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 <jspid...@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
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Computational Biologist
Genentech Research
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