[BioC] biocLite

[Dan Tenenbaum]

On Tue, Sep 27, 2011 at 10:55 AM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> On Tue, Sep 27, 2011 at 1:43 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>> Hi Kasper,
>>
>> On Tue, Sep 27, 2011 at 7:52 AM, Kasper Daniel Hansen
>> <kasperdanielhansen at gmail.com> wrote:
>>> It seems that Rcompression (from omegahat) is not available through
>>> biocLite anymore (or, at least I believe it used to be available).  I
>>> may be missing something here, but didn't we use to be able to get
>>> omegahat packages through biocLite.  Or is this something specific to
>>> Rcompression?
>>>
>>
>> What version of R and what OS are you using?
>>
>> I just did a quick check on Linux and Windows, R-2.13 and R-2.14, and
>> biocinstallRepos() (the function that tells biocLite() where to look)
>> does not include the Omegahat repository on any of them.
>
> I have been checking 2.13 and devel for Linux and OS X.  Just to be
> clear: I see the same as you (that omegahat is not included).  I seem
> to recall that omegahat used to be included, but I am probably
> completely wrong.

We have not  included Omegahat as long as anyone here can remember.
We do point to our own extra repository which includes some Omegahat
packages, but  Rcompression has never been in that repository, at
least since BioC 1.8.

Some Omegahat packages, such as XML, are available in CRAN, which
could account for this, but it doesn't look like Rcompression is one
of them.

Dan



>
> Kasper
>