[BioC] Rsamtools installation error

[Dan Tenenbaum]

On Wed, Jul 11, 2012 at 12:01 PM, Murli [guest] <guest at bioconductor.org> wrote:
>
> Hi,
> I am trying to install Rsamtools (Redhat linux ) and I have been getting the following error
> #######################################
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object '/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>   /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: gzopen64
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ‘/usr/local/lib64/R/library/Rsamtools’
> #########################################
>
> I have libz installed
> /sbin/ldconfig -p|grep libz
>         libz.so.1 (libc6,x86-64) => /lib64/libz.so.1
>         libz.so.1 (libc6,x86-64) => /usr/lib64/libz.so.1
>         libz.so.1 (libc6) => /lib/libz.so.1
>         libz.so.1 (libc6) => /usr/lib/libz.so.1
>         libz.so (libc6,x86-64) => /lib64/libz.so
>         libz.so (libc6,x86-64) => /usr/lib64/libz.so
>         libz.so (libc6) => /lib/libz.so
>         libz.so (libc6) => /usr/lib/libz.so
>
> I checked the LD_LIBRARY_PATH using the following
> R CMD env | grep LD_LIBRARY_PATH
> LD_LIBRARY_PATH=/usr/local/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64
>
> Please let me know if there is anything else that I need to check.


What command are you using to try and install Rsamtools?
Try this command:
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

It seems like the error you are getting is because zlibbioc is not
being installed, but if you used the above command, it would be
installed.

Dan


> Thanks for your help.
> Cheers../Murli
>
>
>
>
>  -- output of sessionInfo():
>
> sessionInfo()
> R version 2.15.0 (2012-03-30)
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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