[BioC] Problems when access elements in mogene10stprobeset.db

[Peng Yu]

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.

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?
  2. how automatically uninstall all the packages in my directory that
are already installed in both places?

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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>>
>
>