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

[Ben Bolker]

  You can use safe=FALSE (the default is TRUE) and extra.args="-o", I
believe.

  Is there a simple way (something like admb --version) to retrieve ADMB
version info?  I believe I'm using revision 76 of the public SVN, which
I *think* is identical to "admb-9.1-linux-gcc4.2-32bit.zip  ( ADMB 9.1
Linux for gcc 4.2 (32 bit); Dec 2009)";

"svn log | head"

 gives

------------------------------------------------------------------------
r74 | jnancheta | 2009-12-31 20:28:45 -0500 (Thu, 31 Dec 2009) | 1 line

[Issue 1] Release of full ADMB source code.  Milestone Dec.2009 completed.

  (this makes me a little bit puzzled where r75 and r76 went, but never
mind ...)

  I'll take a look at the other issue a little later today.

  Ben

John Sibert wrote:
> 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.
> 
> John
> 
> 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     ld: warning: option -s is obsolete and being ignored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
>>>      
>> _______________________________________________
>> Users mailing list
>> Users at admb-project.org
>> http://lists.admb-project.org/mailman/listinfo/users
>>
>>    
> 


-- 
Ben Bolker
bbolker at gmail.com , bolker at mcmaster.ca
http://www.math.mcmaster.ca/~bolker
GPG key: http://www.math.mcmaster.ca/~bolker/benbolker-publickey.asc

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