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 3.2 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 • 833 views
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I had the same issue earlier today and checked out GenomicRanges 1.19.3 directly from svn and installed it.

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Thanks, Laurent - that worked. 

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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.5 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

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thanks, Marc - looks good this morning

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