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

[Michael Stadler]

Hi Herve,

I reinstalled AnnotationDbi 1.25.17, and now things work flawlessly.

Thank you for your help!

Michael


On 09.04.2014 19:25, Hervé Pagès wrote:
> 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
>>
> 

-- 
--------------------------------------------
Michael Stadler, PhD
Head of Computational Biology
Friedrich Miescher Institute
Basel (Switzerland)
Phone : +41 61 697 6492
Fax   : +41 61 697 3976
Mail  : michael.stadler at fmi.ch