Herve,
It works like wonder!
Thank you so much for your kind help!
FYI, here is what did.
Downloaded the latest version of the BiocInstaller package, then upgrades
all currently installed packages to the latest repositories for this version
of R using the following commands.
source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")
Best regards,
Julie
On 10/16/13 6:15 PM, "Hervé Pagès" <hpages at fhcrc.org> wrote:
> 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