[BioC] FW: strange ChIPpeakAnno and rtracklayer interaction.

[Zhu, Lihua (Julie)]

Herve,

Do you know why the following error occurs depending on the order of package
loading? ChIPpeakAnno does not use Granges and this error does not occur in
the previous release.

Error in x[[name, exact = FALSE]] :
  missing '[[' method for Sequence class Granges

Best regards,

Julie

------ Forwarded Message
From: "oleg at stat.berkeley.edu" <oleg at stat.berkeley.edu>
Date: Thu, 21 Oct 2010 18:58:57 -0400
To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
Subject: [BioC] strange ChIPpeakAnno and rtracklayer interaction.

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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------ End of Forwarded Message