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Bioconductor / VariantAnnotation

Annotation of Genetic Variants
https://bioconductor.org/packages/VariantAnnotation
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SNPlocs version in vignette needs updating #63

Closed jwokaty closed 1 year ago

jwokaty commented 1 year ago

From @vjcitn via https://devteam-bioc.slack.com/archives/C4VR9ABBP/p1660139066145949

Error: processing vignette 'VariantAnnotation.Rnw' failed with diagnostics:
 chunk 16 (label = examine_dbSNP) 
Error in library(SNPlocs.Hsapiens.dbSNP.20101109) : 
  there is no package called 'SNPlocs.Hsapiens.dbSNP.20101109'

that happens in 3.16 on lconway. The reason is that that SNPlocs version is I guess retired, but the other platforms have an old version on hand? The vignette can likely be updated to involve a non-defunct SNPlocs.

hpages commented 1 year ago

Taken care of in VariantAnnotation 1.43.3 (see commit 505509cfd5a2e42514504fb95972fb96aa19ff21).