[Bioc-devel] Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

Sonali B Arora sarora at fredhutch.org
Mon Dec 21 22:56:40 CET 2015


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-bounces at r-project.org] on behalf of Sonali B Arora [sarora at fredhutch.org]
> Sent: Monday, December 21, 2015 3:08 PM
> To: bioc-devel at 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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