[BioC] strange ChIPpeakAnno and rtracklayer interaction.

[Vincent Carey]

This is a nice example, concisely generating a problem that I
encountered a couple of weeks ago.  My impression was that the update
method defined in multtest was the culprit.  I can't say why.  But
when I remove the references to multtest in ChIPpeakAnno's DESCRIPTION
and NAMESPACE files, so that multtest is neither loaded nor attached,
and reinstall ChIPpeakAnno, the error does not occur in the second
command sequence given by Oleg.  This does not include Michael's new
fix -- I haven't updated GenomicRanges.

On Fri, Oct 22, 2010 at 6:03 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> `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 Somehow the 'update,ANY' method defined by GenomicRanges is being superseded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 at 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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