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

[Motoki Wu]

Hi Ben,

I got a different error this time (posted below), assuming this is the code you're referring to: https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/R/admb-funs.R?revision=25&root=r2admb

But I think it's just a simple typo. In your new do_admb(), the arguments in the following line of code needs to be flipped: 

sapply(warning,admb_warnings)

After fixing this, it worked!

- Motoki


##### ------- old version

> do_admb("simple2", data = list(nobs = length(x), Y = y, x = x), params = list(a = 2, b = 1), verbose = T, checkparam = "ignore", checkdata = "ignore", objfunname = "f", clean = T, safe = F)
compiling with args: '  ' ...
compile output:
  *** tpl2cpp   simple2  *** adcomp     simple2 g++ -c -O3 -Wno-deprecated -D__GNUDOS__  -Dlinux -DOPT_LIB -DUSE_LAPLACE -fpermissive -I. -I/opt/local/admb/include simple2.cpp   *** adlink     simple2 g++ -s  -L/opt/local/admb/lib simple2.o -ldf1b2o -ladmod -ladt -lado -ldf1b2o -ladmod -ladt -lado -o simple2  
compile log:
ld: warning: option -s is obsolete and being ignored
Error in do_admb("simple2", data = list(nobs = length(x), Y = y, x = x),  : 
  errors detected in compilation: run with verbose=TRUE to view

> traceback()
       2: stop("errors detected in compilation: run with verbose=TRUE to view")
       1: do_admb("simple2", 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)

###### ------- new version

> do_admb("simple2", data = list(nobs = length(x), Y = y, x = x), params = list(a = 2, b = 1), verbose = T, checkparam = "ignore", checkdata = "ignore", objfunname = "f", clean = T, safe = F)
compiling with args: '  ' ...
compile output:
  *** tpl2cpp   simple2  *** adcomp     simple2 g++ -c -O3 -Wno-deprecated -D__GNUDOS__  -Dlinux -DOPT_LIB -DUSE_LAPLACE -fpermissive -I. -I/opt/local/admb/include simple2.cpp   *** adlink     simple2 g++ -s  -L/opt/local/admb/lib simple2.o -ldf1b2o -ladmod -ladt -lado -ldf1b2o -ladmod -ladt -lado -o simple2  
compile log:
ld: warning: option -s is obsolete and being ignored
Error in get(as.character(FUN), mode = "function", envir = envir) : 
  object 'from ADMB: ld: warning: option -s is obsolete and being ignored' of mode 'function' was not found

> traceback()
4: get(as.character(FUN), mode = "function", envir = envir)
3: match.fun(FUN)
2: sapply(warning, admb_warnings)
1: do_admb("simple2", data = list(nobs = length(x), Y = y, x = x), 
       params = list(a = 2, b = 1), verbose = T, checkparam = "ignore", 
       checkdata = "ignore", objfunname = "f", clean = T, safe = T)

####### ------ fixed new version

> do_admb("simple2", data = list(nobs = length(x), Y = y, x = x), params = list(a = 2, b = 1), verbose = T, checkparam = "ignore", checkdata = "ignore", objfunname = "f", clean = T, safe = F)
compiling with args: '  ' ...
compile output:
  *** tpl2cpp   simple2  *** adcomp     simple2 g++ -c -O3 -Wno-deprecated -D__GNUDOS__  -Dlinux -DOPT_LIB -DUSE_LAPLACE -fpermissive -I. -I/opt/local/admb/include simple2.cpp   *** adlink     simple2 g++ -s  -L/opt/local/admb/lib simple2.o -ldf1b2o -ladmod -ladt -lado -ldf1b2o -ladmod -ladt -lado -o simple2  
compile log:
ld: warning: option -s is obsolete and being ignored
writing data and parameter files ...
running compiled executable with args: '  '...
Run output:


Initial statistics: 2 variables; iteration 0; function evaluation 0
Function value   8.0025892e+01; maximum gradient component mag   6.8268e+00
Var   Value    Gradient   |Var   Value    Gradient   |Var   Value    Gradient   
  1  2.00000  6.82682e+00 |  2  1.00000  1.12079e+00 |

 - final statistics:
2 variables; iteration 7; function evaluation 12
Function value   6.9985e+01; maximum gradient component mag   2.0435e-06
Exit code = 1;  converg criter   1.0000e-04
Var   Value    Gradient   |Var   Value    Gradient   |Var   Value    Gradient   
  1 -1.15391  2.04351e-06 |  2  8.90396  7.37683e-08 |
Estimating row 1 out of 2 for hessian
Estimating row 2 out of 2 for hessian





reading output ...
Warning message:
In lapply(X, FUN, ...) :
  from ADMB: ld: warning: option -s is obsolete and being ignored



On Aug 19, 2010, at 10:41 AM, Ben Bolker wrote:

> 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
>