[Bioc-devel] "[[<-" method dispatch and GenomicRanges

[Hervé Pagès]

Hi Michael,

Because of a recent change to IRanges, some information about the
"as.list" method table is now out-of-sync in your installed
AnnotationDbi (granted it was installed before the new IRanges
propagated to you). Re-installing AnnotationDbi should clear this.

I bumped AnnotationDbi version yesterday night (even though
AnnotationDbi has not changed) to help clear this up for other
users. The new version won't become available before tomorrow though.
But, again, this new version (1.25.18) is similar to the current
version (1.25.17), so you can re-install now with
biocLite("AnnotationDbi"). No need to wait until tomorrow.

HTH,
H.

On 04/09/2014 12:23 AM, Michael Stadler wrote:
> Dear Bioc gurus,
>
> Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some
> unit tests, which turns out to be reproducible independent of QuasR and
> might be related to R getting the wrong method for "[[<-".
>
> The following works fine...
> library(GenomicRanges)
> grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
>                     r2=GRanges("chr2",IRanges(3,4)))
> grl[[1]] <- GRanges("chr1",IRanges(10,11))
>
>
> ...but this produces an error:
> library(GenomicRanges)
> library(GenomicFeatures)
> grl <- GRangesList(r1=GRanges("chr1",IRanges(1,2)),
>                     r2=GRanges("chr2",IRanges(3,4)))
> grl[[1]] <- GRanges("chr1",IRanges(10,11))
> #Error in as.list(x, use.names = FALSE) :
> #  could not find function ".as.list.CompressedList"
>
> My guess is that loading the GenomicFeatures library in addition to
> GenomicRanges influences the methods dispatch, but with my limited
> understanding of R and S4 classes I was not able to narrow it further down.
>
> I noticed that I am using a slightly older version of R (r65206)
> compared to the build system (r65358), however I also see the error with
> the most recent release candidate (r65385).
>
> Michael
>
>
> My session info:
> R version 3.1.0 alpha (2014-03-17 r65206)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GenomicFeatures_1.15.15 AnnotationDbi_1.25.17   Biobase_2.23.6
> [4] GenomicRanges_1.15.44   GenomeInfoDb_0.99.30    IRanges_1.21.43
> [7] BiocGenerics_0.9.3      RColorBrewer_1.0-5
>
> loaded via a namespace (and not attached):
>   [1] BBmisc_1.5                BSgenome_1.31.13
>   [3] BatchJobs_1.2             BiocParallel_0.5.19
>   [5] Biostrings_2.31.21        DBI_0.2-7
>   [7] GenomicAlignments_0.99.37 RCurl_1.95-4.1
>   [9] RSQLite_0.11.4            Rcpp_0.11.1
> [11] Rsamtools_1.15.41         XML_3.98-1.1
> [13] XVector_0.3.7             biomaRt_2.19.3
> [15] bitops_1.0-6              brew_1.0-6
> [17] codetools_0.2-8           digest_0.6.4
> [19] fail_1.2                  foreach_1.4.1
> [21] iterators_1.0.6           plyr_1.8.1
> [23] rtracklayer_1.23.22       sendmailR_1.1-2
> [25] stats4_3.1.0              stringr_0.6.2
> [27] tools_3.1.0               zlibbioc_1.9.0
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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