[BioC] subscript out of bounds halting error when Sweaving with weaver And GOstats' HyperGTest
kleiman at rohan.sdsu.edu
Sat Oct 4 23:26:50 CEST 2008
I am trying to Sweave the results section of my masters thesis using
package 'weaver' as an alternative to simply loading a previously stored
R session of objects, i.e, load(file='file.RData'), into an R noweb
code chunk, ...
But when I Sweave (cache) with weaver and then call the GOstats' function,
'HyperGTest' inside a code chunk, I get the following weaver 'subscript
out of bounds' halting error,
$ # run weaver using bash script as described in doc 'weaver_howTo.pdf'
$ ./weaver.sh mythesis-results.Rnw
hgResultlst <- hyperGTest(hgParamslst COMPUTING...
Error: chunk 17 (label=perform.hypergeometric.testing)
Error in .subset2(x, i, exact = exact) : subscript out of bounds
Here's a snippet of code chunk 17, that weaver is complaining about,
<<perform.hypergeometric.testing, echo=FALSE, cache=TRUE>>=
# create list of GOHyperGParams objects for test="over" ...
hgParamslst <- list( BP = over.hgparamsBP, CC = over.hgparamsCC, MF =
# perform hypergeometric testing, store results as list of
GOHyperGResults objects ...
hgResultlst <- lapply(hgParamslst, hyperGTest)
The above hypergeometric testing code runs without error in a regular
basic R session, i.e.,
> # create list of GOHyperGParams objects for test="over" ...
> hgParamslst <- list( BP = over.hgparamsBP, CC = over.hgparamsCC, MF =
> # perform hypergeometric testing, store results as list of
GOHyperGResults objects ...
> hgResultlst <- lapply(hgParamslst, hyperGTest)
but chokes in weaver for some reason, and I don't know why? [its my
first time using weaver]
If anyone could provide me with any insights regarding this matter, that
would be totally
RE: Although loading a previously stored R session of objects does work
it hides all the steps that are used to generate those objects, ..., and
so I thought maybe
weaver could provide a solution to this, by enabling code chunk caching
of my rather
time-intensive GOstats' hyperGTest function calls.
> # print-out sessionInfo()
R version 2.7.2 (2008-08-25)
attached base packages:
 splines tools stats graphics grDevices utils datasets
 methods base
other attached packages:
 GOstats_2.6.0 Category_2.6.0 genefilter_1.20.1
 survival_2.34-1 RBGL_1.16.0 GO.db_2.2.0
 graph_1.18.1 lumiRatV1_1.3.1 lumiRatAll.db_1.2.0
 lumi_1.6.3 mgcv_1.4-1 beadarray_1.8.0
 affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1
 geneplotter_1.18.0 annotate_1.18.0 xtable_1.5-3
 AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4
 lattice_0.17-15 Biobase_2.0.1 limma_2.14.7
loaded via a namespace (and not attached):
 KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.11 grid_2.7.2
MS graduate student
Program in Computational Science
San Diego State University
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