[ADMB Users] Problem running glmmADMB in R 2.9.1 (Windows)

[Tanya Russell]

Hi,

I am new to glmmADMB and I am experiencing problems running the model using the R interface. As follows:

> data(epil2)
> glmm.admb(y~Base*trt+Age+Visit,random=~Visit,group="subject",data=epil2,family="nbinom")
'C:/Users/Tanya' is not recognized as an internal or external command,
operable program or batch file.
Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit, group = "subject",  :
  The function maximizer failed
In addition: Warning messages:
1: In dir.create(dirname) : '_glmm_ADMB_temp_dir_' already exists
2: In file.remove(std_file) :
  cannot remove file 'nbmm.std', reason 'No such file or directory'
3: In shell(paste(.path.package("glmmADMB"), "/admb/", file_name, ".exe",  :
  'C:/Users/Tanya Russell/Documents/R/win-library/2.9/glmmADMB/admb/nbmm.exe -maxfn 500 ' execution failed with error code 1

My feeling is that the error originates from the space in the directory name. Could you please assist me to deal with this issue.

Kind regards, Tanya.

Dr Tanya Russell | Senior Research Fellow | PacMISC | Australian Centre for International and Tropical Health
School of Population Health | The University of Queensland | Public Health Building | Herston Rd | Herston Qld 4006 | Australia
Mob: +61434 286 890 | Email: t.rus...@uq.edu.au

[H. Skaug]

Hi Tanya,

I am sorry, but I do not have other advice to offer than:

- Try another version of R (version 2.5 say)

If this does not work:

- Try another machine.

Hope this helps you.

Hans

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[dave fournier]

I don't know anything about R packaging, but the compressed format seems
to be an incredibly inconvenient format. If the code were simply suppled
as an R script one could trivially edit it to take account of the
space in the path. BTW it won't install for me on the latest R version
for windows. What is the point of that?

[dave fournier]

I know almost nothing about R as already said. However I think one can
fix this by modifying the glmm.admb function sort of like this.

load the glmmadmb package.

sink("modglmmadm.r")
glmm.admb
sink()

then edit the file modglmmadmb.r to put quotes around the string
(or however one deals with spaces in paths in windows).
at the beginning of the file put in
glmm.admb=
then in R type

source("modglmmadmb.r")

and you should have the new modified function which can deal with spaces
in path names. Anyway that is a rough idea.

[Arni Magnusson]

Hans and I are in the process of releasing glmmADMB on CRAN, so it will
install and run on all current machines. Here's the cake-in-the-oven
release:

install.packages("glmmADMB", repos="http://R-Forge.R-project.org")

It may require R 2.11, and my guess is that the space-in-path issue is
probably still there. We will slide that to the top priorities.

Dave's hacker approach may well do the trick for you. We're currently
experimenting with which directories glmmADMB should use and how.

Arni

[dave fournier]

I added " " to the path string and it worked.
Perhaps you could modify the package to look for
additional r scripts as as option.
That would make it easier to modify the package.
For example one might want to do a beta regression mixed model.