[BioC] odd behavior of R

[James W. MacDonald]

Hi Chris,

This question isn't about BioC packages, so this is really not the right 
list. You will probably get better results if you post on R-sig-mac 
(https://stat.ethz.ch/mailman/listinfo/r-sig-mac)

Best,

Jim



On 11/13/2012 10:02 AM, chris [guest] wrote:
> Hi,
>
> I have recently loaded 2.15.2 on MacOS 10.7.5 and I am noticing some strange behavior.  I run my scripts from the documents window and notice that I am getting old variables appearing in the screen in grey at the prompt in the background.  Does anyone know the source of this error?  I have tried restarting and reinstalling, but the error persist.
>
> Here is an example while running GViz.  The words "merge" and "ChrTmm" are variables used in past sessions and just pop up randomly.  They are grey on my screen, while the active code is blue.  Over time, they will become more and more problematic and start to take over the screen:
>
> merge
> merge
> merge
> merge
> merge
> merge
> merge
> chrTmm
> chrTmm
> chrTmi>  grtrack<- GeneRegionTrack(mm9EG, chromosome = chromo, from = lim[1], to = lim[2], name = "Ensemble Genes",showID=TRUE)
>
> Thank you for any insights.
>
> best wishes,
> Chris
>
>   -- output of sessionInfo():
>
> dr
> dr
> dr>  sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (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] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] biomaRt_2.14.0         GenomicFeatures_1.10.0 AnnotationDbi_1.20.2   Biobase_2.18.0         GenomicRanges_1.10.5   IRanges_1.16.4         BiocGenerics_0.4.0
>   [8] reshape_0.8.4          plyr_1.7.1             Gviz_1.2.0
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.36.0    Biostrings_2.26.2  biovizBase_1.6.0   bitops_1.0-4.2     BSgenome_1.26.1    cluster_1.14.3     colorspace_1.2-0   DBI_0.2-5          DESeq_1.10.1
> [10] dichromat_1.2-4    genefilter_1.40.0  geneplotter_1.36.0 Hmisc_3.10-1       labeling_0.1       lattice_0.20-10    munsell_0.4        parallel_2.15.2    RColorBrewer_1.0-5
> [19] RCurl_1.95-3       Rsamtools_1.10.1   RSQLite_0.11.2     rtracklayer_1.18.0 scales_0.2.2       splines_2.15.2     stats4_2.15.2      stringr_0.6.1      survival_2.36-14
> [28] tools_2.15.2       XML_3.95-0.1       xtable_1.7-0       zlibbioc_1.4.0
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099