ms609 ms609 - 2 months ago 17
C Question

Compiling C code that uses R libraries in Netbeans

I've been having trouble debugging some C code that I'm writing as part of an R package. The code compiles and executes when I use

R CMD SHLIB
from the Windows console (i.e. cmd.exe):

>R CMD SHLIB MaximumAgreementForest.c
gcc -m64 -I"C:/PROGRA~1/R/R-32~1.4RE/include" -DNDEBUG -I"d:/RCompile/r-compiling/local/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c MaximumAgreementForest.c -o MaximumAgreementForest.o
gcc -m64 -shared -s -static-libgcc -o MaximumAgreementForest.dll tmp.def MaximumAgreementForest.o -Ld:/RCompile/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LC:/PROGRA~1/R/R-32~1.4RE/bin/x64 -lR


The script also built correctly in Netbeans until I started using the functions
R_alloc
and
C_alloc
from the R libraries. Now it doesn't seem to be able to find the definitions of a number of R-specific functions. When I attempt to build the project in Netbeans the console lists the following:

cd 'C:\Work\Fun\implied_weight\MAF'
C:\MinGW\msys\1.0\bin\make.exe -f Makefile CONF=Debug
"/C/MinGW/msys/1.0/bin/make.exe" -f nbproject/Makefile-Debug.mk QMAKE= SUBPROJECTS= .build-conf
make.exe[1]: Entering directory `/c/Work/Fun/implied_weight/MAF'
"/C/MinGW/msys/1.0/bin/make.exe" -f nbproject/Makefile-Debug.mk dist/Debug/MinGW-Windows/libMAF.dll
make.exe[2]: Entering directory `/c/Work/Fun/implied_weight/MAF'
mkdir -p build/Debug/MinGW-Windows/_ext/5c0
rm -f "build/Debug/MinGW-Windows/_ext/5c0/MaximumAgreementForest.o.d"
gcc -DDEBUG -O2 -Wall -mtune=core2 -c -g -Wall -I/C/Program\ Files/R/R-3.2.4revised/include -MMD -MP -MF "build/Debug/MinGW-Windows/_ext/5c0/MaximumAgreementForest.o.d" -o build/Debug/MinGW-Windows/_ext/5c0/MaximumAgreementForest.o ../MaximumAgreementForest.c
mkdir -p dist/Debug/MinGW-Windows
gcc -DDEBUG -O2 -Wall -mtune=core2 -o dist/Debug/MinGW-Windows/libMAF.dll build/Debug/MinGW-Windows/_ext/5c0/MaximumAgreementForest.o -L/C/Program\ Files/R -L/C/Program\ Files/R/R-3.2.4revised/library -shared
build/Debug/MinGW-Windows/_ext/5c0/MaximumAgreementForest.o: In function `forest_new':
C:\Work\Fun\implied_weight\MAF/../MaximumAgreementForest.c:37: undefined reference to `R_alloc'
build/Debug/MinGW-Windows/_ext/5c0/MaximumAgreementForest.o: In function `forest_plant':
C:\Work\Fun\implied_weight\MAF/../MaximumAgreementForest.c:55: undefined reference to `S_alloc'
[...]
C:\Work\Fun\implied_weight\MAF/../MaximumAgreementForest.c:515: undefined reference to `R_chk_free'
collect2.exe: error: ld returned 1 exit status


My script, a single .c file, contains the lines

#define USE_RINTERNALS
#include <R.h> // which itself #includes R_ext/Memory, R_ext Printf
#include <R_ext/Print.h>
#include <R_ext/Memory.h>
#include <Rinternals.h>


Figuring that Netbeans is failing to point to the relevant libraries, I have tried adding and removing
C:/Program Files/R/R-3.2.4revised/include
and
C:/Program Files/R/R-3.2.4revised/bin/x64
at File→Project Properties→General→Source folders, to no effect.

Under File→Project Properties→Build→C compiler, I have included
C:/Program Files/R/R-3.2.4revised/include
.

When I add
C:/Program Files/R/R-3.2.4revised/bin/x64/R.dll
to Build→Linker→Libraries→Libraries, via the Add Library... option, I receive the error
c:/mingw/bin/../lib/gcc/mingw32/4.8.1/../../../../mingw32/bin/ld.exe: cannot find -lR
, and the linker exits without (before?) complaining about the undefined references.

When I subsequently add "C:/Program Files/R/R-3.2.4revised/bin/x64/", which is already in by System PATH, to Build→Linker→Additional Library Directories, the compiler fails with the message
C:/Program Files/R/R-3.2.4revised/bin/x64/R.dll: file not recognized: File format not recognized


What am I missing... how can I point Netbeans to the relevant R libraries?

Answer

The File format not recognized error is encountered when a 32-bit compiler tries to load to a 64-bit .dll (or vice-versa). Changing the path C:/Program Files/R/R-3.2.4revised/bin/x64/R.dll to C:/Program Files/R/R-3.2.4revised/bin/i386/R.dll resolved the problem.

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