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

Wed Sep 10 21:21:00 CEST 2014

On 09/10/2014 11:37 AM, davide risso wrote:
> 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.

biocLite() already scores high on the tangled code scale.

The problem is that this month's 'devel' will actually be next month's 'release' 
and next year's 'previous version', so it's very hard to know where to look for 
the available version, and how to reliably tell the user what to do to get the 
package.

If it's a simple typo of an available package then install.packages will already 
suggest an alternative.

I wonder where the users are getting the notion that they _should_ be able to 
install RUVSeq in Bioc 2.14? I guess they follow the link in the Nature Methods 
paper to the devel landing page, then follow the 'Installation' instructions 
without paying attention to the various 'development version' flags on the page.

Martin

>
> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Computational Biologist
>>>> Genentech Research
>>>>
>>>>           [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
>>>
>>
>>
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>
>
>

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