[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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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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

Hi,

I have the recently got this warning in my package

combineTranscripts: no visible global function definition for ?seqlevels<-?

How would I fix this warning, when building my package. One of my packages calls the function seqlevels. I think if I explicilty import GenomeInfoDb in my NAMESPACE file it should fix this issue right?

Thanks for the help.

Venkat


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