On 03/24/2015 02:31 AM, Wolfgang Huber wrote:
Before we start a religious war, can we make progress on the pragmatic goal of
making it possible to provide such URLs to people?
There are two concepts
- ‘the package' - a specific version, running in a specific environment,
‘frozen’, etc. (Gabe)
- ‘the package’ - as a concept and a living artifact (me, Bernd, Tim)
Both are useful. And having URLs for both would also be useful.
0. That's (mostly) satisfied with the current scheme and
http://bioconductor.org/packages/3.0/bioc/html/BiocGenerics.html
http://bioconductor.org/packages/release/bioc/html/BiocGenerics.html
http://bioconductor.org/packages/devel/bioc/html/BiocGenerics.html
(hey, no www. -- that's four letters already! Perhaps importantly, there's also
a hard-coded version for devel, 3.1, and for past releases. So as I understand
it the request is for (a) shorter path names and (b) dynamic selection of
release vs. devel, mentioned below, for the <6 month period when the package is
in devel but not yet release. Also noted is Henrik's earlier proposal mentioned
by Sean.
1. 'packages', 'bioc', 'html' all look somehow redundant, so
http://bioconductor.org/release/BiocGenerics.html
http://bioconductor.org/devel/BiocGenerics.html
http://bioconductor.org/3.0/BiocGenerics.html
but also
http://bioconductor.org/release/BiocGenerics/ (implicit index.html)
http://bioconductor.org/BiocGenerics/release/
and their devel and version counterparts would seem quite possible / not
profoundly controversial. Landing pages for specific versions 3.22.7 do not
currently exist, change little across package minor versions, and would not lead
to packages installable via biocLite(), so this idea of Tim's is a non-starter
in my opinion.
Having the 'version' level of the path before the package provides a logical
place to put biocViews for that release. I'd vote for one of the
release/BiocGenerics[.html] schemes.
2. Something like
http://bioconductor.org/BiocGenerics
redirecting to release when available, devel when newly added (Wolfgang's
proposal) would in my opinion be confusing, especially since we continue to have
so much difficulty with version mismatches in user installations. I don't think
having a warning on redirect that 'this package is not available for release'
would be effective either at advertising robust software or at enabling use by
comparatively naive users.
3. In terms of the 'redundant' parts of the path, these are not completely
arbitrary (not that these considerations have to dictate presentation; they do
make one suspect that 'add a redirect and everything will be fine' will result
in a nice plate of spaghetti, especially if there is some desire to retain
backward compatibility).
'packages' separates the package repository from other aspects of
bioconductor.org, and group related concepts ('package', 'help', etc.) at a
similar hierarchical level.
'bioc' serves to distinguish between software ('bioc/'), annotation
('data/annotation') and experiment data ('data/experiment') packages, and these
divide the overall repository into three for the purposes of biocLite() /
install.packages() (this conceptual distinction has been useful, I think).
> biocinstallRepos()
BioCsoft
"http://bioconductor.org/packages/3.1/bioc";
BioCann
"http://bioconductor.org/packages/3.1/data/annotation";
BioCexp
"http://bioconductor.org/packages/3.1/data/experiment";
'html' distinguishes the landing pages from the package tar balls / binary
distributions themselves as returned by contrib.url(biocinstallRepos()), and
from their vignette/, man/ and news/ resources.
4. In terms of best practices, it seems like articles are about particular
versions and should cite the package as such, for instance if only in devel when
the paper is being written as .../3.1/..., but that there is no substantive cost
to also referencing 'current version available [after April, 2015] at
.../release/....
5. At the end of the day I find myself casting my lot for landing pages with the
form
http://bioconductor.org/release/BiocGenerics/
which leads to a little less typing but not the dynamic resolution that started
this (version) of the thread.
Martin
Wolfgang
On Mar 23, 2015, at 18:43 GMT+1, Tim Triche, Jr. <tim.tri...@gmail.com> wrote:
I just meant that the mnemonic link
http://www.bioconductor.org/limma/ (SEO version of limma ;-))
could dump people at something like
http://www.bioconductor.org/release/limma/3.22.7/ (I'd prefer this)
or if need be for backwards compatibility,
http://www.bioconductor.org/packages/3.0/limma/3.22.7/ (seems less good)
instead of
http://www.bioconductor.org/packages/3.0/bioc/html/limma.html (current)
and furthermore the specific version page could note more prominently that
the build of limma being referenced at that particular instance in time may
or may not be the same as was cited in a paper, used in an analysis,
available for download the previous evening, etc. thus citation("limma") is
a Very Good Idea when writing up results that depend upon it. Because even
the WEHI guys could theoretically have a bug that impacted someone's
results (as opposed to the usual case of Didn't Read The Fine Limma Manual)
Does that make more sense? (Probably not, but worth a try)
Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
On Mon, Mar 23, 2015 at 9:29 AM, Dan Tenenbaum <dtene...@fredhutch.org>
wrote:
On March 23, 2015 9:18:57 AM PDT, "Tim Triche, Jr." <tim.tri...@gmail.com>
wrote:
Packages are (read: should be, IMHO) published, citable pieces of
research, though. Imagine if a paper you cite were silently updated
without the doi/citation changing. That wouldn't be good
I don't disagree, but the existing setup does nothing to address that.
Citation('limma'), for example, does.
.../release/... and .../devel/... can change at any time, potentially
overnight (with or without a new BioC release). The only real way to
cite an exact version is to cite that exact version, which is already
the proper way to do things and would remain unaffected by this, at
least AFAIK.
Perhaps a useful addendum would be for the mnemonic
http://bioconductor.org/limma
To redirect to
http://bioconductor.org/packages/limma/whateverTheMostRecentStableVersionMayBe/
And then everything is explicit.
Does that address the competing issues discussed herein?
Note that 'release' and 'devel' are just symlinks to the current release
and devel versions. I.e. currently 3.0 and 3.1 respectively. So you can
always link directly to a specific version.
Dan
Best,
--t
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