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

Gabe Becker becker.gabe at gene.com
Wed Aug 20 01:57:47 CEST 2014


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

> 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.


> 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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> Bioc-devel at r-project.org mailing list
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Computational Biologist
Genentech Research

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