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

[Morgan, Martin]

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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