[R-sig-hpc] Rmpi in "Depends"

[Ramon Diaz-Uriarte]

Dear Hao,

Thanks for your answer.


On Fri, Jul 17, 2009 at 5:02 PM, Hao Yu<hyu at stats.uwo.ca> wrote:
> lamboot is launched in zzz.R at:
>    if (.Platform$OS=="unix"){
>        if(.Call("mpidist",PACKAGE="Rmpi") == 2){
>            if (length(system("lamnodes",TRUE,ignore.stderr = TRUE)) == 0){
>                #cat("\n\tLAM/MPI runtime environment is not operating.\n")
>                #cat("\tStarting LAM/MPI runtime environment.\n")
>                system("lamboot -H",ignore.stderr = TRUE)
>            }
>        }
>    }
>
> One way is to temporally stop lamboot. Another way is to check if user is

So could lamboot be delayed until any of the Rmpi functions are called?

> superuser or not. If there is no significant delay during loading, I will
> try to implement the second approach.
>

That would fix the "installing as root" issue (but would still launch
universes if installed as non-root).

Best,


R.


> Hao
>
>
> Ramon Diaz-Uriarte wrote:
>> Dear Brian,
>>
>> Thanks. Yes, listing as "Suggests" is one approach (what I am doing
>> now, and what some of my other packages in CRAN that use Rmpi do), but
>> it seems somewhat like cheating (the fact is that the package does
>> depend on Rmpi) and not very elegant (I'd rather have the failure at
>> install time than at run time). So something like having the
>> dependency check without actually starting the LAM/MPI universe.
>>
>> Best,
>>
>> R.
>>
>>
>>
>>
>>
>> On Thu, Jul 16, 2009 at 3:29 PM, Brian G. Peterson<brian at braverock.com>
>> wrote:
>>> Ramon Diaz-Uriarte wrote:
>>>>
>>>> Dear All,
>>>>
>>>> I have one package where I listed Rmpi in the "Depends" line in the
>>>> DESCRIPTION file. But this leads to unwanted behavior: installing the
>>>> package will try to start the lam universe (I am using LAM/MPI here).
>>>> This will not work if done as root, and is annoying when done as a
>>>> regular user.
>>>>
>>>> I just checked, and no package in CRAN is listed that has a reverse
>>>> Depends on Rmpi. I've googled around, but haven't been able to locate
>>>> anything, though I think I remember this issue has appeared in the
>>>> past in some list.
>>>>
>>>> Any ideas of the best way to proceed?
>>>>
>>>> Thanks,
>>>>
>>>> R.
>>>>
>>>>
>>>
>>> Sure, list it as "Suggests" in the package DESCRIPTION.
>>> Inside your code, check to see if it is installed, and throw a warning
>>> or
>>> stop() error if the package is not available without starting up the lam
>>> universe.  Make clear in your documentation why you've done this.
>>>
>>> Regards,
>>>
>>>  - Brian
>>>
>>> --
>>> Brian G. Peterson
>>> http://braverock.com/brian/
>>> Ph: 773-459-4973
>>> IM: bgpbraverock
>>>
>>>
>>
>>
>>
>> --
>> Ramon Diaz-Uriarte
>> Structural Biology and Biocomputing Programme
>> Spanish National Cancer Centre (CNIO)
>> http://ligarto.org/rdiaz
>> Phone: +34-91-732-8000 ext. 3019
>>
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>>
>
>
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-- 
Ramon Diaz-Uriarte
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz
Phone: +34-91-732-8000 ext. 3019