Question: ChemmineOB installation failed
0
gravatar for abdullahsaeed92
8 months ago by
abdullahsaeed920 wrote:

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

software error • 249 views
ADD COMMENTlink modified 8 months ago by James W. MacDonald52k • written 8 months ago by abdullahsaeed920

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

ADD REPLYlink written 8 months ago by khoran0

Yes it exists, and the output of .libPaths is /Library/Frameworks/R.framework/Versions/3.5/Resources/library

ADD REPLYlink written 8 months ago by abdullahsaeed920

Did the location of the installed libopenbabel.so get added to the LDLIBRARYPATH? Maybe something like

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib

http://openbabel.org/wiki/Install(sourcecode)

ADD REPLYlink written 8 months ago by shepherl ♦♦ 1.7k

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_PATH the location of the dylib file, so that would be "/usr/local/opt/open-babel/lib/" in this case.

Also, setting the LD_LIBRARY_PATH to this same directory would be worth trying also.

ADD REPLYlink modified 8 months ago • written 8 months ago by khoran0
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