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'update' methods need exporting? #7

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mtmorgan opened this issue May 14, 2018 · 1 comment
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'update' methods need exporting? #7

mtmorgan opened this issue May 14, 2018 · 1 comment

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@mtmorgan
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@mtmorgan mtmorgan commented May 14, 2018

@hpages This support site question seems to be due to 'update' methods not being exported / documented in GenomicRanges (and elsewhere?). This seems to fix the immediate problem.

GenomicRanges master$ git diff
diff --git a/NAMESPACE b/NAMESPACE
index 3fbb6ff..6d9880c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -73,7 +73,7 @@ exportMethods(
     merge,
 
     ## Generics defined in the stats4 package:
-    summary,
+    summary, update,
 
     ## Generics defined in the BiocGenerics package:
     duplicated, match,

For reference: the reproducible example

seqinfo_hg19 = GenomeInfoDb::Seqinfo(genome = 'hg19')

se <- SummarizedExperiment::SummarizedExperiment(
  rowRanges = GenomicRanges::GRanges(c("chr1", "chr2", "chr1"), 
                                     IRanges::IRanges(1:3, width = 1)))

GenomeInfoDb::seqinfo(se) = seqinfo_hg19[GenomeInfoDb::seqlevelsInUse(se)]
#> Error in methods::slot(object, name): no slot of name "call" for this object of class "GRanges"
hpages added a commit that referenced this issue May 14, 2018
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@hpages hpages commented May 14, 2018

I just applied the fix: 20fe2d9 Also ported to the RELEASE_3_7 branch. Thanks @mtmorgan !

@mtmorgan mtmorgan closed this May 17, 2018
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