Error during installation of ChemmineOB R package
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@elisamicarelli-8523
Last seen 3.1 years ago
European Union

Hi, 

I'm trying to install the ChemmineOB packages following this tutorial

https://www.bioconductor.org/packages/3.3/bioc/vignettes/ChemmineOB/inst/doc/ChemmineOB.html

the installation by direct command in R software  [ source("http://bioconductor.org/biocLite.R") biocLite("ChemmineOB") ]

returns this error 

[....]

** 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: unable to load shared object '/home/elisa/R/x86_64-pc-linux-gnu-library/3.2/ChemmineOB/libs/ChemmineOB.so':
  libopenbabel.so.4: impossibile aprire il file oggetto condiviso: File o directory non esistente
Errore: loading failed
Esecuzione interrotta
ERROR: loading failed

 

Since the installation failed I tried to run the following command

R CMD INSTALL --configure-args='--with-openbabel-include=...  --with-openbabel-lib=...' <ChemmineOB package file>

downloading the ChemmineOB package from 

https://www.bioconductor.org/packages/release/bioc/html/ChemmineOB.html

 

but the same error is returned.

I specify also that I have installed also the openbabel tool by command line but I don't know if this is required to install this R package, and also I installed the ChemmineR without any problem.

Someone could explain me how I can fix this problem.

Thanks!

Chemmine Ubuntu OpenBabel • 1.5k views
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Entering edit mode
Thomas Girke ★ 1.7k
@thomas-girke-993
Last seen 8 months ago
United States

The header files might be missing in your install of OpenBabel. On Ubuntu you want to install OpenBabel like this: 

sudo apt-get install libopenbabel-dev

After this, try to install ChemmineOB from R with biocLite(...) or the command-line.

More detail on debugging Linux installs are provided in the README file here: http://bioconductor.org/packages/ChemmineOB/ 

Thomas

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Entering edit mode

Thanks I solved in this way!!!!

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