I am trying to call a C code double_metaphone.c from R in windows. I am familiar with R , but have not tried C yet.
I have compiled the code and created a shared library as follows in windows using Cygwin gcc including the header file double_metaphone.h
gcc -c double_metaphone.c
gcc -shared -o double_metaphone.dll double_metaphone.o
I have used dyn.load to load the dll file as follows
dyn.load("C:/R/double_metaphone.dll")
getLoadedDLLs() lists double_metaphone.dll, however
is.loaded(double_metaphone.dll)
gives the error
Error in is.loaded(double_metaphone.dll) :
object 'double_metaphone.dll' not found
When I try to use .C() or .Call(), I get
Error in .C("double_metaphone") :
C symbol name "double_metaphone" not in load table
I understand this is a problem with C++ code as in Link1, Link, but why can't I access the shared library for calling C code from R? Where am I going wrong?
As per my understanding "is.loaded" checks for the loaded symbols. As per your header, you can try:
is.loaded("DoubleMetaphone")
To call the method. try:
.C("DoubleMetaphone", <your>, <arguments>)
You need compile and link against R for the shared object to be loadable. e.g.
$ gcc -I/YOUR_R_HOME_DIR/include -DNDEBUG -fpic -c double_metaphone.c -o double_metaphone.o
$ gcc -shared -o double_metaphone.dll double_metaphone.o -L/YOUR_R_HOME_DIR/lib -lR
Or simply
$ R CMD SHLIB double_metaphone.c
As Dirk said, R-exts gives you more details.
And you want to consider Rcpp for writing compiled code in R, which benefits you further down the road.
Related
Good Day Everyone,
N.B - This problem has been solved - I have provided my own solution in the answer section however the solution provided by Jonathan is much shorter. Nevertheless, this was the following question I originally posted:
I am basically trying to compile a serial library (for UART communication) on Linux however I am not really sure how to correctly compile (I have mentioned what I have done so far below), any suggestions would be highly valuable. I am using the serialib library - which is composed of 2 main files (serialib.h and serialib.cpp) , you may directly view the source code of these files here (scroll all the way to the bottom and view the files in new tabs): http://serialib.free.fr/html/classserialib.html
I transferred these files (serialib.h and serialib.cpp) to my BeagleBone Black micro-controller which is running Debian (Wheezy) , g++/gcc (Debian 4.6.3-14) 4.6.3. I wrote my own program (uart.cpp is my file name) to access the functions provided by this library, this is what I wrote:
#include <iostream>
#include "serialib.h"
#ifdef __linux__
#define DEVICE_PORT "/dev/ttyO1"
#endif
int main()
{
serialib LS;
return 0;
}
So as you can see I am trying to access the 'seriallib' class. serialib.h, serialib.cpp and uart.cpp are all in the home directory. I also manually added the iostream library in serialib.cpp as I did not see it being declared in the original source code.
Now I am really unsure of how to compile such external libraries but so far I tried the following steps:
g++ -c -Wall -Werror -fPIC serialib.c to convert to PIC which gives the following error:
distcc[3142] (dcc_parse_hosts) Warning: /home/debian/.distcc/zeroconf/hosts contained no hosts; can't distribute work
distcc[3142] (dcc_zeroconf_add_hosts) CRITICAL! failed to parse host file.
distcc[3142] (dcc_build_somewhere) Warning: failed to distribute, running locally instead
g++ serialib.cpp -L /home/debian/serialib.h which gives the following error:
/usr/lib/gcc/arm-linux-gnueabihf/4.6/../../../arm-linux-gnueabihf/crt1.o: In function _start':
(.text+0x30): undefined reference tomain'
collect2: ld returned 1 exit status
distcc[3210] ERROR: compile serialib.cpp on localhost failed
As of now I am still finding out how to compile this and if I manage to work this out then I'll post my solution here too. Once again any suggestion will be highly valuable. Thank you all :) .
g++ -c -Wall -Werror -fPIC serialib.c to convert to PIC which gives the following error:
The "error" is not an error, it's a warning, telling you that your distcc setup is broken, but that it compiled locally.
That command doesn't "convert to PIC", it compiles the file serialib.c and produces a compiled object file, serialib.o
g++ serialib.cpp -L /home/debian/serialib.h
This is just nonsense. It tries to build a program from serialib.cpp and use the directory /home/debian/serialib.h (which isn't a directory!) to find libraries.
