Best,
David
On Mon, Jul 12, 2010 at 9:24 PM, Dirk Eddelbuettel <[email protected]
<mailto:[email protected]>> wrote:
David,
On 12 July 2010 at 20:50, David Rosengarten wrote:
| 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)
Cool. One down. Good to know.
| 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
You want += here to add your values, not = as that would erase prior
values.
Else use new definitions (eg GSL_CFLAGS) which you later insert into
the CXXFLAGS definition.
| 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
Yes. You effectively everything we need to build with RInside. Not a
good plan :)
| for my program metrop.cpp. The only thing regarding R that I have
in my code
| as of now is #include <RInside.h>.
But that implies Rcpp as well as R so you need headers from three
places,
libs from three places, rpath entries ... all before you even
mentioned GSL.
Dirk
| Best,
| David
|
| On Mon, Jul 12, 2010 at 5:38 PM, Dirk Eddelbuettel <[email protected]
<mailto:[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] <mailto:[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]
<mailto:[email protected]>
| |
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
|
| --
| Regards, Dirk
|
|
--
Regards, Dirk
_______________________________________________
Rcpp-devel mailing list
[email protected]
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
