[R] Error during wrapup: cannot open the connection

[Martin Morgan]

On 05/25/2010 08:52 AM, Sheila Reynolds wrote:
> Follow-up : one of my colleagues (who is not experiencing this problem)
> noticed that I had an older version of impute than he did, so I have now
> installed impute_1.22.0, but I still get the same error.

Hi Sheila --

Apparently your 'data' list wants an element logged2=TRUE, which I
discovered with

> samr.obj <- samr ( data, resp.type="Two class unpaired", nperms=100 )
perm= 1
Error in !logged2 : invalid argument type
> traceback()
2: foldchange.twoclass(xstar, ystar, data$logged2)
1: samr(data, resp.type = "Two class unpaired", nperms = 100)

aha, looks like data$logged2 is being accessed!

> data <- list ( x=x, y=y, geneid=as.character(1:nrow(x)),
+               genenames=paste("g",as.character(1:nrow(x))),
+               logged2=TRUE)
> samr.obj <- samr ( data, resp.type="Two class unpaired", nperms=100 )

I'd guess that the 'cannot open connection' is a consequence of the
error, and not directly relevant to your problem.

Martin

> 
> thanks,
> 
> Sheila
> 
> 
> On Mon, May 24, 2010 at 3:01 PM, Sheila Reynolds <
> sheilamoorereynolds at gmail.com> wrote:
> 
>>
>> I am trying to use a new (to me) package (samr) and even when I try to run
>> a very simple example, I get this "cannot open the connection" error.
>>
>> The reason I am writing to r-help rather than to the authors of samr is I
>> think this may be a more general R problem rather than a samr-specific
>> problem.  Perhaps something with my installation and write access to some
>> particular place ?  I am currently running on a Windows box (where I do not
>> have administrator privileges) but have been meaning to shift over to a
>> linux box, perhaps this will push me there faster.
>>
>> In any case, if anyone has a suggestion on where I should look to solve
>> this, I'd greatly appreciate it.  Below is what I tried and what happened
>> (with the error highlighted in bold red font).
>>
>> thanks in advance,
>>
>> Sheila
>>
>>
>>
>>> library (samr)
>> Loading required package: impute
>>>
>>> ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>> - -
>>> ## testing the two class unpaired example from the man pages ...
>>>
>>> set.seed(100)
>>> x <- matrix ( rnorm(1000*20), ncol=20 )
>>> dd <- sample ( 1:1000, size=100 )
>>> u <- matrix ( 2*rnorm(100), ncol=10, nrow=100 )
>>> x[dd,11:20] <- x[dd,11:20] + u
>>> y <- c(rep(1,10),rep(2,10))
>>>
>>> data <- list ( x=x, y=y, geneid=as.character(1:nrow(x)),
>> +                genenames=paste("g",as.character(1:nrow(x))) )
>>>
>>> samr.obj <- samr ( data, resp.type="Two class unpaired",
>> +                    nperms=100, logged2=TRUE )
>> Error in samr(data, resp.type = "Two class unpaired", nperms = 100, logged2
>> = TRUE) :
>>   unused argument(s) (logged2 = TRUE)
>> Error during wrapup: cannot open the connection
>>>
>>>
>>> samr.obj <- samr ( data, resp.type="Two class unpaired",
>> +                    nperms=100 )
>> perm= 1
>> Error in !logged2 : invalid argument type
>> *Error during wrapup: cannot open the connection*
>>> sessionInfo()
>> R version 2.11.0 (2010-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] samr_1.28    impute_1.0-5
>>>
>>
>>
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793