Error during wrapup: cannot open the connection

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.

samr.obj <- samr ( data, resp.type="Two class unpaired", nperms=100 )

traceback()

data <- list ( x=x, y=y, geneid=as.character(1:nrow(x)),

samr.obj <- samr ( data, resp.type="Two class unpaired", nperms=100 )

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

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