[BioC] Problems when access elements in mogene10stprobeset.db

[Peng Yu]

On Sat, Aug 8, 2009 at 12:37 AM, Martin Morgan<mtmorgan at fhcrc.org> wrote:
> Peng Yu wrote:
>> Hi,
>>
>> I removed the directory that my own package installations are in, that
>> is where 'mogene10stprobeset.db' was. The I found that there were
>> 'mogene10stprobeset.db' in the system already. Therefore, I run my
>> scripts mogeneID.R, which now gives me the correct results. My
>> original problem was because that there are packages installed in the
>> system and packages installed in my home directory. Somehow, there are
>> some conflicts in between.
>
> It is not likely to be a conflict -- R works happily with user and
> system libraries. Likely the package(s) in your local library were
> installed incorrectly or were corrupted during use.
>
>> The reason that I have my own installations is that our system admin
>> may not install packages in time. So I have to install the packages in
>> my own directory, when he is not available. However, he may later
>> install the same packages in the systems. I am wondering what is the
>> correct way to maintain the consistencies between the two
>> installations. For example, two questions are
>>   1. how to figure what packages are installed in both places?
>
>  pkgs = installed.packages()
>  dups = pkgs[duplicated(pkgs[,c("Package", "Version")]), "Package"]
>
>>   2. how automatically uninstall all the packages in my directory that
>> are already installed in both places?
>
>  remove.packages(dups)
>
> I would not do this 'automatically'.

Is there a reason why you would not do this 'automatically'?

Regards,
Peng