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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