On Thu, Feb 25, 2010 at 10:43 AM, Patrick Aboyoun <[email protected]>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 >> >> >>> >>> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
