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MSKCC cBio cluster documentation
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R unable to load shared object #429

Closed rgejman closed 8 years ago

rgejman commented 8 years ago

Hello! I am trying to install a bioconductor library in R like so:

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("mzR")

Unfortunately I get a strange error that I cannot debug. It seems to be related to libnetcdf:

....
installing to /cbio/ski/scheinberg/home/rgejman/R/x86_64-pc-linux-gnu-library/3.2/mzR/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'close' from package 'base' in package 'mzR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
    unable to load shared object '/cbio/ski/scheinberg/home/rgejman/R/x86_64-pc-linux-gnu-library/3.2/mzR/libs/mzR.so':
      libnetcdf.so.7: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/cbio/ski/scheinberg/home/rgejman/R/x86_64-pc-linux-gnu-library/3.2/mzR'

Any idea what might be going on?

juanperin commented 8 years ago

Please send this to hpc-request@cbio.mskcc.org

Juan

On Jul 22, 2016, at 6:55 AM, Ron Gejman notifications@github.com wrote:

Hello! I am trying to install a bioconductor library in R like so:

source("http://bioconductor.org/biocLite.R") biocLite() biocLite("mzR")

Unfortunately I get a strange error that I cannot debug. It seems to be related to libnetcdf:

`installing to /cbio/ski/scheinberg/home/rgejman/R/x86_64-pc-linux-gnu-library/3.2/mzR/libs * R * inst * preparing package for lazy loading Creating a generic function for 'close' from package 'base' in package 'mzR' * help ** installing help indices * building package indices * installing vignettes * testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/cbio/ski/scheinberg/home/rgejman/R/x86_64-pc-linux-gnu-library/3.2/mzR/libs/mzR.so': libnetcdf.so.7: cannot open shared object file: No such file or directory Error: loading failed Execution halted ERROR: loading failed

removing '/cbio/ski/scheinberg/home/rgejman/R/x86_64-pc-linux-gnu-library/3.2/mzR' ` Any idea what might be going on?

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tatarsky commented 8 years ago

This was handled via FB.