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':<div><br></div><div><div>linux-vdso.so.1 => (0x00007fff720dd000)</div><div>
<span style="white-space:pre-wrap"> </span>libR.so => /usr/lib/R/lib/libR.so (0x00007f351598d000)</div><div>
<span style="white-space:pre-wrap"> </span>libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f3514ff2000)</div><div><span style="white-space:pre-wrap"> </span>liblapack.so.3gf => /usr/lib/atlas/liblapack.so.3gf (0x00007f35143ea000)</div>
<div><span style="white-space:pre-wrap"> </span>libRcpp.so => /usr/local/lib/R/site-library/Rcpp/lib/libRcpp.so (0x00007f3514192000)</div><div><span style="white-space:pre-wrap"> </span>libRInside.so => /usr/local/lib/R/site-library/RInside/lib/libRInside.so (0x00007f3513f7d000)</div>
<div><span style="white-space:pre-wrap"> </span>libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f3513c68000)</div><div><span style="white-space:pre-wrap"> </span>libm.so.6 => /lib/libm.so.6 (0x00007f35139e5000)</div>
<div><span style="white-space:pre-wrap"> </span>libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f35137ce000)</div><div><span style="white-space:pre-wrap"> </span>libc.so.6 => /lib/libc.so.6 (0x00007f351344a000)</div>
<div><span style="white-space:pre-wrap"> </span>libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f351315d000)</div><div><span style="white-space:pre-wrap"> </span>libreadline.so.6 => /lib/libreadline.so.6 (0x00007f3512f1c000)</div>
<div><span style="white-space:pre-wrap"> </span>libpcre.so.3 => /lib/libpcre.so.3 (0x00007f3512ced000)</div><div><span style="white-space:pre-wrap"> </span>libbz2.so.1.0 => /lib/libbz2.so.1.0 (0x00007f3512adc000)</div>
<div><span style="white-space:pre-wrap"> </span>libz.so.1 => /lib/libz.so.1 (0x00007f35128c5000)</div><div><span style="white-space:pre-wrap"> </span>libdl.so.2 => /lib/libdl.so.2 (0x00007f35126c0000)</div>
<div><span style="white-space:pre-wrap"> </span>/lib64/ld-linux-x86-64.so.2 (0x00007f3515f18000)</div><div><span style="white-space:pre-wrap"> </span>libncurses.so.5 => /lib/libncurses.so.5 (0x00007f351247d000)</div>
<div><br></div><div>and the examples run now. Thanks so much for your help.</div><div><br></div><div>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:</div>
<div><br></div><div><div>CFLAGS = <span class="Apple-tab-span" style="white-space:pre"> </span>-I/usr/include/gsl</div><div>LDFLAGS = <span class="Apple-tab-span" style="white-space:pre"> </span>-lgsl -lgslblasnative</div>
<div>CC = <span class="Apple-tab-span" style="white-space:pre"> </span>g++</div><div>%: %.cpp</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>$(CC) $(CFLAGS) $(LDFLAGS) $< -o $@</div></div><div>
<br></div><div>as well as 'rm -f *~ *.o core a.out' in clean:, but upon 'make' I am getting the error</div><div><br></div><div><div>metrop.cpp:14:21: error: RInside.h: No such file or directory</div><div>make: *** [metrop] Error 1</div>
</div><div><br></div><div>for my program metrop.cpp. The only thing regarding R that I have in my code as of now is #include <RInside.h>.</div><div><br></div><div>Best,</div><div>David</div><br><div class="gmail_quote">
On Mon, Jul 12, 2010 at 5:38 PM, Dirk Eddelbuettel <span dir="ltr"><<a href="mailto:edd@debian.org" target="_blank">edd@debian.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi David,<br>
<br>
Thanks for hanging in there -- I think you just found a real bug on our side!<br>
<div><br>
On 12 July 2010 at 17:21, David Rosengarten wrote:<br>
| The result of sudo apt-get install r-base-core is:<br>
|<br>
| Reading package lists... Done<br>
| Building dependency tree <br>
| Reading state information... Done<br>
| r-base-core is already the newest version.<br>
| r-base-core set to manually installed.<br>
| The following packages were automatically installed and are no longer required:<br>
| linux-headers-2.6.32-21-generic linux-headers-2.6.32-21 dkms<br>
| Use 'apt-get autoremove' to remove them.<br>
| 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.<br>
|<br>
| So, it looks like I should already have the shared libraries installed. I<br>
| originally installed the R packages from the Ubuntu Software Center, and then I<br>
| installed Rcpp and RInside using install.packages() in R. Does this give any<br>
| new information, or should I try uninstalling everything and starting from<br>
| scratch?<br>
<br>
</div>It's perfect. I had to scratch my head for a moment, but then I got an idea.<br>
<br>
Here is the story I currently suspect:<br>
<br>
1) r-base-core is built using shared libraries, but these are private to R<br>
<br>
2) R itself sets a LD_LIBRARY_PATH in the shell script /usr/bin/R so all<br>
is good for normal R use<br>
<br>
3) I _used to_ add a file /etc/ld.so.conf.d/libR.conf which made the<br>
'hidden' location of R visible to the system<br>
<br>
4) Unfortunately, this is considered cheating and bad use by the so-called<br>
Debian Policy my Debian R package has to conform to so I had to stop<br>
that.<br>
<br>
5) Because of 3), my systems still have /etc/ld.so.conf.d/libR.conf which<br>
is why 'ldd rinside_sample0' resolves all shared libs for, but because<br>
of 4) you no longer do !<br>
<br>
To fix this, try placing these two line in a file /etc/ld.so.conf.d/libR.conf<br>
(without the leading psace, though)<br>
<br>
# make libR.so visible to ld.so<br>
/usr/lib/R/lib<br>
<br>
On amd64, you could also use<br>
<br>
# make libR.so visible to ld.so<br>
/usr/lib64/R/lib<br>
