[Bioc-devel] Consistency between miRNATarget and MiRaGE

Hervé Pagès hpages at fhcrc.org
Sat Dec 21 10:07:06 CET 2013

Hi tag,

We now have a RELEASE_2_13 branch for data experiment packages like
we do for software packages.

The release version of the miRNATarget package lives in that branch:


The devel version of the package still lives in (this has not changed):


I've rolled back the release version of miRNATarget to revision 2631,
which corresponds to version 0.99.5. This brings it back to the state
it was in release before you did the recent changes (which were intended
to be for devel only). However, I've bumped its version to 1.1.2
because versions needs to go up. So the only difference between version
0.99.5 and version 1.1.2 is the version number.

I've also bumped the version of the devel package to 1.1.3 so it stays
ahead of the package in release.

Please let me know if you have questions or concerns about this.


On 12/13/2013 10:19 AM, Hervé Pagès wrote:
> 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:
>    http://bioconductor.org/checkResults/2.14/data-experiment-LATEST/
>    http://bioconductor.org/checkResults/2.13/data-experiment-LATEST/
> 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.
> Cheers,
> H.
> 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
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
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