`Hi,

Somehow the 'update,ANY' method defined by GenomicRanges is being superseded
by stats::update() (which is the ANY method in all other packages). If I
change update,ANY to update,GenomicRanges, everything works. I'll go ahead
and commit this change, but this still seems like an issue with the methods
package. Not sure why it only happens with ChIPpeakAnno.

Michael

On Thu, Oct 21, 2010 at 3:58 PM, <oleg@stat.berkeley.edu> wrote:

> Hi, all
>
> I wanted to annotate my peaks using ChIPpeakAnno with a table from UCSC
> genome browser that I was going to import using rtracklayer package.  The
> code runs fine if I do this:
>
> library(ChIPpeakAnno)
> library(rtracklayer)
> session=browserSession()
> genome(session)='hg19'
> query=ucscTableQuery(session,'refGene')
>
>
> BUT: if I exchange the order in which I load libraries in a new R session,
> it crashes:
>
> library(rtracklayer)
> library(ChIPpeakAnno)
> session=browserSession()
> genome(session)='hg19'
> > query=ucscTableQuery(session,'refGene')
> Error in x[[name, exact = FALSE]] :
>  missing '[[' method for Sequence class GRanges
> >
>
>
> So there seems to be some sort of weird interaction between ChIPpeakAnno
> and rtracklayer that causes errors if ChIPpeakAnno is loaded AFTER
> rtracklayer but not before.
>
> It also seems that in general, I need to load ChIPpeakAnno before ANY
> OTHER packages I use because for example this works:
>
> library(ChIPpeakAnno)
> library(BSgenome.Hsapiens.UCSC.hg19)
> library(ShortRead)
> library(rtracklayer)
> session=browserSession()
> genome(session)='hg19'
> query=ucscTableQuery(session,'refGene')
>
> but this doesn't:
>
> library(BSgenome.Hsapiens.UCSC.hg19)
> library(ChIPpeakAnno)
> library(ShortRead)
> library(rtracklayer)
> session=browserSession()
> genome(session)='hg19'
> query=ucscTableQuery(session,'refGene')
> Error in x[[name, exact = FALSE]] :
>  missing '[[' method for Sequence class GRanges
>
>
> Session info for this last session is below. Just letting you know that
> this problem exists.
>
> Oleg.
>
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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] rtracklayer_1.9.11                  RCurl_1.4-3
>  [3] bitops_1.0-4.1                      ShortRead_1.7.30
>  [5] Rsamtools_1.1.17                    lattice_0.19-13
>  [7] ChIPpeakAnno_1.5.5                  limma_3.5.21
>  [9] org.Hs.eg.db_2.4.6                  GO.db_2.4.5
> [11] RSQLite_0.9-2                       DBI_0.2-5
> [13] AnnotationDbi_1.11.9
>  BSgenome.Ecoli.NCBI.20080805_1.3.16
> [15] multtest_2.5.14                     Biobase_2.9.2
> [17] biomaRt_2.5.1                       BSgenome.Hsapiens.UCSC.hg19_1.3.16
> [19] BSgenome_1.17.7                     Biostrings_2.17.48
> [21] GenomicRanges_1.1.38                IRanges_1.7.39
>
> loaded via a namespace (and not attached):
> [1] grid_2.12.0     hwriter_1.2     MASS_7.3-8      splines_2.12.0
> [5] survival_2.35-8 XML_3.2-0
> >
>
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