[R] RSQLite and undefined symbol:sqlite3_bind_in

[Marc Carlson]

Hi Maya,

You might want to post emails about specialized bioconductor packages to 
the bioconductor mailing list.  You can sign up for it here:

http://www.bioconductor.org/docs/mailList.html

Please post your question over there and also tell us: how did you 
install RSQLite?  Did you use biocLite() for that as well or did you use 
another method?


    Marc


Maya Bercovich wrote:
> Hi All,
>
> I tried to install AnnotationDBI
> like so:
> source("http://bioconductor.org/biocLite.R")
> biocLite("AnnotationDbi")
> and got this error:
> ....
>
> Loading required package: RSQLite
> Error in dyn.load(file, ...) :
>    unable to load shared library '/RHEL3/local/lib64/R/library/ 
> RSQLite/libs/RSQLite.so':
>    /RHEL3/local/lib64/R/library/RSQLite/libs/RSQLite.so: undefined  
> symbol: sqlite3_bind_int
> Error: package 'RSQLite' could not be loaded
> Execution halted
> ERROR: lazy loading failed for package 'AnnotationDbi'
> ** Removing '/RHEL3/local/lib64/R/library/AnnotationDbi'
>
> The downloaded packages are in
>          /RHEL3/tmp/Rtmp6ex1Pz/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies =  
> dependencies,  :
>    installation of package 'AnnotationDbi' had non-zero exit status
>  >
>
> However, I did install RSQLite and the installation finished with no  
> errors.
>
> But:
>
>  > require(RSQLite)
> Loading required package: RSQLite
> Error in dyn.load(file, ...) :
>    unable to load shared library '/usr/local/lib64/R/library/RSQLite/ 
> libs/RSQLite.so':
>    /usr/local/lib64/R/library/RSQLite/libs/RSQLite.so: undefined  
> symbol: sqlite3_bind_int
>
> The library and file do exist with 755 permissions.
>
> My session info:
>
>  > sessionInfo()
> R version 2.6.2 (2008-02-08)
> 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.U 
> TF-8;LC_MONETARY=en_US.UTF-8;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_ID 
> ENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] DBI_0.2-4
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17 tools_2.6.2
>  >
>
> Has anyone a clue?
> I am not a R user, just the IT person who has to install it, so if  
> you need additional info from inside R, please let me know how to get  
> it.
>
>
> Thanks a lot,
> Maya
>
>
>
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>
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