[Rcpp-devel] RInside
Dirk Eddelbuettel
edd at debian.org
Tue Jul 13 02:21:55 CEST 2010
David,
On 12 July 2010 at 16:38, Dirk Eddelbuettel 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 !
That was a good theory, but it turns out that we also have a softlink in
/usr/lib/ which connects /usr/lib/libR.so to /usr/lib/R/lib/libR.so so
libR.so remains still visible even after I remove my
/etc/ld.so.conf.d/libR.conf
Hence, I don't have a good explanation as to why things to do not work at
your end. They should. They sure do here:
edd at max:~/svn/rinside/pkg/inst/examples/standard$ rm rinside_sample0
edd at max:~/svn/rinside/pkg/inst/examples/standard$ make 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/include" -g -O2 -Wall 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
edd at max:~/svn/rinside/pkg/inst/examples/standard$ ldd rinside_sample0
linux-vdso.so.1 => (0x00007fffe19c9000)
libR.so => /usr/lib/libR.so (0x00007fe40e15a000)
libblas.so.3gf => /usr/lib/gotoblas2/libblas.so.3gf (0x00007fe40da4f000)
liblapack.so.3gf => /usr/lib/gotoblas2/liblapack.so.3gf (0x00007fe40d05d000)
libRcpp.so => /usr/local/lib/R/site-library/Rcpp/lib/libRcpp.so (0x00007fe40cdfb000)
libRInside.so => /usr/local/lib/R/site-library/RInside/lib/libRInside.so (0x00007fe40cbe6000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007fe40c8d1000)
libm.so.6 => /lib/libm.so.6 (0x00007fe40c64e000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fe40c437000)
libc.so.6 => /lib/libc.so.6 (0x00007fe40c0b3000)
libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007fe40bdc6000)
libreadline.so.6 => /lib/libreadline.so.6 (0x00007fe40bb85000)
libpcre.so.3 => /lib/libpcre.so.3 (0x00007fe40b956000)
libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007fe40b745000)
libz.so.1 => /lib/libz.so.1 (0x00007fe40b52e000)
libdl.so.2 => /lib/libdl.so.2 (0x00007fe40b329000)
/lib64/ld-linux-x86-64.so.2 (0x00007fe40e6f0000)
libpthread.so.0 => /lib/libpthread.so.0 (0x00007fe40b10c000)
libncurses.so.5 => /lib/libncurses.so.5 (0x00007fe40aec8000)
edd at max:~/svn/rinside/pkg/inst/examples/standard$ ./rinside_sample0
Hello, world!
edd at max:~/svn/rinside/pkg/inst/examples/standard$
Dirk
| 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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| | Rcpp-devel mailing list
| | Rcpp-devel at lists.r-forge.r-project.org
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|
| --
| Regards, Dirk
| _______________________________________________
| Rcpp-devel mailing list
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--
Regards, Dirk
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