tmp   x")]
    if (length(cred) > 0) 
        stop("errors detected in compilation: run with verbose=TRUE to view")

For the variable cred, I get a warning:
   ld: warning: option -s is obsolete and being ignored

Getting rid of the -s argument should work, but also, shouldn't the negation (!) be removed to actually detect the error?


- Motoki

ps: my session (admb-9.1.556-macos10.6-xcode3.2-intel-32bit.dmg)

x <- rnorm(20, 5, 2)
y <- rnorm(20, 2, 9)
do_admb("simple", data = list(nobs = length(x), Y = y, x = x), params = list(a = 2, b = 1), verbose = T, checkparam = "ignore", checkdata = "ignore", objfunname = "f", clean = F)

> R.Version()[c(1,13)]
[1] "x86_64-apple-darwin9.8.0"

[1] "R version 2.11.1 (2010-05-31)"

On Aug 18, 2010, at 6:14 PM, Ben Bolker wrote:

>  For any R users out there trying to get up the learning curve with
> ADMB: I've put a new version of "R2admb" on r-forge (hence you should be
> able to install from within R via
> install.packages("R2admb",repos="http://r-forge.r-project.org") . It's
> supposed to handle as much as possible of the work of passing R objects
> to AD Model Builder, compiling/linking/running, getting the results back
> into R, and analyzing them.  You still need to write the PROCEDURE
> section of the TPL file, but R2admb can write most of the PARAMETER and
> DATA sections automatically, on the basis of the data and parameter
> lists you pass it.  The package includes a 'vignette' (R-speak for a PDF
> document with examples); after installing and loading
> [library("R2admb")] the package, you can access it via vignette("R2admb").
>  Bug reports, wish lists, comments are all welcome.
>  Ben Bolker
> _______________________________________________
> Users mailing list
> Users at admb-project.org
> http://lists.admb-project.org/mailman/listinfo/users

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