[Bioc-devel] Changes S4Vectors etc.

[Leonard Goldstein]

Hi Martin and Hervé,

The problem lies in the pre-built binaries. Installing SGSeq from source
fixes the installation. I bumped the version number for SGSeq to trigger a
rebuild, but I guess other packages are affected as well. Among SGSeq
dependencies it looks like Rsamtools needs a version bump too.

Thanks,

Leonard


On Thu, Feb 9, 2017 at 4:19 AM, Martin Morgan <martin.morgan at roswellpark.org
> wrote:

> On 02/09/2017 06:25 AM, Hervé Pagès wrote:
>
>> 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.
>>
>
> See also https://support.bioconductor.org/p/92201/#92205 where
>
> GeneSetCollection extends 'list', which extends 'vector'
>
> GSEABase Depends: on annotate which Depends: on AnnotationDbi which
> Imports: S4Vectors.
>
> S4Vectors defines a class union on vector_OR_factor (previously
> vectorORfactor). Consequently, GeneSetCollection extends vector_OR_factor.
>
> Class definitions are cached at package installation time, so GSEABase
> class definitions became out-of-date when S4Vectors was updated.
>
> A conservative approach is to bump the version of all packages that depend
> on S4Vectors, even GSEABase which is three steps away from S4Vectors. I
> believe that this involves
>
>   db = available.packages(repos=BiocInstaller::biocinstallRepos()[1])
>   revdeps = tools::package_dependencies("S4Vectors", db, recursive=TRUE,
>       reverse=TRUE)
>
> which is
>
> > length(revdeps$S4Vectors)
> [1] 662
>
> packages!
>
> Leonard could find candidates for re-installation with
>
> > mydep = tools::package_dependencies("SGSeq", db, recursive=TRUE)
> > mydep$SGSeq[mydep$SGSeq %in% revdeps$S4Vectors]
>  [1] "IRanges"              "GenomicRanges"        "Rsamtools"
>  [4] "SummarizedExperiment" "AnnotationDbi"        "Biostrings"
>  [7] "GenomicAlignments"    "GenomicFeatures"      "GenomeInfoDb"
> [10] "rtracklayer"          "XVector"              "biomaRt"
> [13] "DelayedArray"
>
> Martin
>
>
>
>> 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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>>>
>>>
>>
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