Question: cummerbund installation error- R package version
1
gravatar for jashapiro
3.9 years ago by
jashapiro • 10
United States
jashapiro • 10 wrote:

The current version of cummerbund in the toolshed (package_cummerbund_2_8_2) has a dependency on the R digest package, which it specifies to download from http://cran.r-project.org/src/contrib/digest_0.6.7.tar.gz , The R package has recently been updated to 0.6.8, so the url is no longer valid, and the cummerbund package fails to install. 

Is there a simple way to specify the updated url in the package? 

Update: I see that this is updated in the github repository: 

https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_cummerbund_2_8_2/tool_dependencies.xml

How long does it generally take for such updates to propagate to the toolshed?

toolshed software error • 1.8k views
ADD COMMENT • link • modified 3.9 years ago by Dave B. ♦ 410 • written 3.9 years ago by jashapiro • 10
3
gravatar for Dave B.
3.9 years ago by
Dave B. ♦ 410
United States
Dave B. ♦ 410 wrote:

Thanks for the notification, I've corrected the dependency and the cummerbund library should now install correctly.

ADD COMMENT • link written 3.9 years ago by Dave B. ♦ 410

Thanks, but sadly, that is not quite enough, as I now discover: There are actually a few other packages that have also been updated. The changeset below may contain all of the appropriate updates (though I have not checked its completeness).

https://github.com/galaxyproject/tools-iuc/commit/c6433913f3863b1afd7a5202a9828ec558ab90f1

ADD REPLY • link written 3.9 years ago by jashapiro • 10
3

Fortunately, the IUC expected this, and preemptively hosted all dependent libraries elsewhere. I've updated the xml to download and install them from that host.

ADD REPLY • link written 3.9 years ago by Dave B. ♦ 410
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