[Bioc-devel] Changes S4Vectors etc.

Leonard Goldstein goldstein.leonard at gene.com
Thu Feb 9 01:18:13 CET 2017

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.


> 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
> 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

[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
 [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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