Question: ChemmineOB cannot find installed open-babel
0
gravatar for yun YAN
4.5 years ago by
yun YAN20
Canada
yun YAN20 wrote:

I have installed ChemmineOB and also open-babel but when the package is called inside R console, it seems that my open-babel is not found. Actually open-babel could be called by using its command line in terminal. I got confused and any suggestions will help a lot. 

Thank you so much. 

 

install open-babel

brew install open-babel

locate OPEN_BABEL_INCDIR and OPEN_BABEL_LIBDIR

OPEN_BABEL_INCDIR is /usr/local/Cellar/open-babel/2.3.2/lib/openbabel/2.3.2, where files likealias.hdescriptor.hpointgroup.hatom.h etc.

OPEN_BABEL_LIBDIR is /usr/local/Cellar/open-babel/2.3.2/lib/openbabel/2.3.2, where files likeAPIInterface.sofastsearchformat.sooutformat.soCSRformat.so, etc.

install ChemmineOB

R CMD INSTALL --configure-args='--with-openbabel-include=/usr/local/Cellar/open-babel/2.3.2/include/openbabel-2.0/openbabel --with-openbabel-lib=/usr/local/Cellar/open-babel/2.3.2/lib/openbabel/2.3.2' ChemmineOB_1.2.9.tgz

Errors reported

Error : .onLoad failed in loadNamespace() for 'ChemmineOB', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ChemmineOB/libs/ChemmineOB.so': dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/ChemmineOB/libs/ChemmineOB.so, 10): Symbol not found: __ZN9OpenBabel10FastSearch11FindSimilarEPNS_6OBBaseERSt8multimapIdjSt4lessIdESaISt4pairIKdjEEEdd
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/library/ChemmineOB/libs/ChemmineOB.so
Expected in: /usr/local/lib/libopenbabel.4.dylib in /Library/Frameworks/R.framework/Versions/3.1/Resources/library/ChemmineOB/libs/ChemmineOB.so
Error: package or namespace load failed for ‘ChemmineOB’

Environment

R version 3.1.1 (2014-07-10) -- "Sock it to Me"

Platform: x86_64-apple-darwin13.1.0 (64-bit) Mac OS X 10.9.5

Xcode 6.0.1

chemmineob openbabel • 2.0k views
ADD COMMENTlink modified 4.5 years ago by Dan Tenenbaum8.2k • written 4.5 years ago by yun YAN20
Answer: ChemmineOB cannot find installed open-babel
1
gravatar for Dan Tenenbaum
4.5 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:

I suggest you uninstall the brew-provided version of Open Babel and install it instead from here:

 

http://sourceforge.net/projects/openbabel/files/openbabel/2.3.1/OpenBabel-2.3.1.mac.zip/download

This is the version of Open Babel used by the Mac build machines at Bioconductor.

Then install ChemmineOB as follows:

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

biocLite("ChemmineOB")

That will install the binary version of ChemmineOB, which is already compiled. 

I just tried these steps on my own machine and they worked fine.

Dan

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Dan Tenenbaum8.2k

This worked for me; thanks, Dan.

ADD REPLYlink written 2.6 years ago by paulymer0

I do this way on mac os but still getting error? Error: package or namespace load failed for ‘ChemmineOB’: .onLoad failed in loadNamespace() for 'ChemmineOB', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ChemmineOB/libs/ChemmineOB.so': dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ChemmineOB/libs/ChemmineOB.so, 10): Library not loaded: /usr/local/opt/open-babel/lib/libopenbabel.5.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ChemmineOB/libs/ChemmineOB.so Reason: image not found

ADD REPLYlink written 14 days ago by abdullahsaeed920
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