You don't need to "compile a library" you can just compile both the source files and link them together into a program. Either:
g++ -c serialib.cpp
g++ -c uart.cpp
g++ serialib.o uart.o -o uart
Or all in one command:
g++ serialib.cpp uart.cpp -o uart
You should read An Introduction to GCC to understand the commands, not just enter bogus commands without understanding them.
I have found a solution to this problem, hope this helps for all the future readers with similar problems. I have my own source code uart.cpp (Given in the question) which I want to compile, the external library is serialib that contains two main files (serialib.h and serialib.cpp), you will want to replace the following commands with respect to the files you have
Step 1: Compiling with position independent code
g++ -c -Wall -Werror -fpic serialib.cpp
Step 2: Creating a shared library
g++ -shared -o libserialib.so serialib.o , here the library is libserialib.so.
Step 3: Linking your source code with library
g++ -L /home/debian -lserialib uart.cpp -o uart
g++ -L /home/debian -Wall -o test uart.cpp -lserialib
You may save the library at a different path and you may have a different name of course. Suppose you have a library called libabc.so at the directory /home/user/myDir then the commands will be like:
g++ -L /home/user/myDir -labc your_code.cpp -o your_code
g++ -L /home/user/myDir -Wall -o test your_code.cpp -labc
test is out own program, lserialib is actually looking for libserialib.so and not serialib.o as gcc/g++ assumes all libraries start with lib and end with .so or .a and you can see the same goes for labc as it will look for libabc.so thus it is important to make sure your library name begins with lib and ends with .so or .a
Step 4: Making library available at run time
Here we provide the path where the library is actually stored, I saved it in the directory /home/debian which is why my command looks like:
export LD_LIBRARY_PATH=/home/debian:$LD_LIBRARY_PATH
if your library is saved at /path/to/file then the command will look like:
export LD_LIBRARY_PATH=/path/to/file:$LD_LIBRARY_PATH
This is to help the loader find the shared library and to view this path: echo $LD_LIBRARY_PATH and to unset this: unset LD_LIBRARY_PATH
To execute the program type either ./test or ./uart and in case of any modification to the main source code (uart.cpp in this case) , simply repeat step 3. I found the following link very useful: http://www.cprogramming.com/tutorial/shared-libraries-linux-gcc.html . Thank you to all of you who took time to read this question and especially those who gave me suggestions. If anyone has more or better solutions, feel free to post them here to assist future readers :).
I originally wanted to compile SQLCipher statically since it seems like it is easier to link up, but I have been unsuccessful at that. The only place I can find that discusses compiling SQLCipher on OS X is this blog post, but even he was not able to get the static compiling to work.
I was able to get the dynamic compiling working for the SQLCipher and I am able to use the sqlcipher command line program as mentioned in the blog, but now I want to use sqlcipher in a compiled C++ program. I have never dealt directly with dynamic compiling in the command line so I am a bit lost.
It looks like it produces a libtool file libsqlcipher.la so I am wondering how I should import it in C++ #include "libsqlcipher.h"? Looking around at tutorials for libtool they mostly mention how to compile it but I have not found any simple examples of how to link it.
I attempted something like this based on what I saw but I got a couple of errors:
libtool g++ -o test EncryptDatabases.cpp sqlcipher/libsqlcipher.la
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool: can't open file: g++ (No such file or directory)
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool: file: EncryptDatabases.cpp is not an object file (not allowed in a library)
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/libtool: file: sqlcipher/libsqlcipher.la is not an object file (not allowed in a library)
Not an answer yes, but too long for a comment.
As far as I remember first libtool should be explicitly told to compile source file into a "library object":
libtool --mode=compile g++ -c EncryptDatabases.cpp -o EncryptDatabases.lo
then it should link the binary:
libtool --mode=link g++ -o test EncryptDatabases.lo sqlcipher/libsqlcipher.la
See the docs
I have to build a small program to run on a set-top box, and for that I use a specific build toolchain: toolchain-final-mipsisa32r2el-timesys-linux-gnu
The build is composed of 2 parts: one lib static .a file and an executable that use the library.
