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class definitions became out-of-date when S4Vectors was updated.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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