Error compiling Rglpk on Windows - c

Question

I need to use the R package Rglpk in a project and need to modify the package - in particular, I need to add a time limit control parameter option to the interface (it is a option in GLPK v4.5.2 itself, but Rglpk 0.5-2 does not support this parameter). This will allow R to call GLPK and limit the search time to be user specified (i.e., search time <= t).
I have modified Rglpk code and have successfully compiled the package on Mac OS X v10.9.2 and verified that it worked as expected. My project needs to run on Windows and I have not been able to compile the modified Rglpk package, or for that matter the unmodified package (Rglpk 0.5-2), on Windows. I have tried uploading the original package to Win Builder (http://win-builder.r-project.org/), but I have received the same errors.
The following is a summary of what I have done on Windows 7 (my machine):
(1) Download the Rglpk 0.5-2 package source from http://cran.r-project.org/web/packages/Rglpk/index.html
(2) Unzip the file to a directory. All the code is in a directory called Rglpk.
(3) Start RStudio v0.98.490. I have devtools v1.4.1 installed, Rtools v3.1 installed, and R v3.0.2
(4) Open a new project and select the Rglpk directory mentioned in (2).
(5) Under the 'Build' menu, select 'Build and Reload'. The result of this is that the package compiles and is loaded:
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (Rglpk)
(6) Under the 'Build' menu, select 'Check Package'. The result is that the installation fails. The log file is shown below.
I have tried to compile another package that has C code and have not been able to compile it either. The package I tried to compile is devtools v1.5 The error that came back in that case is 'LoadLibrary failure: %1 is not a valid Win32 application.'
Does anyone have any experience compiling R packages on Windows that include C code? I have been able to compile packages that involve only R code, but it seems C code is troublesome.
Any help would be appreciated.
Log File
* using R version 3.0.2 (2013-09-25)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'Rglpk/DESCRIPTION' ... OK
* this is package 'Rglpk' version '0.5-2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
src/GLPK/alloc.o src/GLPK/amd/amd_1.o src/GLPK/amd/amd_2.o
src/GLPK/amd/amd_aat.o src/GLPK/amd/amd_control.o
src/GLPK/amd/amd_defaults.o src/GLPK/amd/amd_dump.o
src/GLPK/amd/amd_info.o src/GLPK/amd/amd_order.o
src/GLPK/amd/amd_post_tree.o src/GLPK/amd/amd_postorder.o
src/GLPK/amd/amd_preprocess.o src/GLPK/amd/amd_valid.o
src/GLPK/bignum.o src/GLPK/cfg.o src/GLPK/cfg1.o
src/GLPK/colamd/colamd.o src/GLPK/dmp.o src/GLPK/env.o
src/GLPK/error.o src/GLPK/ffalg.o src/GLPK/fhv.o src/GLPK/fhvint.o
src/GLPK/glpapi01.o src/GLPK/glpapi02.o src/GLPK/glpapi03.o
src/GLPK/glpapi04.o src/GLPK/glpapi05.o src/GLPK/glpapi06.o
src/GLPK/glpapi07.o src/GLPK/glpapi08.o src/GLPK/glpapi09.o
src/GLPK/glpapi10.o src/GLPK/glpapi11.o src/GLPK/glpapi12.o
..... (more lines are here, I have removed them for brevity)
src/GLPK/triang.o src/GLPK/wclique.o src/GLPK/wclique1.o
src/GLPK/zlib/adler32.o src/GLPK/zlib/compress.o
src/GLPK/zlib/crc32.o src/GLPK/zlib/deflate.o src/GLPK/zlib/gzclose.o
src/GLPK/zlib/gzlib.o src/GLPK/zlib/gzread.o src/GLPK/zlib/gzwrite.o
src/GLPK/zlib/inffast.o src/GLPK/zlib/inflate.o
src/GLPK/zlib/inftrees.o src/GLPK/zlib/trees.o
src/GLPK/zlib/uncompr.o src/GLPK/zlib/zio.o src/GLPK/zlib/zutil.o
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rglpk' can be installed ... ERROR
Installation failed.
The contents of the 00install.out file are:
* installing *source* package 'Rglpk' ...
** libs
*** arch - i386
gcc -m32 -I"C:/PROGRA~1/R/R-30~1.2/include" -DNDEBUG -IGLPK -IGLPK/amd -IGLPK/colamd -IGLPK/minisat -IGLPK/proxy -IGLPK/zlib -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rglpk_initialize.c -o Rglpk_initialize.o
gcc -m32 -I"C:/PROGRA~1/R/R-30~1.2/include" -DNDEBUG -IGLPK -IGLPK/amd -IGLPK/colamd -IGLPK/minisat -IGLPK/proxy -IGLPK/zlib -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rglpk_read_file.c -o Rglpk_read_file.o
Rglpk_read_file.c: In function 'Rglpk_read_file':
Rglpk_read_file.c:84:6: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
Rglpk_read_file.c: In function 'Rglpk_retrieve_MP_from_file':