The lib is correctly build with the following option:
mipsisa32r2el-timesys-linux-gnu-gcc -c --param max-inline-insns-single=2400
-o ../../../build/LinuxHost_STB_release/_outLib/STB.o -O2 -fno-strict-aliasing
-Winline -Wall -I../../../Modules -I../../../Source
-I/opt/toolchains/toolchain-final-mipsisa32r2el-timesys-linux-gnu/include
-I -fno-rtti ../../../Source/STBLib/STB.cpp
if I run nm on the libSTB.a, I saw the function define in STB.cpp as:
0000000000000124 T STB_Create
0000000000000460 T STB_Destroy
To compile and link the executable, I use the following command line:
mipsisa32r2el-timesys-linux-gnu-c++ -o ../../../build/LinuxHost_STB_release/STBExample
--sysroot=/opt/toolchains/toolchain-final-mipsisa32r2el-timesys-linux-gnu/
-I/opt/toolchains/toolchain-final-mipsisa32r2el-timesys-linux-gnu/include
-L../../../build/LinuxHost_STB_release
-lSTB ../../../Source/STBLib/STBExample.c
But I get the following linker error:
STBExample.c:(.text+0x488): undefined reference to `STB_Create'
Any idea of where I made a mistake or on how to investigate ?
As explained by #H2CO3 and #Joe Z, the problem was in the parameter ordering.
Additional static lib set with -lmust be place AFTER the .c file. As in the following example, a switch of the 2 last arguments solved the issue.
mipsisa32r2el-timesys-linux-gnu-c++ -o ../../../build/LinuxHost_STB_release/STBExample
--sysroot=/opt/toolchains/toolchain-final-mipsisa32r2el-timesys-linux-gnu/
-I/opt/toolchains/toolchain-final-mipsisa32r2el-timesys-linux-gnu/include
-L../../../build/LinuxHost_STB_release
../../../Source/STBLib/STBExample.c -lSTB
I am trying to compile a project that depends on the Xerces XML Parser. The project compiles for Windows without any difficulty, but I'm having some trouble compiling it with g++ in Cygwin.
In order to use Xerces, I am trying to compile my code against the static library libxerces-c.a. But when I do so, I get errors that look like this:
/tmp/cc2QGvMh.o:test.cpp:(.text+0x3a): undefined reference to `xercesc_2_8::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)'
I've inspected the static library using ar, and confirmed that it contains the DOMImplementationRegistry.o file that defines the function that I am calling.
ar -t libxerces-c.a
...
DOMImplementationImpl.o
DOMImplementationRegistry.o
DOMLocatorImpl.o
...
I've also extracted the object files from the library, and used 'nm' to make sure that the function I am calling actually exists:
ar -x libxerces-c.a
nm --demangle DOMImplementationRegistry.o
...
00000080 T xercesc_2_8::getDOMImplSrcVectorMutex()
00000300 T xercesc_2_8::DOMImplementationRegistry::getDOMImplementation(unsigned short const*)
000002a0 T xercesc_2_8::DOMImplementationRegistry::addSource(xercesc_2_8::DOMImplementationSource*)
...
Since I can compile everything for Windows but not with g++, I thought that the error could be in the linker order (similar to the problem described in this question). However, even after changing the linker order, I am still getting the same compiler error. I have tried both
g++ -o test.exe test.cpp -Llib -lxerces-c
and
g++ -o test.exe test.cpp lib/libxerces-c.a
Any ideas?
Your project uses method from xercesc_2_6 namespace as pointed by compiler error message but your library offers xercesc_2_8 version. Problem is probably caused by mismatch between headers you use and library object file.
You didn't say the source of the archive. If it isn't compiled with cygwin, it could be a name mangling problem. Compiling the library from source might well fix this.
It could also be that the archive is built incorrectly so that it has internal resolution problems. Try giving the library name twice.
g++ -o test.exe test.cpp lib/libxerces-c.a lib/libxerces-c.a
If this works, the archive is broken and you should look for or build a new one.
Try the linker option --enable-stdcall-fixup (see 'man ld'). It will care for name mangling and calling conventions:
g++ -o test.exe test.o -Wl,--enable-stdcall-fixup -Llib -lxerces-c
EDIT: I suppose I should clarify, in case it matters. I am on a AIX Unix box, so I am using VAC compilers - no gnu compilers.
End edit
I am pretty rusty in C/C++, so forgive me if this is a simple question.
I would like to take common functions out of a few of my C programs and put them in shared libraries or shared objects. If I was doing this in perl I would put my subs in a perl module and use that module when needed.
For the sake of an example, let's say I have this function:
int giveInteger()
{
return 1034;
}
Obviously this is not a real world example, but if I wanted to share that function, how would I proceed?
