[Bioc-devel] biocLite message "R package not available" is confusing

Thanks Martin,

yes, you're right about the "use the devel version," but perhaps
biocLite could check if the package is available in the devel, just to
distinguish between a package that is not in Bioconductor (mistyping?)
and one that is not yet available in release.

Just my two cents.

Davide

On Wed, Sep 10, 2014 at 11:19 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

On 09/10/2014 10:39 AM, davide risso wrote:

I just wanted to add my support to Josef request.

During the last few weeks I received several emails from users asking
me if I "plan to make a version of RUVSeq compatible with R 3.1." (My
RUVSeq package is in devel).

I understand the error comes directly from install.packages, but is
there a way for biocLite to catch this before passing it to
install.packages? Perhaps throwing a different error, like "The
package xxx is not available in the release version of Bioconductor.
Use the devel version."

The current error message is not just confusing, it's incorrect.

I don't think we'd say 'use the devel version' but we could say something
about 'not available for this version of Bioconductor'; I'll also think
about getting this 'fixed' upstream (it's not the version of R, but the
repositories specified in the call to install.packages)

Martin

Best,
davide

On Tue, Aug 19, 2014 at 4:57 PM, Gabe Becker <becker.gabe at gene.com> wrote:

Josef,

The problems with reviewers you are describing sound very frustrating
(for
the author and the reviewer) but I suspect you think that biocLite is
doing
somethign that it is not (reimplementing the actual package installation
machinery in R). Responses inline.


On Tue, Aug 19, 2014 at 4:40 PM, Josef Spidlen <jspidlen at bccrc.ca> wrote:

Hi,
I believe that the "R package ... is not available for R ..." message as
produced by biocLite is a bit confusing for "new-ish" BioConductor
users,
and I have a suggestion how things could be improved.

Imagine that a brand new package is submitted to BioConductor and a
related
manuscript to some journal. Your typical reviewer as well as most other
users that heard about the package will search for it and end up
somewhere
under http://bioconductor.org/packages/devel/bioc/..... From there, they
will simply copy&paste
source("http://bioconductor.org/biocLite.R")
biocLite("myFancyPackage")
into their R 3.1 console, which will tell them that the package is not
available for their version of R despite the fact that the actual
package
"depends" on, say, R >= 2.10.0.

This message is from install.packages, which biocLite calls, not biocLite
itself. The message is the generic "the repository you pointed at doesn't
have a version of the package you wanted installable on your system"
(types
of packages not withstanding).

Your typical user may try several versions of R and than either give up,
or
contact the maintainer. Your manuscript reviewer will reject the
manuscript
as the "package is not available". Trust me, I have seen both happen,
and I
have answered several questions explaining how a package that is still
just
"a development version" can be installed.

In order to make things less confusing, I would suggest that future
versions of biocLite check also the development section of BioConductor
(if
a package cannot be found in the current release), and possibly produce
a
message that is more informative, e.g.,
"R package ... is still in development; you can either try again after
the
next BioConductor release in October|April 20xx, or you can follow these
steps to install the development version now: ..."

You can't (safely) mix package versions from Bioc-devel and Bioc-release,
so the instructions there would be "use bioc devel". I could easily be
put
in the availability section of a paper "it will be available as a devel
package until X/Y/ZZZZ, after which it will be a fully released bioc
package"

And (less important), if biocLite "knew" which packages are from CRAN
rather than BioConductor (cache the names of the ~6,000 CRAN packages?),
then it could also produce errors like "R package ... seems like a CRAN
package; you may want to try install.packages to install it"). That may
help some users as well.

biocLite does/can know where the packages come from, but again, it is
just
calling install.packages, and will happily install CRAN packages for you
without any trouble.

~G

That's just my 2c :-).

Cheers,
Josef


--
Josef Spidlen, Ph.D.
Staff Scientist, Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
Tel. +1 604-675-8000, ex. 7755

          [[alternative HTML version deleted]]

--
Computational Biologist
Genentech Research

          [[alternative HTML version deleted]]

--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793