[Rcpp-devel] RInside
Dirk Eddelbuettel
edd at debian.org
Mon Jul 12 23:38:55 CEST 2010
Hi David,
Thanks for hanging in there -- I think you just found a real bug on our side!
On 12 July 2010 at 17:21, David Rosengarten wrote:
| The result of sudo apt-get install r-base-core is:
|
| Reading package lists... Done
| Building dependency tree
| Reading state information... Done
| r-base-core is already the newest version.
| r-base-core set to manually installed.
| The following packages were automatically installed and are no longer required:
| linux-headers-2.6.32-21-generic linux-headers-2.6.32-21 dkms
| Use 'apt-get autoremove' to remove them.
| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
|
| So, it looks like I should already have the shared libraries installed. I
| originally installed the R packages from the Ubuntu Software Center, and then I
| installed Rcpp and RInside using install.packages() in R. Does this give any
| new information, or should I try uninstalling everything and starting from
| scratch?
It's perfect. I had to scratch my head for a moment, but then I got an idea.
Here is the story I currently suspect:
1) r-base-core is built using shared libraries, but these are private to R
2) R itself sets a LD_LIBRARY_PATH in the shell script /usr/bin/R so all
is good for normal R use
3) I _used to_ add a file /etc/ld.so.conf.d/libR.conf which made the
'hidden' location of R visible to the system
4) Unfortunately, this is considered cheating and bad use by the so-called
Debian Policy my Debian R package has to conform to so I had to stop
that.
5) Because of 3), my systems still have /etc/ld.so.conf.d/libR.conf which
is why 'ldd rinside_sample0' resolves all shared libs for, but because
of 4) you no longer do !
To fix this, try placing these two line in a file /etc/ld.so.conf.d/libR.conf
(without the leading psace, though)
# make libR.so visible to ld.so
/usr/lib/R/lib
On amd64, you could also use
# make libR.so visible to ld.so
/usr/lib64/R/lib
The run 'sudo ldconfig' and repeat 'ldd rinside_sample0'. It should now find
libR.so, and if so, you should be able to run all examples.
If this hunch is wrong we need to look somewhere else. If the hunch is
right, I need to modify the examples so that libR.so gets an Rpath invocation
as we do for libRcpp.so and libRInside.so.
Hope this helps, Dirk
|
| Thanks,
| David
|
| On Mon, Jul 12, 2010 at 4:52 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
|
|
| David,
|
| Thanks for bringing the discussion here with is more topical for Rcpp and
| RInside.
|
| On 12 July 2010 at 16:34, David Rosengarten wrote:
| | Hi,
| |
| | I originally emailed the r-sig-debian list and was directed here. I
| am
| | trying to run the examples in /RInside/examples/standard such as
| | rinside_sample_0, but I am getting the error:
| |
| | error while loading shared libraries: libR.so: cannot open shared object
| file:
| | No such file or directory
| |
| | Does anyone know how to deal with this? I was told to include the
| output of
| | 'make' and 'ldd ./rinside_sample0', so they are as follows:
| |
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample0.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample0
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample1.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample1
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample2.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample2
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample3.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample3
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample4.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample4
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample5.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample5
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample6.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample6
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample7.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample7
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_sample8.cpp
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/
| Rcpp/
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local
| /lib/R
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_sample8
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_test0.cpp -L
| | /usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/Rcpp
| /lib
| | -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local/lib
| /R/
| | site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_test0
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include
| -I/usr/
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s
| rinside_test1.cpp -L
| | /usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/Rcpp
| /lib
| | -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local/lib
| /R/
| | site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/
| site-library/
| | RInside/lib -o rinside_test1
| |
| | linux-vdso.so.1 => (0x00007fff30bff000)
| | libR.so => not found
| | libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f50d2512000)
| | liblapack.so.3gf => /usr/lib/atlas/liblapack.so.3gf (0x00007f50d190a000)
| | libRcpp.so => /usr/local/lib/R/site-library/Rcpp/lib/libRcpp.so
| | (0x00007f50d16b2000)
| | libRInside.so => /usr/local/lib/R/site-library/RInside/lib/libRInside.so
| | (0x00007f50d149d000)
| | libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f50d1188000)
| | libm.so.6 => /lib/libm.so.6 (0x00007f50d0f05000)
| | libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f50d0cee000)
| | libc.so.6 => /lib/libc.so.6 (0x00007f50d096a000)
| | libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f50d067d000)
| | /lib64/ld-linux-x86-64.so.2 (0x00007f50d2ecd000)
| | libR.so => not found
| | libR.so => not found
|
| There is your problem.
|
| | I have R and r-base-dev installed, so I don't understand why this is
| happening.
| | Any help would be much appreciated.
|
| You may have R, but I suspect you do not have R built with shared
| libraries.
| The quickest fix, given that you started on r-sig-debian, may be
|
| $ sudo apt-get install r-base-core
|
| Else you can of course rebuild R from source etc, but you have to tell
| configure to use --enable-R-shlib or else you cannot embed R. And
| RInside wants to embed R, so you can't the latter witout the former.
|
| Hope this helps.
|
| --
| Regards, Dirk
|
|
|
| ----------------------------------------------------------------------
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--
Regards, Dirk
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