On Nov 12, 2009, at 5:19 PM, Seth Falcon wrote:
Hi Michael,
Sorry I don't have more, but a few hints are below...
On 11/12/09 2:48 PM, Michael Muratet wrote:
which grinds along for awhile and then I get a "subscript out of
bounds"
error in a method with which I am unfamiliar. See traceback:
> traceback()
18: stop("subscript out of bounds")
17: .nextMethod(x = x, i = i, ...)
16: .Call("R_nextMethodCall", call, callEnv, PACKAGE = "methods")
15: callNextMethod()
14: x...@ranges[i]
13: x...@ranges[i]
12: seqi...@sread[colonies]
11: seqi...@sread[colonies]
10: .local(run, ...)
9: SeqScore(run = run, int = int, seqInit = seq, colonies =
1:dim(int)[1],
cycles = 1:ncycles)
8: SeqScore(run = run, int = int, seqInit = seq, colonies =
1:dim(int)[1],
cycles = 1:ncycles)
7: .local(run, ...)
6: OneBatch(run, path, lane, tiles[fn + 1:nfiles], outpath, prefix)
5: OneBatch(run, path, lane, tiles[fn + 1:nfiles], outpath, prefix)
4: ForkBatch(run = rolenv.1, sp.1, outpath = "./", prefix = "rs.1",
nthreads = 2, nfiles = 2, lane = lane, tiles = 1:2)
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("batch_analysis.R")
I haven't been able to locate the method where the error occurs.
Maybe
it's in R itself somewhere. Can anyone point me in the right
direction?
Frames 11, 12 are from the Rolexa package, I believe. Line 213 of
Rolexa/R/Model.R has:
siseq = seqi...@sread[colonies]
Then frames 13, 14 jump to either IRanges or Biostrings code (or
both).
Have you been able to run a perhaps smaller example without the fork
package?
Seth
Yes, I am able to execute the process manually. I will take a look at
it again this morning and if I can figure it out I will write a script
to do it manually and serially.
Thanks
Mike
I'm not familiar with fork, but assuming that it is forking the R
process, one might be suspicious of using fork with packages that
use external pointers such as Biostrings. Since R is not multi-
threaded, package code is not setup for concurrent access... Or this
might have nothing to do with the issue you are seeing :-P
+ seth
--
Seth Falcon
Program in Computational Biology | Fred Hutchinson Cancer Research
Center
Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
[email protected]
(256) 327-0473 (p)
(256) 327-0966 (f)
Room 4005
601 Genome Way
Huntsville, Alabama 35806
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