Re: [R] RSQLite and undefined symbol:sqlite3_bind_in

From: Marc Carlson <mcarlson_at_fhcrc.org>
Date: Mon, 19 May 2008 11:02:24 -0700

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
>
>
>
> [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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>
>



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Mon 19 May 2008 - 18:56:22 GMT

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