[BioC] Problems when access elements in mogene10stprobeset.db

[Martin Morgan]

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'.

Martin

> 
> Regards,
> Peng
> 
> PS: I have $R_LIBS that is set to a directory that I have write permission.
> 
> On Thu, Aug 6, 2009 at 4:41 PM, Marc Carlson<mcarlson at fhcrc.org> wrote:
>> Hi Peng,
>>
>> I have run the following;
>>
>> library(mogene10stprobeset.db)
>> sessionInfo()
>> all_probes<-ls(mogene10stprobesetENTREZID)
>> set.seed(0xa1beef)
>> probes <-sample(all_probes, 5)
>> print(probes)
>> mogene10stprobesetENTREZID[[probes[1]]]
>>
>>
>> And it runs fine for me.  So I don't think there is anything wrong with
>> your R script, unless there is more than you have shown us here.  The
>> one thing I noticed was that my version of R was slightly newer than
>> yours.  But a problem like you report here should have alerted a lot
>> more people if it were caused by R.
>>
>>  Marc
>>
>>
>>
>> Peng Yu wrote:
>>> Hi,
>>>
>>> Below this email is the R script and the output that I got after
>>> running the script. Can somebody take a look help me figure out why I
>>> get an error message? I followed in the instructions in
>>> AnnotationDbi.pdf.
>>>
>>> Regards,
>>> Peng
>>>
>>> $ cat mogeneID.R
>>> library(mogene10stprobeset.db)
>>> sessionInfo()
>>> all_probes<-ls(mogene10stprobesetENTREZID)
>>> set.seed(0xa1beef)
>>> probes <-sample(all_probes, 5)
>>> print(probes)
>>> mogene10stprobesetENTREZID[[probes[1]]]
>>>
>>> $ Rscript mogeneID.R
>>> Loading required package: methods
>>> Loading required package: Biobase
>>> Loading required package: utils
>>>
>>> Welcome to Bioconductor
>>>
>>>   Vignettes contain introductory material. To view, type
>>>   'openVignette()'. To cite Bioconductor, see
>>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>
>>> Loading required package: affy
>>> Loading required package: affyio
>>> Loading required package: AnnotationDbi
>>> Loading required package: DBI
>>> R version 2.9.1 (2009-06-26)
>>> x86_64-unknown-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices datasets  utils     methods   base
>>>
>>> other attached packages:
>>> [1] mogene10stprobeset.db_2.0.2 RSQLite_0.7-1
>>> [3] DBI_0.2-4                   AnnotationDbi_1.6.1
>>> [5] makecdfenv_1.22.0           affyio_1.12.0
>>> [7] affy_1.22.1                 Biobase_2.4.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] preprocessCore_1.6.0
>>> [1] "10377734" "10527109" "10489285" "10353981" "10371859"
>>> Error in names(colnames) <- colmetanames(x) :
>>>   attempt to set an attribute on NULL
>>> Calls: [[ ... as.list -> as.list -> .tagCol -> tagname -> tagname
>>> Execution halted
>>>
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>>>
>>
> 
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