[BioC] Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db'; RS-DBI driver -database locked

[Marc Carlson]

Hi Manikhandan,

I still cannot reproduce this problem.  I have loaded all the latest
versions of the packages that you have in your sessionInfo() and none of
them causes any problems for me.  But the error says that your
annotation database is locked.  And so I wonder if you might have other
R sessions (or other things) open which are tapping into (and possibly
writing to) this same library?  So you might want to start over, and be
sure to try and kill any rogue R processes that may be present, it might
also be a good idea to start fresh by moving the .RData file from the
directory you use to launch R.  Another thing to try is to remove your
previous annotation packages (in particular org.Hs.eg.db since that one
is giving this error) with remove.packages().  That way you can get a
fresh start when you try to use biocLite() to install these packages.


  Marc


On 06/29/2010 09:57 AM, Manikhandan Mudaliar wrote:
> Marc Carlson <mcarlson at ...> writes:
>
>   
>> Hi Manikhandan,
>>
>> I am unable to reproduce this problem.  Can you please give us your
>> sessionInfo() as described in the posting guide? 
>>
>> http://www.bioconductor.org/docs/postingGuide.html
>>
>> I can tell you that none of the human chip packages will work without
>> the org.Hs.eg.db package installed so getting this installed is going to
>> be critical to your success. 
>>
>>   Marc
>>     
>
> Marc Carlson <mcarlson at ...> writes:
>
>   
>> Hi Manikhandan,
>>
>> I am unable to reproduce this problem.  Can you please give us your
>> sessionInfo() as described in the posting guide? 
>>
>> http://www.bioconductor.org/docs/postingGuide.html
>>
>> I can tell you that none of the human chip packages will work without
>> the org.Hs.eg.db package installed so getting this installed is going to
>> be critical to your success. 
>>
>>   Marc
>>     
>
>
> Dear Marc,
>
> Thanks very much.
>
> My sessionInfo:
>
>   
>> sessionInfo()
>>     
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> 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=C              LC_MESSAGES=en_US.UTF-8  
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C           
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C      
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods 
> [8] base    
>
> other attached packages:
>  [1] e1071_1.5-24          class_7.3-2           samr_1.28           
>  [4] impute_1.22.0         bridge_1.12.1         rama_1.22.1         
>  [7] RankProd_2.20.0       AnnotationDbi_1.10.1  Biostrings_2.16.5   
> [10] IRanges_1.6.6         preprocessCore_1.10.0 affyio_1.16.0       
> [13] plgem_1.20.0          MASS_7.3-6            siggenes_1.22.0     
> [16] multtest_2.4.0        simpleaffy_2.24.0     gcrma_2.20.0        
> [19] genefilter_1.30.0     RColorBrewer_1.0-2    affydata_1.11.10    
> [22] affy_1.26.1           Biobase_2.8.0       
>
> loaded via a namespace (and not attached):
> [1] annotate_1.26.0 DBI_0.2-5       RSQLite_0.9-1   survival_2.35-8
> [5] tools_2.11.1    xtable_1.5-6  
>   
>>     
> Thanks.
>
> Regards,
> Mani
>
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