Question

devel version: rtracklayer depends on GenomicRanges 1.19.3 but that's not available

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Janet Young ▴ 740

@janet-young-2360

Last seen 5.1 years ago

Fred Hutchinson Cancer Research Center,…

Hi there,

I'm guessing you folks know this already, and have probably already fixed it for the overnight builds, but thought I'd bring it up just in case.

I've re-installed R from scratch today (new linux version on the servers here). I'm now having trouble installing packages in the devel version: rtracklayer won't install because it depends on GenomicRanges version 1.19.3 but only 1.19.2 is currently available (looks like the build failed for 1.19.3). This also means I can't install any of the BSgenome packages as they're dependent on rtracklayer.

thanks,

Janet

rtracklayer genomicranges bioclite • 1.3k views

ADD COMMENT • link updated 10.2 years ago by Marc Carlson ★ 7.2k • written 10.2 years ago by Janet Young ▴ 740

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I had the same issue earlier today and checked out GenomicRanges 1.19.3 directly from svn and installed it.

ADD REPLY • link 10.2 years ago Laurent Gatto 1.6k

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Thanks, Laurent - that worked.

ADD REPLY • link 10.2 years ago Janet Young ▴ 740

score 1 · Answer 1 · 2014-11-03

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 8.4 years ago

United States

Hi Janet,

I just checked in some revisions for GenomicRanges that should resolve this issue. It was caused because the interface for AnnotationHub in devel is quite different from before. So some of the vignette chunks in GenomicRanges needed to be updated.

Marc

ADD COMMENT • link 10.2 years ago Marc Carlson ★ 7.2k

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thanks, Marc - looks good this morning

ADD REPLY • link 10.2 years ago Janet Young ▴ 740