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I want to use rpy2 import R package 'iqspr' which I have aleady installed and test on my Rstudio, this package works fine.

Here are the errors I am getting.

from rpy2.robjects.packages import importr

java=importr('rJava')
iqspr=importr('iqspr')

errors 

/Library/Python/2.7/site-packages/rpy2-2.8.3-py2.7-macosx-10.11-intel.egg/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so':
  dlopen(/usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from: /usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so
  Reason: image not found

  warnings.warn(x, RRuntimeWarning)
/Library/Python/2.7/site-packages/rpy2-2.8.3-py2.7-macosx-10.11-intel.egg/rpy2/rinterface/__init__.py:185: RRuntimeWarning: Error: .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so':
  dlopen(/usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from: /usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so
  Reason: image not found

  warnings.warn(x, RRuntimeWarning)
Traceback (most recent call last):
  File "/Users/yang/Desktop/Chemical compounds design important materials/chemical_compound_design.py", line 4, in <module>
    java=importr('rJava')
  File "/Library/Python/2.7/site-packages/rpy2-2.8.3-py2.7-macosx-10.11-intel.egg/rpy2/robjects/packages.py", line 453, in importr
    env = _get_namespace(rname)
rpy2.rinterface.RRuntimeError: Error: .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so':
  dlopen(/usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from: /usr/local/lib/R/3.3/site-library/rJava/libs/rJava.so
  Reason: image not found
jwpfox
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杨秀锋
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1 Answers1

0

Issues involving RStudio and rJava were reported in the past (for example rJava load error in RStudio/R after "upgrading" to OSX Yosemite), and it is quite possible that the cause is similar.

Try doing

export LD_LIBRARY_PATH=/usr/local/lib/R/3.3/site-library/rJava/libs/:{LD_LIBRARY_PATH}

before starting Python.

Community
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lgautier
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