[Bioc-devel] Consistency between miRNATarget and MiRaGE

Hervé Pagès hpages at fhcrc.org
Fri Dec 13 19:19:33 CET 2013

Hi tag,

The data-experiment repository doesn't use a trunk/branch organization
like the software repo, so the devel and release builds both point to
trunk. You can see this in the "svn info" box ("URL" field) at the top
of the HTML reports:


It's not a good situation but so far package maintainers were more
or less able to work around this.

Anyway, seems like it's time for us to consider branching the
data-experiment repo. It has actually been requested for a while.
We're working on this and will announce on this list when it's ready.


On 12/10/2013 12:21 AM, Y-h. Taguchi wrote:
> Dear Maintainers,
> Thank you very much for your every efforts to maintain this fantastic project!
> Before explaining a concern with my package, please let me explain about mine.
> My package, MiRaGE, is a little bit different from the standard
> Software Packages.
> MiRaGE needs to import experiment package miRTarget that includes
> essential data frames to execute MiRaGE, i.e., in spite of the name of
>   experiment package, mIRNATarget includes important/essential data
> sets for MiRaGE.
> (This exceptional structure was decided during the negotiation  with
> Maintainers when MiRaGE was released for the first time)
> Recently, I updated both software package MiRaGE (1.5.1->1.5.2) and
> experiment package miRNATarget (0.99.5 -> 1.1.0) in development.
> I expected that both are reflected to development only, but today I
> found that miRNATarget in release was also updated to 1.1.0 !
> Because of this, MiRaGE in release does not work properly and is not a
> original release version 1.4.0 anymore, since MiRaGE 1.4.0 must import
> miRNATarget 0.99.5 that did disappear.
> Please advise me how to keep consistency between software package and
> experimental package for both release and development.
> Since in vignette, I have clearly advised users to use data set not in
> experiment package but that in my own web site, if users follow my
> advises, it is OK.
> But, if not, MiRaGE in the present release does not work properly any
> more because of unintended update of miRNATarget in the present
> release.
> yours, tag.

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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