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

Let me add my opinion: we do not have perfect (easy) reproducibility with
Bioc because we can only (easily) download the tar ball corresponding to
the latest commit in a given branch.  I am ok with that.  What I (and
Alejandro) is concerned about is the inability to install even that.

There is a clear candidate for which version of the CRAN package we should
store: the version we use when we run R CMD check.  This is the version we
implicitly say things are working with.

Best,
Kasper


On Fri, Apr 25, 2014 at 7:41 AM, Herv?? Pag??s <hpages at fhcrc.org> wrote:

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

--
Herv?? Pag??s

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
Phone:  (206) 667-5791
Fax:    (206) 667-1319

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