[Bioc-devel] namespace GenomicRanges

Karl Stamm karl.stamm at gmail.com
Wed Dec 2 22:42:54 CET 2015

Happened to look if my package rgsepd was building correctly, and it
seems as if some kind of change to a dependency is causing an
installation error for me. I was explicitly importing and calling
GenomicRanges::assay() for a year, and this month it is not exported.

Error : object ‘assay’ is not exported by 'namespace:GenomicRanges'

It appears to be fixed by removing the specification for that assay
function, and now I'm using a generic, probably provided from another
package. What happened here?

On a related note, should I be notified of a build error? When a similar
problem occurred last month with biomart changing their interface, the
build was failing for an unknown length of time. The fix was quick and easy
but I didn't see the problem right away. Maybe I'm not on the correct RSS
feeds, or how would a dev see his package having problems? Given the
problem occurred by the build server updating a dependency, I wasn't
actively working on anything.

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