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 <[email protected]> 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 <[email protected]> > 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 > | [email protected] > | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > -- > Regards, Dirk >
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