Re: [Bioc-devel] Short URLs for packages?
#5 is what I was thinking of when I responded. A simple RewriteRule, if anyone
still uses Apache.
Release vs devel and/or 3.0 vs 3.1 vs 3.2, e.g.
http://bioconductor.org/release/BiocGenerics/
Pointing analogously to
http://bioconductor.org/3.0/BiocGenerics/
seems like a good minimal standard (project + version + package)
--t
On Mar 24, 2015, at 4:14 AM, Martin Morgan mtmor...@fredhutch.org wrote:
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.
Re: [Bioc-devel] Short URLs for packages?
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.
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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[Bioc-devel] Rtools warning on tracker page
Hi After uploading our package to the tracker, it built successfully on all systems with no errors. But we have the following Rtools related WARNING: WARNING: Rtools is required to build R packages, but no version of Rtools compatible with R 3.2.0 was found. (Only the following incompatible version(s) of Rtools were found:2.13,2.14,2.15,2.16) Is it possible this is related to the build environment on the tracker page? We can't think how it could be related to our package. I have already mailed the BioC team about this, but I thought I'd post it here also to see if anyone else has the same issue. (our package is called 'CausalR'). Best Regards, Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Short URLs for packages?
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
Re: [Bioc-devel] Short URLs for packages?
On Tue, Mar 24, 2015 at 7:28 AM, Wolfgang Huber whu...@embl.de wrote: 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. But we already have dynamic resolution. Even http://bioconductor.org/release/BiocGenerics will point to different package versions (e.g. after bugfixes) as time goes by. So the attribute “release” is dynamically resolved. All I am asking for is another attribute that means “the best that we currently have”, i.e. release if it exists and devel otherwise. I didn’t expect so much disagreement on so mundane an issue. And there are plenty of ways of doing this outside the Bioc webpage, any of the public ’tiny URL’ services, through my own webpage, or by just telling people to google the package name. I just think there are a couple of subtleties here. I certainly don't begrudge people wanting to type less and find packages easier. But if a naive user with a default (read: release) Bioc installation goes to http://bioconductor.org/CoolAwesomePkg and see's that it is available in bioconductor but then can't install it because it is only in devel, are they going to be less confused, or more? I don't know the answer to that, but I think it's something to consider. Also, as I have said elsewhere, though I acknowledge that you seem to disagree, I think such urls are substantially less appropriate for credit/citation in publications. A link that brought users to the version in question, but which - if not current - had a prominent link to the current version would be better imho. On 24 Mar 2015, at 12:14, Martin Morgan mtmor...@fredhutch.org wrote: 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/…. I don’t agree. This would mean that for each later version of the same package, even just after a trivial typo fix, there is either no article, or another one would have to be written. I don’t think this has an easily formalized solution, some good judgement is required. E.g. try to apply the above reasoning to http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003118 I agree that there can be a bit of a beard problem* here. If people follow the Bioc development guidelines, though, I think a pretty good rule of thumb can be had: bugfix version changes (in the major.minor-bugfix nomenclature) are (relatively unambiguously) the same software from a publication standpoint, while package versions with minor or major version differences are not. This doesn't mean that a new article need to be written, imo, just that awareness that the article discussed a different version of the software - and that users should see the NEWS file or current documentation for fully up-to-date information - is important. Not to harp on you personally, Wolfgang, because your paper with Simon about DESeq was ahead of its time (and ours, sadly) on many of these issues, but the API and default behavior of DESeq have changed substantially (and for the better!) since its publication [1]. As a never-going-to-happen pipedream, this would be even more straight-forward if Bioc package version numbers were of the form (BiocVersion.PkgVersion-bugfix). Then the automatic incrementing of package versions for bioc releases wouldn't muddy the waters here. * The philosophical issue where some men obviously have beards, and some men obviously don't, but there is no exact number of facial hairs at which one unambiguously transitions from not having a beard to having one. [1] http://blog.revolutionanalytics.com/2014/08/gran-and-switchr-cant-send-you-back-in-time-but-they-can-send-r-sort-of.html ~G -- Gabriel Becker, Ph.D Computational Biologist Genentech Research [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Rtools warning on tracker page
The builder for submitted packages uses the devtools package and this is a bug in devtools: https://github.com/hadley/devtools/issues/717 You can ignore it. Dan - Original Message - From: Glyn Bradley glyn.x.brad...@gsk.com To: bioc-devel@r-project.org Sent: Tuesday, March 24, 2015 3:03:36 AM Subject: [Bioc-devel] Rtools warning on tracker page Hi After uploading our package to the tracker, it built successfully on all systems with no errors. But we have the following Rtools related WARNING: WARNING: Rtools is required to build R packages, but no version of Rtools compatible with R 3.2.0 was found. (Only the following incompatible version(s) of Rtools were found:2.13,2.14,2.15,2.16) Is it possible this is related to the build environment on the tracker page? We can't think how it could be related to our package. I have already mailed the BioC team about this, but I thought I'd post it here also to see if anyone else has the same issue. (our package is called 'CausalR'). Best Regards, Glyn This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Short URLs for packages?
I just think there are a couple of subtleties here. I certainly don't begrudge people wanting to type less and find packages easier. But if a naive user with a default (read: release) Bioc installation goes to http://bioconductor.org/CoolAwesomePkg and see's that it is available in bioconductor but then can't install it because it is only in devel, are they going to be less confused, or more? I don't know the answer to that, but I think it's something to consider. We have (and already had many times) exactly this problem. A paper is published and refers to a new BioC-package. The naive user is not able to find the package. We want to show the naive user that this package is indeed part of bioconductor and point him/her to a way to install the package. The devel-webpage makes a clear statement on top saying “This is the development version of BiocGenerics; for the stable release version, see MyPackage.” If this is not prominent enough, one can highlight this with yellow color. Also, as I have said elsewhere, though I acknowledge that you seem to disagree, I think such urls are substantially less appropriate for credit/citation in publications. A link that brought users to the version in question, but which - if not current - had a prominent link to the current version would be better imho. This discussion is off-topic. The versioning system of Bioconductor provides a sufficient way to cite the right version of the packages to ensure reproducible research. We (try to) do this in the papers as well. We do not request that short URLs should replace the correct citation of package versions. Here, we ask for a stable, short URL that links to the most current, stable version of the package (which is in devel for the time between acceptance and first release of the package). Most users reading about a bioconductor package want to install the current version of the package, that is best tested,with the lowest number of bugs, installable on a current machine, with a current version of R, … . We want to put a stable URL into a paper, that does not need to be changed anymore, when the BioC-package moves from devel to release. There is no way to change the paper after publication. Bernd ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