<br>
The run 'sudo ldconfig' and repeat 'ldd rinside_sample0'. It should now find<br>
libR.so, and if so, you should be able to run all examples.<br>
<br>
If this hunch is wrong we need to look somewhere else. If the hunch is<br>
right, I need to modify the examples so that libR.so gets an Rpath invocation<br>
as we do for libRcpp.so and libRInside.so.<br>
<br>
Hope this helps, Dirk<br>
<div><div></div><div><br>
<br>
<br>
<br>
|<br>
| Thanks,<br>
| David<br>
|<br>
| On Mon, Jul 12, 2010 at 4:52 PM, Dirk Eddelbuettel <<a href="mailto:edd@debian.org" target="_blank">edd@debian.org</a>> wrote:<br>
|<br>
|<br>
| David,<br>
|<br>
| Thanks for bringing the discussion here with is more topical for Rcpp and<br>
| RInside.<br>
|<br>
| On 12 July 2010 at 16:34, David Rosengarten wrote:<br>
| | Hi,<br>
| |<br>
| | I originally emailed the r-sig-debian list and was directed here. I<br>
| am<br>
| | trying to run the examples in /RInside/examples/standard such as<br>
| | rinside_sample_0, but I am getting the error: <br>
| |<br>
| | error while loading shared libraries: libR.so: cannot open shared object<br>
| file:<br>
| | No such file or directory<br>
| |<br>
| | Does anyone know how to deal with this? I was told to include the<br>
| output of<br>
| | 'make' and 'ldd ./rinside_sample0', so they are as follows:<br>
| |<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample0.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample0<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample1.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample1<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample2.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample2<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample3.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample3<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample4.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample4<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample5.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample5<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample6.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample6<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample7.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample7<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_sample8.cpp<br>
| | -L/usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/<br>
| Rcpp/<br>
| | lib -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local<br>
| /lib/R<br>
| | /site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_sample8<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_test0.cpp -L<br>
| | /usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/Rcpp<br>
| /lib<br>
| | -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local/lib<br>
| /R/<br>
| | site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_test0<br>
| | g++ -I/usr/share/R/include -I/usr/local/lib/R/site-library/Rcpp/include<br>
| -I/usr/<br>
| | local/lib/R/site-library/RInside/lib -g -O2 -Wall -s<br>
| rinside_test1.cpp -L<br>
| | /usr/lib64/R/lib -lR -lblas -llapack -L/usr/local/lib/R/site-library/Rcpp<br>
| /lib<br>
| | -lRcpp -Wl,-rpath,/usr/local/lib/R/site-library/Rcpp/lib -L/usr/local/lib<br>
| /R/<br>
| | site-library/RInside/lib -lRInside -Wl,-rpath,/usr/local/lib/R/<br>
| site-library/<br>
| | RInside/lib -o rinside_test1<br>
| |<br>
| | linux-vdso.so.1 => (0x00007fff30bff000)<br>
| | libR.so => not found<br>
| | libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x00007f50d2512000)<br>
| | liblapack.so.3gf => /usr/lib/atlas/liblapack.so.3gf (0x00007f50d190a000)<br>
| | libRcpp.so => /usr/local/lib/R/site-library/Rcpp/lib/libRcpp.so<br>
| | (0x00007f50d16b2000)<br>
| | libRInside.so => /usr/local/lib/R/site-library/RInside/lib/libRInside.so<br>
| | (0x00007f50d149d000)<br>
| | libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f50d1188000)<br>
| | libm.so.6 => /lib/libm.so.6 (0x00007f50d0f05000)<br>
| | libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f50d0cee000)<br>
| | libc.so.6 => /lib/libc.so.6 (0x00007f50d096a000)<br>
| | libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007f50d067d000)<br>
| | /lib64/ld-linux-x86-64.so.2 (0x00007f50d2ecd000)<br>
| | libR.so => not found<br>
| | libR.so => not found<br>
|<br>
| There is your problem.<br>
|<br>
| | I have R and r-base-dev installed, so I don't understand why this is<br>
| happening.<br>
| | Any help would be much appreciated.<br>
|<br>
| You may have R, but I suspect you do not have R built with shared<br>
| libraries.<br>
| The quickest fix, given that you started on r-sig-debian, may be<br>
|<br>
| $ sudo apt-get install r-base-core<br>
|<br>
| Else you can of course rebuild R from source etc, but you have to tell<br>
| configure to use --enable-R-shlib or else you cannot embed R. And<br>
| RInside wants to embed R, so you can't the latter witout the former.<br>
|<br>
| Hope this helps.<br>
|<br>
| --<br>
| Regards, Dirk<br>
|<br>
|<br>
|<br>
</div></div>| ----------------------------------------------------------------------<br>
| _______________________________________________<br>
| Rcpp-devel mailing list<br>
| <a href="mailto:Rcpp-devel@lists.r-forge.r-project.org" target="_blank">Rcpp-devel@lists.r-forge.r-project.org</a><br>
| <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</a><br>
<font color="#888888"><br>
--<br>
Regards, Dirk<br>
</font></blockquote></div><br>
</div>