[Bioc-devel] Changes S4Vectors etc.

[Martin Morgan]

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class definitions became out-of-date when S4Vectors was updated.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
>>
>>>
>>
>>     [[alternative HTML version deleted]]
>>
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