[Bioc-sig-seq] error with export {rtracklayer}

[Patrick Aboyoun]

Joseph,
It appears that you are using R 2.10.1 with a mix of BioC 2.5 packages 
and BioC 2.6 packages. For R 2.10.1, you should only have BioC 2.5 
packages installed. One solution is to run biocLite to install the BioC 
2.5 versions of IRanges and Biostrings.

BSgenome_1.14.2    - BioC 2.5
rtracklayer_1.6.0  - BioC 2.5
ShortRead_1.4.0    - BioC 2.5

IRanges_1.5.49     - BioC 2.6
Biostrings_2.15.22 - BioC 2.6


The other solution is to move to R-devel and use BioC 2.6 packages.


Patrick


On 2/25/10 10:25 AM, joseph wrote:
> Hello
>
> I need help to fix an error when trying to export a bedGraph:
>    
>> export(cvge_test, "cvge_test.bedGraph")
>>      
> Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
>
> more information on what I did:
>    
>> test
>>      
> class: AlignedRead
> length: 871819 reads; width: 13..34 cycles
> chromosome: chr7 chr12 ... chr19 chrM
> position: 99250659 60363973 ... 12084236 16156
> strand: + + ... - -
> alignQuality: NumericQuality
> alignData varLabels: similar mismatch
>
> cvge_test = coverage(test)
>    
>> cvge_test
>>      
> SimpleRleList of length 22
> $chr1
> 'integer' Rle of length 197182846 with 26843 runs
>    Lengths: 3008620      26    5998      32 ...       1       1       1      14
>    Values :       0       1       0       2 ...       4       6       8      10
> $chr10
> 'integer' Rle of length 129992419 with 17807 runs
>    Lengths: 3074426      23   12686      29 ...       3      26       3       1
>    Values :       0       1       0       1 ...       1       4       3       2
> ...
>
> ##make bedGraph
>    
>> export(cvge_test, "cvge_test.bedGraph")
>>      
> Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
>
>
>
>    
>> sessionInfo()
>>      
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.4.0    lattice_0.17-26    BSgenome_1.14.2    Biostrings_2.15.22
> [5] IRanges_1.5.49     rtracklayer_1.6.0  RCurl_1.3-1        bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.1 grid_2.10.1   hwriter_1.1   XML_2.6-0
>    
>>      
>
>
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>
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