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abdullahsaeed92
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@abdullahsaeed92-20444
Last seen 5.7 years ago
I installled chemmineR and ChemmineOB on my mac osx (10.13.x) like this:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChemmineR", version = "3.8")
Then after installing chemmineR, I installed openbabel from there: http://sourceforge.net/projects/openbabel/files/openbabel/2.3.1/OpenBabel-2.3.1.mac.zip/download
and after this I installed ChemmineOB, this way:
BiocManager::install("ChemmineOB", version = "3.8")
After this on R command line:
library("ChemmineR")
library("ChemmineOB")
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
First, can you check to see if the file /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ChemmineOB/libs/ChemmineOB.so exists or not?
Also, can you show me the output of ".libPaths()"?
Thanks. Kevin
Yes it exists, and the output of .libPaths is /Library/Frameworks/R.framework/Versions/3.5/Resources/library
Did the location of the installed libopenbabel.so get added to the LDLIBRARYPATH? Maybe something like
http://openbabel.org/wiki/Install(sourcecode)
Upon closer inspection of the error message, I see that it is actually failing to load /usr/local/opt/open-babel/lib/libopenbabel.5.dylib, not the ChemmineOB.so as it first seemed to me. First, confirm that file does exist. I'm not really a mac developer, but this stack overflow page seems to have some helpful suggestions:
https://stackoverflow.com/questions/17703510/dyld-library-not-loaded-reason-image-not-found
One suggestions is to set the environment variable
DYLD_LIBRARY_PATHthe location of the dylib file, so that would be "/usr/local/opt/open-babel/lib/" in this case.Also, setting the
LD_LIBRARY_PATHto this same directory would be worth trying also.