[Bioc-devel] r+w permissions in release branches

[Wolfgang Huber]

Hi Martin
to come back to the original trigger for this thread: it was not concerns for reproducibility, but the fact that a Bioc package in the current release stopped working because a CRAN package has changed in the meanwhile.
What’s the most practical solution to this specific problem?
	Best wishes
	Wolfgang




On 23 Apr 2014, at 19:41, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> On 04/22/2014 09:47 AM, Kasper Daniel Hansen wrote:
>> I think we should have a CRAN snapshot (or a subset of CRAN used in Bioc)
>> inside each Bioc release; I don't know how hard that is to manage from a
>> technical point of view.
> 
> I followed this thread with some interest.
> 
> It would be surprisingly challenging to update even a 2.13 package -- the build machines have moved on to other tasks, unconstrained by the unique system dependencies needed for 2.13 builds.
> 
> The idea of a 'forever' repository snapshot seems possible, but would the snapshot be at the beginning of the release and hence miss the few but important bug fixes introduced during the release, or at the end of the release, which might be after the time required for the purposes of replication? Either way it is certain that the peanut butter would land face down for one's particular need. Also, the need for the user to satisfy system dependencies becomes increasingly challenging, even with a binary repository. I don't think a central 'Bioc' solution would really address the problem of reproducibility.
> 
> It is not that 'hard' for an individual group to create a snapshot of Bioc and CRAN, using rsync
> 
>  http://www.bioconductor.org/about/mirrors/mirror-how-to/
>  http://cran.r-project.org/mirror-howto.html‎
> 
> and to use install.packages() or even biocLite to access these (see ?setRepositories). This would again require that the system dependencies for these packages are satisfied in some kind of frozen fashion.
> 
> A more robust possibility is of course a virtual machine, such as the AMI (or a customized version) we provide
> 
>  http://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids
> 
> although these have only a subset of packages installed by default.
> 
> The CRAN thread referenced earlier included this post
> 
>  https://stat.ethz.ch/pipermail/r-devel/2014-March/068605.html
> 
> which I think makes an important distinction between exact replication and scientific reproducibility; it is the latter that must be the most interesting, and the former that we somehow seem to stumble over. The thread also mentions best practices -- version control
> 
>  http://bioconductor.org/developers/how-to/source-control/
> 
> disciplined approach to deprecation
> 
>  http://bioconductor.org/developers/how-to/deprecation/
> 
> package versioning
> 
>  http://bioconductor.org/developers/how-to/version-numbering/
> 
> and the Bioc-style approach to release that we as developers can act on to enhance reproducibility. What other best practices can we more forcefully / conveniently adopt within the project?
> 
> Martin
> 
>> 
>> Best,
>> Kasper
>> 
>> 
>> On Tue, Apr 22, 2014 at 6:06 PM, Julian Gehring <julian.gehring at embl.de>wrote:
>> 
>>> Hi,
>>> 
>>> For most problems discussed here, it seems that having a fixed version of
>>> package is sufficient rather than a specific version.  If the idea of a
>>> snapshot with each bioc release would work (which still means one version
>>> per package), so would requiring that version within the package (one would
>>> just need to agree which version this is).
>>> 
>>> Best wishes
>>> 
>>> Julian
>>> 
>>> 
>>>  what if two Bioc packages require different version of the ‘same’ CRAN
>>>> package?
>>>> AfaIu, the infrastructure is not designed to deal with multiple versions
>>>> of a package.
>>>> 
>>>> Nor would I as a user expect to have less-than-the-most recent versions
>>>> of CRAN packages in my library just because some other package says so…
>>>> 
>>>> Just to throw in another, and probably silly suggestion: the Bioconductor
>>>> repository could keep ‘snapshots’ of CRAN packages compatible with each
>>>> release, but they would have to be name-mangled in some way. The potential
>>>> for confusion is enormous.
>>>> 
>>> 
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> 
>> 
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>> 
>> 
>> 
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> 
> 
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