On Thu, Feb 25, 2010 at 10:43 AM, Patrick Aboyoun <paboyoun@fhcrc.org>wrote:

> 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.
>
>
I would encourage this for rtracklayer, as lots of bugs have been fixed
since last release.

>
> 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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>>
>>
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