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

Ben Bolker bolker at ufl.edu
Sat Aug 21 08:43:10 PDT 2010

  That's not exactly the situation in which the errors/warnings occur.
  They happen when one runs tpl2rem on a RE model that is "too simple":
as pointed out by Tom Wainwright on March 10
this is reproducible in the "liver_gamma" example that comes with ADMB:

> tpl2rem liver_gamma

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   xxalloc2.tmp   xxalloc3.tmp   xxalloc4.tmp
xxalloc5.tmp    xxtopm.tmp    xxalloc6.tmp > liver_gamma.cpp

  At least, it happens with my installation (release 9.1, running on
Ubuntu 10.04).

    Ben Bolker

dave fournier wrote:
> Ben Bolker wrote:
> Hi,
> For the example  simple.tpl
> If I type
>      tpl2cpp  simple
> on linux is just works.
>     tpl2rem simple
> produces an (warning or error) message since there are no random effects in
>  simple.
> In neither case is the mesage exactly the same as what you have.
>             Cheers,
>            Dave
>> dave fournier wrote:
>>> You are getting the message
>>>      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")]
>>> because the indicated file is only created when using a particular
>>> option in the tpl file. It is not really an error because everything is
>>> working fine.
>>   It's a bit confusing, but the R error actually occurred (I think) due
>> to the warning about safe mode ("-s") being obsolete/redundant. I've
>> added an (UNTESTED) bit of code on SVN that's supposed to pass warnings
>> from ADMB through to R's warning() system rather than considering them
>> errors and stopping.  The complicated bit that Motoki quoted is used to
>> avoid an error when those (non-error) error messages pop up, by
>> explicitly ignoring them.
>>   Motoki, could you test the latest version with safe=TRUE and
>> safe=FALSE and see if it works properly (i.e. warning when safe=TRUE,
>> running cleanly when safe=FALSE) ... ? (If I knew how to easily provoke
>> a non-fatal warning from ADMB, I would test it myself ...)
>>   It would be really nice (wish list) if things that are not really
>> errors would not produce error messages ... that would help those of us
>> who are relatively new to ADMB and hence relatively clueless focus on
>> the things that are really wrong with our models ...
>>   cheers
>>     Ben Bolker

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

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