Rglpk_read_file.c:192:6: warning: 'status' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"C:/PROGRA~1/R/R-30~1.2/include" -DNDEBUG -IGLPK -IGLPK/amd -IGLPK/colamd -IGLPK/minisat -IGLPK/proxy -IGLPK/zlib -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Rglpk_solve.c -o Rglpk_solve.o
Rglpk_solve.c: In function 'R_glp_solve':
Rglpk_solve.c:25:10: warning: variable 'kl' set but not used [-Wunused-but-set-variable]
gcc -m32 -shared -s -static-libgcc -o Rglpk.dll tmp.def Rglpk_initialize.o Rglpk_read_file.o Rglpk_solve.o GLPK/libglpk.a -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-30~1.2/bin/i386 -lR
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLPK/libglpk.a(glpmpl04.o)' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLPK/libglpk.a(error.o)' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLPK/libglpk.a(glpmpl03.o)' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLPK/libglpk.a(alloc.o)' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: i386:x86-64 architecture of input file `GLPK/libglpk.a(glpenv07.o)' is incompatible with i386 output
c:/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe:
.....
Error: 64-bit reloc in dll
Error: 64-bit reloc in dll
Error: 64-bit reloc in dll
.....
Rglpk_initialize.o:Rglpk_initialize.c:(.text+0x33): undefined reference to `glp_term_hook'
Rglpk_initialize.o:Rglpk_initialize.c:(.text+0x44): undefined reference to `glp_version'
Rglpk_read_file.o:Rglpk_read_file.c:(.text+0x10): undefined reference to `glp_delete_prob'
Rglpk_read_file.o:Rglpk_read_file.c:(.text+0x4f): undefined reference to `glp_term_out'
Rglpk_read_file.o:Rglpk_read_file.c:(.text+0x60): undefined reference to `glp_delete_prob'
Rglpk_read_file.o:Rglpk_read_file.c:(.text+0x65): undefined reference to `glp_create_prob'
.....
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x4326): undefined reference to `strcpy'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x4d39): undefined reference to `strcpy'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x4dc5): undefined reference to `strcpy'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x4e05): undefined reference to `floor'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x4e16): undefined reference to `floor'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x502e): undefined reference to `floor'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x50e2): undefined reference to `sprintf'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x5111): undefined reference to `sprintf'
.....
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x990): undefined reference to `exp'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0x9e0): undefined reference to `log'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0xa30): undefined reference to `log10'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0xaee): undefined reference to `sin'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0xb4e): undefined reference to `cos'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0xb65): undefined reference to `atan'
GLPK/libglpk.a(glpmpl03.o):glpmpl03.c:(.text+0xb79): undefined reference to `atan2'
.....
GLPK/libglpk.a(deflate.o):deflate.c:(.text+0x2ec0): undefined reference to `memcpy'
GLPK/libglpk.a(deflate.o):deflate.c:(.text+0x2ed5): undefined reference to `memcpy'
GLPK/libglpk.a(deflate.o):deflate.c:(.text+0x2ee7): undefined reference to `memcpy'
GLPK/libglpk.a(zutil.o):zutil.c:(.text+0x47): undefined reference to `malloc'
GLPK/libglpk.a(zutil.o):zutil.c:(.text+0x54): undefined reference to `free'
collect2: ld returned 1 exit status
ERROR: compilation failed for package 'Rglpk'

Answer 1

It looks like a couple things are going wrong:
Object files are getting pre-compiled, but not cleaned out.
Because these object files are being pre-compiled, and it looks like they were compiled for 64-bit architecture, when you try to use these in a 32-bit build, the installation process barfs.
The fix here is going to be deleting all of those *.o files (they need to be compiled as part of the R CMD build step, I imagine), and the resulting tarball can then be R CMD checked.
You should consider installing a more up-to-date version of RStudio and devtools, and ensure you use devtools to handle the build process -- it might be able to help you out here.