[BioC] Error loading rat2302.db

[Marc Carlson]

Hi Mike,

Your sessionInfo() hints that you might have a missing dependency (IOW 
you may not have org.Rn.eg.db installed).

You can install it this way:

biocLite("org.Rn.eg.db")



   Marc




On 11/15/2012 11:18 AM, James W. MacDonald wrote:
> Hi Mike,
>
> On 11/15/2012 2:07 PM, Mike [guest] wrote:
>> Every time I try to load rat2302.db I get the same error:
>>
>>> library("rat2302.db")
>> Error : .onLoad failed in loadNamespace() for 'rat2302.db', details:
>>    call: sqliteExecStatement(con, statement, bind.data)
>>    error: RS-DBI driver: (error in statement: no such table: chrlengths)
>> Error: package/namespace load failed for ‘rat2302.db’
>
> Looks like you might have a borked package. Did you try re-installing?
>
> I get:
>
> > library(rat2302.db)
> Loading required package: org.Rn.eg.db
>
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] rat2302.db_2.8.1 org.Rn.eg.db_2.8.0
> [3] BiocInstaller_1.8.3 affycoretools_1.31.2
> [5] KEGG.db_2.8.0 GO.db_2.8.0
> [7] AnnotationDbi_1.20.2 affy_1.36.0
> [9] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.2
> [11] DBI_0.2-5 limma_3.14.1
> [13] oligo_1.22.0 Biobase_2.18.0
> [15] oligoClasses_1.20.0 BiocGenerics_0.4.0
>
> Best,
>
> Jim
>
>
>>
>>
>> I have looked everywhere on the message boards and internet with no 
>> luck finding a solution. Any help is greatly appreciated!
>>
>> Best,
>> Mike
>>
>>   -- output of sessionInfo():
>>
>>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United 
>> States.1252    LC_MONETARY=English_United States.1252 
>> LC_NUMERIC=C                           LC_TIME=English_United 
>> States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] org.Hs.eg.db_2.8.0   RSQLite_0.11.2       DBI_0.2-5            
>> AnnotationDbi_1.20.2 Biobase_2.18.0       BiocGenerics_0.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.16.4  parallel_2.15.1 stats4_2.15.1
>>
>> -- 
>> Sent via the guest posting facility at bioconductor.org.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>