[BioC] Does this message means that I need to update R or BioC?

[Peng Yu]

Hi Patrick,

The problem was because that the BioC packages were not updated. It
seems that the problem is solved after all the packages are updated.

Regards,
Peng

On Wed, Aug 5, 2009 at 4:55 PM, Patrick Aboyoun<paboyoun at fhcrc.org> wrote:
> Peng,
> We don't have any utility to check the version numbers of all installed
> packages because as long as you don't install the development version of
> BioC with the release version of R and you routinely run the commands
>
> biocLite(<<character vector of package names>>)
>
> to install packages and
>
> update.packages(repos = biocinstallRepos())
>
> to update the BioC packages you will be current for your version of R.
>
> Could you put your current situation in context? How have you been managing
> your packages and what is the current state of your R installation?
>
>
> Patrick
>
>
>
> Peng Yu wrote:
>>
>> Hi Patrick,
>>
>> Would you please let me know what is the command to check the BioC
>> version?
>>
>> Regards,
>> Peng
>>
>> On Wed, Aug 5, 2009 at 12:02 PM, Patrick Aboyoun<paboyoun at fhcrc.org>
>> wrote:
>>
>>>
>>> Peng,
>>> In addition to the versioning of R and Bioconductor packages, we also
>>> version the biocLite.R script on biocondunctor.org
>>>
>>> "biocinstall version 2.4.11" because we sometimes change the behavior of
>>> the
>>> functions in that script, such as which BioC packages are recommended, so
>>> providing the printout that you gave is ideal for us to pinpoint problems
>>> users encounter.
>>>
>>>
>>> Patrick
>>>
>>>
>>> Sean Davis wrote:
>>>
>>>>
>>>> On Wed, Aug 5, 2009 at 12:14 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>>>
>>>>
>>>>
>>>>>
>>>>> Hi,
>>>>>
>>>>> I got the following message. I don't understand what it means. Can
>>>>> somebody let me know its meaning?
>>>>>
>>>>>
>>>>>
>>>>>>
>>>>>>   source("http://bioconductor.org/biocLite.R")
>>>>>>   biocLite("pd.mogene.1.0.st.v1")
>>>>>>
>>>>>>
>>>>>
>>>>> Running biocinstall version 2.4.11 with R version 2.9.0
>>>>> Your version of R requires version 2.4 of Bioconductor.
>>>>>
>>>>>
>>>>>
>>>>
>>>> Version 2.4 is the current release of bioconductor.  biocLite() will do
>>>> the
>>>> right thing, generally.  What you want to try to avoid is mixing
>>>> bioconductor versions together.  If you use biocLite() all the time, you
>>>> shouldn't have any problems.
>>>>
>>>> Sean
>>>>
>>>>       [[alternative HTML version deleted]]
>>>>
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>>>>
>>>>
>>>
>>>
>>
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>
>