[R-sig-ME] glmmADMB troubles

[Ross Boylan]

On 3/2/2013 3:04 PM, Ben Bolker wrote:
> On 13-02-28 01:15 PM, Ross Boylan wrote:
>> On 2/27/2013 8:05 PM, Ben Bolker wrote:
>>> Ross Boylan <ross at ...> writes:
>    [snip: not including version without NAs removed, since we already
> know what the issue is there]
>
>>> r <- glmmadmb(sexActs~(1|id), sexpartner[!is.na(sexpartner$sexActs),],
>>> debug=TRUE)
>> platform: windows 32
>> executable name: glmmadmb.exe
>> bin_loc:
>> c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe
>>
>> using temp directory
>> C:\Users\rdboylan\AppData\Local\Temp\Rtmpy2JsMY\glmmADMB17085c19f4d
>> creating temp directory
>> changed working directory to
>> C:/Users/rdboylan/AppData/Local/Temp/Rtmpy2JsMY/glmmADMB17085c19f4d
>> Command line:
>> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe"
>> -maxfn 500 -maxph 5 -noinit -shess
>> Error in system(cmd, intern = intern, wait = wait | intern,
>> show.output.on.console = wait,  :
>>    'C:/Program' not found
>    I'm a little bit baffled here.  What happens if you use save.dir to
> save the input files to a temporary directory and run
>
> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe"
> -maxfn 500 -maxph 5 -noinit -shess
>
> from the command line?

> r <- glmmadmb(sexActs~(1|id), sexpartner[!is.na(sexpartner$sexActs),], debug=TRUE, save.dir="I:/LAMOC/Ross/")
platform: windows 32
executable name: glmmadmb.exe
bin_loc: c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe
changed working directory to I:/LAMOC/Ross
Command line: "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500 -maxph 5 -noinit -shess
Error in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
   'C:/Program' not found

Then from a Windows Command Prompt (not cygwin)
H:\> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32
/glmmadmb.exe" -maxfn 500 -maxph 5 -noinit -shess
Error trying to open data input file glmmadmb.dat
  Error trying to read in model data
  This is usual caused by a missing DAT file
H:\>I:

I:\>cd LAMOC/Ross

I:\LAMOC\Ross> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/b
/windows32/glmmadmb.exe" -maxfn 500 -maxph 5 -noinit -shess

Initial statistics: 1 variables; iteration 0; function evaluation 0; phase 1
Function value   8.9003579e+04; maximum gradient component mag  -5.3609e+02
Var   Value    Gradient   |Var   Value    Gradient   |Var   Value    Gradient

   1  0.00000 -5.36095e+02 |

  - final statistics:
1 variables; iteration 8; function evaluation 14
Function value   5.0576e+04; maximum gradient component mag   6.2393e-08
Exit code = 1;  converg criter   1.0000e-04
Var   Value    Gradient   |Var   Value    Gradient   |Var   Value    Gradient

   1 112.5711  6.23928e-08 |
etc

So it seems to work, provided I start in the save.dir. Note that is the 
directory that R is running in.
glmmadmb.exe is still running as I hit send.

>
>   What is the result of .Platform (and .Platform$OS in particular)

> .Platform
$OS.type
[1] "windows"

$file.sep
[1] "/"

$dynlib.ext
[1] ".dll"

$GUI
[1] "RTerm"

$endian
[1] "little"

$pkgType
[1] "win.binary"

$path.sep
[1] ";"

$r_arch
[1] "i386"

Ross

>
>   It looks conceivably like R is misdiagnosing your system as *not* being
> windows, as that's the only way system() should be running.  Are you
> running under Cygwin (you say it's installed below) ...  ?
>
>> changed working directory to i:/LAMOC/Ross
>> removed temp directory
>> C:\Users\rdboylan\AppData\Local\Temp\Rtmpy2JsMY\glmmADMB17085c19f4d
>>> glmmADMB:::get_bin_loc()
>> $bin_loc
>> [1]
>> "c:/Users/rdboylan/Documents/R/R-2.15.2/site-library/glmmADMB/bin/windows32/glmmadmb.exe"
>>
>>
>> $platform
>> [1] "windows"
>>
>> P.S. about lme4; I don't have a build environment and so trying the
>> github version will not be my first move.
>> Although perhaps lack of a build environment is why the second version
>> is failing.  I do have cygwin installed, althoughI would not expect R to
>> know how to find it.
>    lme4 should be installable from lme4.r-forge.r-project.org/repos now,
> as stated in a message earlier today.
>