[Bioc-devel] Changes S4Vectors etc.

[Hervé Pagès]

Hi Leonard,

mmh... I can't reproduce this and it doesn't show up on the build report
either. But I got another strange error when I tried to *install*
SGSeq: something about TxFeatures not being able to extend GenomicRanges
because of incompatible type for the elementMetadata slot.

I got rid of it by re-installing GenomicRanges from svn.
I guess I had some stalled class definition somewhere in a cache.

Looks like maybe you also have a stalled class definition somewhere
in a cache for one of SGFeatureCounts's parent classes. Not sure which
one though :-/

Maybe I forgot to bump a package version somewhere after I renamed
characterORNULL -> character_OR_NULL? Re-installing S4Vectors, IRanges,
GenomicRanges, and SummarizedExperiment directly from svn might help.

Cheers,
H.

On 02/08/2017 04:18 PM, Leonard Goldstein wrote:
> Hi Hervé,
>
> It looks like there have been some changes in bioc-devel (S4Vectors etc.)
> that break the SGSeq package (see below). I'm not sure whether this is
> something that needs to be addressed in SGSeq or its dependencies. I'd be
> grateful for any pointers. Thanks for your help.
>
> Leonard
>
> --
>> example(makeSGFeatureCounts, "SGSeq")
>
> mkSGFC> sgfc <- makeSGFeatureCounts(sgf_pred, si,
> mkSGFC+   matrix(0L, length(sgf_pred), nrow(si)))
> Error in checkSlotAssignment(object, name, value) :
>   assignment of an object of class "NULL" is not valid for slot 'NAMES' in
> an object of class "SGFeatureCounts"; is(value, "characterORNULL") is not
> TRUE
>>
>> sessionInfo()
> R Under development (unstable) (2017-02-06 r72129)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X El Capitan 10.11.6
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] SGSeq_1.9.1                SummarizedExperiment_1.5.5
>  [3] DelayedArray_0.1.4         Biobase_2.35.0
>  [5] Rsamtools_1.27.12          Biostrings_2.43.4
>  [7] XVector_0.15.2             GenomicRanges_1.27.22
>  [9] GenomeInfoDb_1.11.9        IRanges_2.9.18
> [11] S4Vectors_0.13.13          BiocGenerics_0.21.3
>
> loaded via a namespace (and not attached):
>  [1] igraph_1.0.1             Rcpp_0.12.9              AnnotationDbi_1.37.2
>
>  [4] magrittr_1.5             zlibbioc_1.21.0
>  GenomicAlignments_1.11.9
>  [7] BiocParallel_1.9.5       lattice_0.20-34          tools_3.4.0
>
> [10] grid_3.4.0               DBI_0.5-1                digest_0.6.12
>
> [13] Matrix_1.2-8             GenomeInfoDbData_0.99.0  rtracklayer_1.35.5
>
> [16] bitops_1.0-6             RUnit_0.4.31             biomaRt_2.31.4
>
> [19] RCurl_1.95-4.8           memoise_1.0.0            RSQLite_1.1-2
>
> [22] compiler_3.4.0           GenomicFeatures_1.27.6   XML_3.98-1.5
>
>>
>
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>
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-- 
Hervé Pagès

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