I'm pretty sure I have 2 options:
Put my shared function in a file, and have it compile with my main program at compile time. If I ever make changes to my shared function, I would have to recompile my main program.
Put my shared function in a file, and compile it as a shared library (if I have my terms correct), and have my main program link to that shared library. Any changes I make to my shared library (after compiling it) would be integrated into my main program at runtime without re-compiling my main program.
Am I correct on that thinking?
If so, how can I complish either/both of those methods? I've searched a lot and I seem to find information how how I could have my own program link to someone else's shared library, but not how to create my own shared functions and compile them in a way I can use them in my own program.
Thanks so much!
Brian
EDIT: Conclusion
Thanks everyone for your help! I thought I would add to this post what is working for me (for dynamic shared libraries on AIX) so that others can benefit:
I compile my shared functions:
xlc -c sharedFunctions.c -o sharedFunctions.o
Then make it a shared object:
xlc -qmkshrobj -qexpfile=exportlist sharedFunctions.o
xlc -G -o libsharedFunctions.so sharedFunctions.o -bE:exportlist
Then link it another program:
xlc -brtl -o mainProgram mainProgram.c -L. -lsharedFunctions
And another comment helped me find this link, which also helped:
http://publib.boulder.ibm.com/infocenter/comphelp/v7v91/topic/com.ibm.vacpp7a.doc/proguide/ref/compile_library.htm
Thanks again to all who helped me out!
Yeah you are correct. The first is called a static library, while the second is called a shared library, because the code is not bound to the executable at compile time, but everytime again when your program is loaded.
Static library
Compile your library's code as follows:
gcc -c *.c
The -c tells the program not to link the object file, but just leaves you with object files for each .c file that was compiled. Now, archive them into one static library:
ar rcs libmystuff.a *.o
man ar will tell you what the rcs options mean. Now, libmystuff.a is a archive file (you can open it with some zip-file viewers) which contain those object files, together with an index of symbols for each object file. You can link it to your program:
gcc *.c libmystuff.a -o myprogram
Now, your program is ready. Note that the order of where the static libraries appear in the command matter. See my Link order answer.
Shared library
For a shared library, you will create your library with
gcc -shared -o libmystuff.so *.c
That's all it takes, libmystuff.so is now a shared object file. If you want to link a program to it, you have to put it into a directory that is listed in the /etc/ld.so.conf file, or that is given by the -L switch to GCC, or listed in the LD_LIBRARY_PATH variable. When linking, you cut the lib prefix and .so suffix from the library name you tell gcc.
gcc -L. -lmystuff *.c -o myprogram
Internally, gcc will just pass your arguments to the GNU linker. You can see what arguments it pass using the -### option: Gcc will print the exact arguments given to each sub process.
For details about the linking process (how some stuff is done internally), view my Linux GCC linker answer.
You've got a third option. In general, your C++ compiler should be able to link C routines. The necessary options may vary from compiler to compiler, so R your fine M, but basically, you should be able to compile with g++ as here:
$ g++ -o myapp myapp.cpp myfunc.c giveint.c
... or compile separately
$ gcc -c myfunc.c
$ gcc -c giveint.c
$ g++ -c myapp.cpp
$ g++ -o myapp myapp.o myfunc.o
You also need to include your declaration of the functions; you do that in C++ as
extern "C" {
int myfunc(int,int);
int giveInterger(void);
}
You need to distinguish between recompiling and relinking.
If you put giveInteger() into a separate (archive) library, and then modify it later, you'll (obviously) need to recompile the source file in which it is defined, and relink all programs that use it; but you will not need to recompile such programs [1].
For a shared library, you'll need to recompile and relink the library; but you will not have to relink or recompile any of the programs which use it.
Building C++ shared libraries on AIX used to be complicated; you needed to use makeC++SharedLib shell script. But with VAC 5.0 and 6.0 it became quite easy. I believe all you need to do is [2]:
xlC -G -o shr.o giveInteger.cc
xlC -o myapp main.cc shr.o
[1] If you write correct Makefile (which is recommended practice), all of this will happen automatically when you type make.
[2] There is a certain feature of AIX which may complicate matters: by default shared libraries are loaded into memory, and "stick" there until subsequent reboot. So you may rebuild the shr.o, rerun the program, and observe "old" version of the library being executed. To prevent this, a common practice is to make shr.o world-unreadable:
chmod 0750 shr.o