[Rcpp-devel] RInside

David Rosengarten save.of.ten at gmail.com
Tue Jul 13 02:50:46 CEST 2010


Well I'm not quite sure why it's different for me then, but your theory
fixed it!  This is the result of 'ldd rinside_sample0':

linux-vdso.so.1 =>  (0x00007fff720dd000)
libR.so => /usr/lib/R/lib/libR.so (0x00007f351598d000)
 libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f3514ff2000)
liblapack.so.3gf => /usr/lib/atlas/liblapack.so.3gf (0x00007f35143ea000)
 libRcpp.so => /usr/local/lib/R/site-library/Rcpp/lib/libRcpp.so
(0x00007f3514192000)
libRInside.so => /usr/local/lib/R/site-library/RInside/lib/libRInside.so
(0x00007f3513f7d000)
 libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f3513c68000)
libm.so.6 => /lib/libm.so.6 (0x00007f35139e5000)
 libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f35137ce000)
libc.so.6 => /lib/libc.so.6 (0x00007f351344a000)
 libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f351315d000)
libreadline.so.6 => /lib/libreadline.so.6 (0x00007f3512f1c000)
 libpcre.so.3 => /lib/libpcre.so.3 (0x00007f3512ced000)
libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007f3512adc000)
 libz.so.1 => /lib/libz.so.1 (0x00007f35128c5000)
libdl.so.2 => /lib/libdl.so.2 (0x00007f35126c0000)
 /lib64/ld-linux-x86-64.so.2 (0x00007f3515f18000)
libncurses.so.5 => /lib/libncurses.so.5 (0x00007f351247d000)

and the examples run now.  Thanks so much for your help.

As a further question (sorry for all the trouble), do you know how I can
adapt the makefile so that a program will compile with the gsl libraries?  I
tried adding:

CFLAGS = -I/usr/include/gsl
LDFLAGS = -lgsl -lgslblasnative
CC = g++
%: %.cpp
$(CC) $(CFLAGS) $(LDFLAGS) $< -o $@

as well as 'rm -f *~ *.o core a.out' in clean:, but upon 'make' I am getting
the error

metrop.cpp:14:21: error: RInside.h: No such file or directory
make: *** [metrop] Error 1

for my program metrop.cpp.  The only thing regarding R that I have in my
code as of now is #include <RInside.h>.

Best,
David

On Mon, Jul 12, 2010 at 5:38 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> 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
> |
> |
> |
> | ----------------------------------------------------------------------
> | _______________________________________________
> | Rcpp-devel mailing list
> | Rcpp-devel at lists.r-forge.r-project.org
> | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
>
> --
>  Regards, Dirk
>
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