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Hi All,
I am Xing Zeng, currently a undergrad summer intern student in Professor Hoffman's lab. I am currently trying to use segtools to analyze the result by segway, but I ran into some trouble.
I try to run segtools, but I get this:
xzeng@mhoffman7:( /scratch/segway-semi/result/0614$ segtools-gmtk-parameters params.params
Loading gmtk transitions...Opening connection to R environment.
/users/xzeng/.local/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/robject.py:5: UserWarning: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
rpy2.rinterface.initr()
/users/xzeng/.local/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/robject.py:5: UserWarning: During startup -
rpy2.rinterface.initr()
/users/xzeng/.local/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/robject.py:5: UserWarning: Warning message:
rpy2.rinterface.initr()
/users/xzeng/.local/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/robject.py:5: UserWarning: package ‘stats’ in options("defaultPackages") was not found
rpy2.rinterface.initr()
/users/xzeng/.local/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/functions.py:106: UserWarning: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/library/stats/libs/stats.so':
libRlapack.so: cannot open shared object file: No such file or directory
res = super(Function, self).__call__(*new_args, **new_kwargs)
/users/xzeng/.local/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/functions.py:106: UserWarning: Error: package or namespace load failed for ‘lattice’
res = super(Function, self).__call__(*new_args, **new_kwargs)
Fatal error: Failed to load R package: /users/xzeng/.local/lib/python2.7/site-packages/segtools-1.1.9-py2.7.egg/segtools/R/common.R
I tried search around and debug for solution.
Seems like adding library folder to LD_LIBRARY_PATH would not work as some claim dyn.load does not use it (and it didn't work on my side either).
Some fix this problem by create a link named /usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/modules/libRlapack.so link to the lapack.so file in that same folder but I lack the administrative privalege to do so.
I also try to check dependencies of stat.so file using the following command:
xzeng@mhoffman7:( /scratch/segway-semi/result/0614$ R CMD ldd /usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/library/stats/libs/stats.so
linux-vdso.so.1 => (0x00007ffff85ff000)
libRlapack.so => /usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/lib/libRlapack.so (0x00007f286aa08000)
libgfortran.so.3 => /usr/lib64/libgfortran.so.3 (0x00007f286a715000)
libm.so.6 => /lib64/libm.so.6 (0x00007f286a491000)
libR.so => /usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/lib/libR.so (0x00007f2869ecf000)
libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00007f2869cb9000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f2869a9c000)
libc.so.6 => /lib64/libc.so.6 (0x00007f2869708000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f2869503000)
libreadline.so.6 => /lib64/libreadline.so.6 (0x00007f28692c0000)
librt.so.1 => /lib64/librt.so.1 (0x00007f28690b8000)
/lib64/ld-linux-x86-64.so.2 (0x000000317ba00000)
libtinfo.so.5 => /lib64/libtinfo.so.5 (0x00007f2868e96000)
It does seems like stat.so should find the libRlapack.so and the file is indeed in that location.
So I am wondering if anyone have seens this or know what causes it. Any ideas would be helpful.
Thanks!