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

[Hervé Pagès]

Hi,

See the latest software builds for BioC 2.13:

   http://bioconductor.org/checkResults/2.13/bioc-20140405/

The number of packages that needed to be installed on the build
system in order to build and check the 750 BioC software packages
is displayed in the right-most column of the top table:

   1510 on zin1 (Linux)
   1486 on moscato1 (Windows)
   1500 on perceval (Mac)

If you click on these numbers, you get the full list of packages
plus their version.

Once you've subtracted the 750 software packages + the number of data
annotation and data experiment packages (a few more hundreds) from
these numbers, that gives you the number of CRAN packages that
BioC 2.13 depends on. Not that many really (only a very small fraction
of the 5400 CRAN packages).

If we hosted only this small subset of CRAN packages under

   http://bioconductor.org/packages/2.13/cran

next to the other 4 frozen repos

   http://bioconductor.org/packages/2.13/bioc
   http://bioconductor.org/packages/2.13/data/annotation
   http://bioconductor.org/packages/2.13/experiment
   http://bioconductor.org/packages/2.13/extra

and have biocLite() modified to point to

    http://bioconductor.org/packages/2.13/cran

instead of

   http://cran.fhcrc.org

then anybody that has R 3.0.3 could *easily* install and run
BioC 2.13 now or in 5 years from now.

Cheers,
H.


On 04/24/2014 08:09 AM, Steve Lianoglou wrote:
> Hi all,
>
> Just saw this tangentially related link to "packrat" which seems something
> analogous to a virtualenv (of sorts) for R by the Rstudio folks, which I
> thought might be useful
>
> It actually doesn't solve anybody's problem here, but as I said ...
> tangential :-)
>
> http://rstudio.github.io/packrat/
>
>
> On Thursday, April 24, 2014, Wolfgang Huber <whuber at embl.de> wrote:
>
>> Hi Kasper
>>
>> you are right, I had misunderstood the problem.
>> In that case I agree with Martin that the problem resolves into components
>> that are either intractable, already addressed by deprecation policies, or
>> not very important.
>> Sorry for the noise.
>>
>>          Wolfgang
>>
>> On 24 Apr 2014, at 15:18, Kasper Daniel Hansen <
>> kasperdanielhansen at gmail.com> wrote:
>>
>>> Wolfgang,
>>>
>>> Alejandro did not have a problem with the current release, but with the
>> most recent prior release.  His issue is precisely because it is no longer
>> the current (stable) release.
>>>
>>> Kasper
>>>
>>>
>>> On Thu, Apr 24, 2014 at 3:05 PM, Wolfgang Huber <whuber at embl.de> wrote:
>>> 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 pract
>
>
>

-- 
Hervé Pagès

Program in Computational Biology
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