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

[Patrick Aboyoun]

Peng,
If you are still having this problem then

source("http://bioconductor.org/biocLite.R")
update.packages(repos = biocinstallRepos())


will prompt you for updating all the out of date packages.


Patrick



Peng Yu wrote:
> 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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>>>       
>>     
>
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