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girke-lab / ChemmineOB

OpenBabel wrapper package for R
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Cannot install ChemmineOB #11

Closed joannazbijewska closed 7 years ago

joannazbijewska commented 7 years ago

I've tried probably almost all possible ways to install the ChemmineOB package - from Bioconductor, through building via devtools, from github package and the way it is described in the install file in the original release. However, all the time I'm getting this error message:

" ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'ChemmineOB', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: cannot load shared object '/home/joanna/R/i686-pc-linux-gnu-library/3.3/ChemmineOB/libs/ChemmineOB.so': /home/joanna/R/i686-pc-linux-gnu-library/3.3/ChemmineOB/libs/ChemmineOB.so: undefined symbol: _ZN9OpenBabel11OBTypeTable9GetToTypeB5cxx11Ev ERROR: loading failed Execution halted ERROR: loading failed

I'm installing under Ubuntu 16.04 LTS. Could you, please advise me some way to deal with it? I would love to use this package ASAP.

khoran commented 7 years ago

It cannot find the openbabel library most likely. If it's installed in a non-standard location (like in your home directory somewhere), you'll have to set some environment variables each time you use ChemmineOB (you could set them in your shell profile to load when you login if you want). First, find out where openbabel is installed, I'll refer to that directory as "". Then set the following 3 environment variables:

export LD_LIBRARY_PATH=/build/lib export BABEL_LIBDIR=$LD_LIBRARY_PATH export BABEL_DATADIR=/data

The /build/lib should have lots of *.so files and the

/data should have lots of *.txt and *.par files in it. Once these environment variables are set you should be able to install and use ChemmineOB. Kevin On 01/21/2017 05:22 AM, joannazbijewska wrote: > > I've tried probably almost all possible ways to install the ChemmineOB > package - from Bioconductor, through building via devtools, from > github package and the way it is described in the install file in the > original release. However, all the time I'm getting this error message: > > " > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'ChemmineOB', details: > call: dyn.load(file, DLLpath = DLLpath, ...) > error: cannot load shared object > '/home/joanna/R/i686-pc-linux-gnu-library/3.3/ChemmineOB/libs/ChemmineOB.so': > /home/joanna/R/i686-pc-linux-gnu-library/3.3/ChemmineOB/libs/ChemmineOB.so: > undefined symbol: _ZN9OpenBabel11OBTypeTable9GetToTypeB5cxx11Ev > ERROR: loading failed > Execution halted > ERROR: loading failed > > * removing ‘/home/joanna/R/i686-pc-linux-gnu-library/3.3/ChemmineOB’ > " > > Could you, please advise me some way to deal with it? I would love to > use this package ASAP. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > , or mute the > thread > . >