[R] RSQLite and undefined symbol:sqlite3_bind_in

From: Maya Bercovich <mayab_at_tauex.tau.ac.il>
Date: Mon, 19 May 2008 09:28:58 +0300


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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