subscript out of bounds halting error when Sweaving with weaver And GOstats' HyperGTest
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@elliot-kleiman-2565
Last seen 6.8 years ago
Hi BioC, 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 Execution halted 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 = over.hgparamsMF ) # perform hypergeometric testing, store results as list of GOHyperGResults objects ... hgResultlst <- lapply(hgParamslst, hyperGTest) @ Note: 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 = over.hgparamsMF ) > # 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 awesome! Thanks, ... Elliot RE: Although loading a previously stored R session of objects does work with Sweaving, 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() > sessionInfo() R version 2.7.2 (2008-08-25) i686-pc-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=C;L C_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GOstats_2.6.0 Category_2.6.0 genefilter_1.20.1 [4] survival_2.34-1 RBGL_1.16.0 GO.db_2.2.0 [7] graph_1.18.1 lumiRatV1_1.3.1 lumiRatAll.db_1.2.0 [10] lumi_1.6.3 mgcv_1.4-1 beadarray_1.8.0 [13] affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 [16] geneplotter_1.18.0 annotate_1.18.0 xtable_1.5-3 [19] AnnotationDbi_1.2.2 RSQLite_0.7-0 DBI_0.2-4 [22] lattice_0.17-15 Biobase_2.0.1 limma_2.14.7 loaded via a namespace (and not attached): [1] 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 http://www.csrc.sdsu.edu/
GO weaver GO weaver • 881 views
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