R dyn.load gives "undefined symbol" error - r

Question

I am writing a shared library that itself uses the uthash library in C under Ubuntu. I am going to use this shared library in R. For this purpose I have created a package.c file where the main code is stored. In order to use CALLOC function (a part of the uthash) I have included uthash.h in the beginning of package.c. In the body of package.c the CALLOC function is called.
I can build package.c without any problem by running:
R CMD SHLIB package.c
This is the output of the above command in the console:
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c package.c -o package.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o package.so package.o -L/usr/local/lib/R/lib -lR
It produces two files "package.o" and "package.so". I load package.so in R using dyn:
dyn.load("package.so")
But it gives the following error message:
Error in dyn.load("package.so") :
unable to load shared object '/home/me/package/package.so':
/home/me/package/package.so: undefined symbol: memoryMap
I searched for a solution and found this. According to what is written there, here is the the output of "ldd package.so" and "nm -g package.so" commands:
"ldd package.so" output:
$ ldd package.so
linux-vdso.so.1 (0x00007ffd283da000)
libR.so => not found
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fd3643b4000)
/lib64/ld-linux-x86-64.so.2 (0x00007fd3649a8000)
"nm -g package.so" outout:
$ nm -g package.so
0000000000202088 B __bss_start
U calloc##GLIBC_2.2.5
w __cxa_finalize##GLIBC_2.2.5
0000000000202088 D _edata
0000000000202090 B _end
00000000000016d8 T _fini
U free##GLIBC_2.2.5
0000000000001260 T getSteadyStateDistribution_R
w __gmon_start__
00000000000008b0 T _init
U INTEGER
w _ITM_deregisterTMCloneTable
w _ITM_registerTMCloneTable
U malloc##GLIBC_2.2.5
U memcpy##GLIBC_2.14
U memoryMap
U __printf_chk##GLIBC_2.3.4
U REAL
U Rf_error
U Rf_isNull
U Rf_length
0000000000000d70 T simulate
0000000000000e50 T simulate_R
U __stack_chk_fail##GLIBC_2.4
0000000000000aa0 T stateTransition
U unif_rand
I have also read this post but still could not find a solution for my problem.
Edit:
Here is an example to reproduce the error:
#include <R.h>
#include <Rinternals.h>
#include "uthash.h"
typedef struct
{
// a pointer to the allocated memory
void * ptr;
// used by the hash table
UT_hash_handle hh;
} AllocatedMemory;
// map that stores all allocated memory pointers
// to free them on interrupt
extern AllocatedMemory * memoryMap;
static inline void* CALLOC(size_t n, size_t sz)
{
void * ptr = calloc(n, sz);
if (ptr == NULL)
error("Out of memory!");
AllocatedMemory * m = calloc(1, sizeof(AllocatedMemory));
m->ptr = ptr;
HASH_ADD_PTR(memoryMap, ptr, m);
return ptr;
}
SEXP example_R(SEXP vec_R) {
unsigned int n = length(vec_R);
unsigned int * v = CALLOC(n, sizeof(unsigned int));
}
If the above code is stored in "example.c", compile it using:
R CMD SHLIB example.c
It will produce the files example.o and example.so. Then load the so file in R:
dyn.load('example.so')

Answer 1

Here is the minimal change to make your example compile and load i.e. link dynamically:
$ diff -u question.orig.c question.c
--- question.orig.c 2022-12-22 09:41:46.483509755 -0600
+++ question.c 2022-12-22 09:44:45.217420621 -0600
## -12,7 +12,8 ##
// map that stores all allocated memory pointers
// to free them on interrupt
-extern AllocatedMemory * memoryMap;
+AllocatedMemory memoryMapInstance;
+AllocatedMemory *memoryMap = &memoryMapInstance;
static inline void* CALLOC(size_t n, size_t sz)
$
Instead of the reference to an extern instance you fail to supply, but one instance (cheaply) on the stack and define the pointer you need as its address. In a real program you would allocate this on the heap.
Another remaining error is that your example_R is wrong as you claim to take and return a SEXP. But we leave this for another time.
Now with a simple wrapper questions.sh
#!/bin/bash
R CMD SHLIB question.c
R -e 'dyn.load("question.so")'
we get another warning because the return from CALLOC is unused -- but no longer an error on load.
$ ./question.sh
ccache gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O3 -Wall -pipe -pedantic -Wno-ignored-attributes -std=gnu99 -c question.c -o question.o
question.c: In function ‘example_R’:
question.c:34:20: warning: unused variable ‘v’ [-Wunused-variable]
34 | unsigned int * v = CALLOC(n, sizeof(unsigned int));
| ^
question.c:35:1: warning: control reaches end of non-void function [-Wreturn-type]
35 | }
| ^
ccache gcc -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o question.so question.o -L/usr/lib/R/lib -lR
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> dyn.load("question.so")
>
>
$
No error.
(You can ignore the compiler settings, and use of ccache I have locally. The warning is real.)