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

John Sibert sibert at hawaii.edu
Thu Aug 19 10:04:24 PDT 2010

The warning about the -s is caused by a change to the admb script making 
the "safe" option the default. So you do not need to specify -s to 
invoke the safe library. You need to use admb -o to build your 
application with the "optimized" (meaning no subscript checking mostly) 
library. I have no idea how to change the option in Ben's package.


On 08/18/2010 06:51 PM, Motoki Wu wrote:
> 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     ld: warning: option -s is obsolete and being ignored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?
> Thanks
> - 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)]
> $platform
> [1] "x86_64-apple-darwin9.8.0"
> $version.string
> [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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John Sibert
Emeritus Researcher, SOEST
University of Hawaii at Manoa

Visit the ADMB project http://admb-project.org/

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