[BioC] GenomicFeatures- disjointExons error

Hervé Pagès hpages at fhcrc.org
Thu Oct 17 00:15:59 CEST 2013


Hi Julie,

I cannot reproduce this but I notice that you have a mix of BioC 2.12
(previous release) and BioC 2.13 (current release) packages. For example
DEXSeq 1.6.0 and Biobase 2.20.1 belong to BioC 2.12.

Make sure your installation is up-to-date by running:

     library(BiocInstaller)
     biocLite()

and then double-check that everything is OK with:

     biocValid()

Then try disjointExons() again and let us know if the problem persists.

Cheers,
H.


On 10/16/2013 02:34 PM, Zhu, Lihua (Julie) wrote:
> Herve,
>
> I encountered the following error with disjointExons. Could you please
> help? Thanks!
>
> Best regards,
>
> Julie
>
> library("GenomicRanges")
> library("Rsamtools")
> library("GenomicFeatures")
> mse <- makeTranscriptDbFromBiomart( biomart="ensembl",
>    dataset="mmusculus_gene_ensembl" )
> Download and preprocess the 'transcripts' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Download and preprocess the 'splicings' data frame ... OK
> Download and preprocess the 'genes' data frame ... OK
> Prepare the 'metadata' data frame ... OK
> Make the TranscriptDb object ... OK
>
> exonicParts <- disjointExons( mse, aggregateGenes=TRUE )
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>    base
>
> other attached packages:
>   [1] DEXSeq_1.6.0           biomaRt_2.18.0
>          GenomicFeatures_1.14.0 AnnotationDbi_1.24.0   Biobase_2.20.1
>   [6] Rsamtools_1.12.4       Biostrings_2.28.0      GenomicRanges_1.14.1
>    XVector_0.2.0          IRanges_1.20.0
> [11] BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>   [1] bitops_1.0-6       BSgenome_1.28.0    DBI_0.2-7
>           hwriter_1.3        RCurl_1.95-4.1     RSQLite_0.11.4
>   [7] rtracklayer_1.20.4 statmod_1.4.18     stats4_3.0.2
>        stringr_0.6.2      tools_3.0.2        XML_3.95-0.2
> [13] zlibbioc_1.6.0

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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