Hi Martin,
Thanks for the quick explanation. I got the latest version of the
packages mentioned below from svn - and installed them using Herve's
HTS core package stack
(http://www.bioconductor.org/help/newsletters/2015_October/#hts-core-package-stack)
and I don't see the problem any more.
> library(AnnotationHub)
> ah =AnnotationHub()
snapshotDate(): 2015-11-19
> ah = query(ah , c("Homo sapiens", "org", "GRCH37", "FASTA","75"))
> hg37_rrna = ah[["AH10879"]]
require(“Rsamtools”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/10879’
‘https://annotationhub.bioconductor.org/fetch/14665’
retrieving 2 resources
|======================================================================|
100%
|======================================================================|
100%
There were 50 or more warnings (use warnings() to see the first 50)
Val, thanks for adding the stack to the newsletter !
FYI - I dont see it here -
http://www.bioconductor.org/packages/devel/bioc/html/S4Vectors.html
under the documentation section.
Thanks and Regards,
Sonali.
On 12/21/2015 1:33 PM, Morgan, Martin wrote:
Hi Sonali --
relistToClass was originally in IRanges
Packages such as Biostrings that Depend: or Import: IRanges and then create a
'relistToClass' method created a methods table on INSTALLATION, noting that the
generic is in IRanges.
The 'relistToClass' generic was moved from IRanges to S4Vectors, with
appropriate version bumps for these packages.
Loading the 'old' version of Biostrings (library(Biostrings)) now sees a new
generic in S4Vectors, but has the old methods table that thinks the methods are
being added to the IRanges generic.
This results in the warning "multiple methods tables found for ‘relistToClass’".
The end-user solution is to re-install the Biostrings package
(biocLite("Biostrings")). This will use the correct methods table.
Any package that defines a method on relistToClass requires updating; there are similar problems with 'space' and 'unlist'. I believe the
'core' packages requiring updating (defining methods, but svn revision older than r111605) include c("GenomicRanges",
"rtracklayer", "GenomicAlignments", "Biostrings", "BSgenome", "VariantAnnotation").
Please let me know if the problem continues after re-installing these packages.
I have bumped the versions of each of these packages, so that biocLite() after
tomorrow-ish should force these to be re-installed.
Usually 'multiple methods tables' is a warning; AnnotationHub:::.require
promotes the warning to an error.
Martin
________________________________________
From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Sonali B Arora
[sar...@fredhutch.org]
Sent: Monday, December 21, 2015 3:08 PM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple
methods tables found for ‘relistToClass’
Hi everyone,
I am trying to get a FaFile from AnnotationHub - It fails with the
following error
library(AnnotationHub)
ah =AnnotationHub()
ah = query(ah , c("Homo sapiens", "org", "GRCH37", "FASTA","75"))
hg37_rna = ah[["AH10879"]]
> hg37_rna = ah[["AH10879"]]
require(“Rsamtools”)
Error: failed to load 'AnnotationHub' resource
name: AH10879
title: Homo_sapiens.GRCh37.75.ncrna.fa
reason: require(“Rsamtools”) failed: multiple methods tables found
for ‘relistToClass’
> sessionInfo()
R Under development (unstable) (2015-10-15 r69519)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
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=en_US.UTF-8 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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomeInfoDb_1.7.3 IRanges_2.5.18 S4Vectors_0.9.15
[4] AnnotationHub_2.3.6 BiocGenerics_0.17.2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.2 AnnotationDbi_1.33.3
[3] magrittr_1.5 zlibbioc_1.17.0
[5] xtable_1.8-0 R6_2.1.1
[7] stringr_1.0.0 httr_1.0.0
[9] tools_3.3.0 Biobase_2.31.3
[11] DBI_0.3.1 htmltools_0.2.6
[13] digest_0.6.8 interactiveDisplayBase_1.9.0
[15] shiny_0.12.2 curl_0.9.4
[17] RSQLite_1.0.0 mime_0.4
[19] stringi_1.0-1 BiocInstaller_1.21.2
[21] httpuv_1.3.3
--
Thanks and Regards,
Sonali
Office: C2-169
http://tinyurl.com/sonali-hb-calendar
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