I have fink installed to get the source code from the cvs, and I have installer R from source. It builds and works correctly.
Now, the python modules that I want (either RSPython or Rpy) need R to be installed with a shared library [ libR.so ]
So, I untared/gzipped the source in th e/sw/src directory, entered the R source directory, and ran:
make distclean ./configure --enable-R-shlib make
I have the CFLAGS and and LDFLAGS set to /sw/include and /sw/lib, respectively.
The configuration goes Ok, and make works until i get this error:
-L/sw/lib/gcc/powerpc-apple-darwin6.8/3.4 -L/sw/lib/gcc/powerpc-apple-darwin6.8/3.4/../../.. -lfrtbegin -lg2c -lSystem -lpcre -lbz2 -lz -lreadline -ldl -lncurses -lm
ld: warning multiple definitions of symbol _BC
/sw/lib/libreadline.dylib(terminal.so) definition of _BC
/sw/lib/libncurses.dylib(lib_termcap.lo) definition of _BC
ld: warning multiple definitions of symbol _UP
/sw/lib/libreadline.dylib(terminal.so) definition of _UP
/sw/lib/libncurses.dylib(lib_termcap.lo) definition of _UP
ld: warning multiple definitions of symbol _PC
/sw/lib/libreadline.dylib(terminal.so) definition of _PC
/sw/lib/libncurses.dylib(lib_tputs.lo) definition of _PC
ld: Undefined symbols:
restFP
saveFP
make[3]: *** [R.bin] Error 1
make[2]: *** [R] Error 2
make[1]: *** [R] Error 1
make: *** [R] Error 1
I get the same error if I rerun the same series of commands, but without trying to configure the compile to produce a dynamic library.
So, it is great the fink can download and compile the source, but I don't understand why i can't compile it myself. Is there some place the Makefile for
a fink compile are left, so I can compare the two?
Thanks,
JP
On Monday, Oct 20, 2003, at 14:03 Europe/Madrid, Alexander K. Hansen wrote:
Try "dpkg -S util.h". This will check everything that Fink has installed for util.h, and you'll be able to see if R installed it somewhere.
Now that I think about it, I believe there's an application that comes with the Developer Tools that will let you change the visibility of folders--it's a command-line app called SetFile.
On Monday, October 20, 2003, at 05:59 AM, JP Glutting wrote:
Ok, it is there (a pain that I can search it using the stupid finder). I tried setting CFLAGS -L/usr/include and LDFLAGS -L/usr/lib , but I get the same error.
The compiling system can't seem to find the util.h header file. The only thinking that I can think is that it is a local R file that is included with the source
code of R.
On Friday, Oct 17, 2003, at 23:18 Europe/Madrid, Alexander K. Hansen wrote:
No.
If you don't have /usr then there's no way your compiler would work at all, and Fink would definitely have bombed.
If you used the Finder, it wouldn't show up--that directory is hidden. Try using
ls /usr/include
from a terminal.
On Friday, October 17, 2003, at 04:40 PM, JP Glutting wrote:
Hmm, this is odd. First, I think you meant /sw/include instead of /usr/include, correct? I don't seem to have a usr directory >>> anywhere.
I don't seem to have a util.h file in the /sw/include directory. i do have a util.h file in the /System/Library/Perl/darwin/CORE/ but that does not seem like that is what I am looking for...
The R installation does have it's own include directory, (/sw/lib/R/include/R_ext/ contains a file Utils.h - capitalized - but this also seems an unlikely candidate, since it says it is checking for the gcc default output, not something related to R.
Do you know how the header files were installed in your /sw/include directory? I am going to try installing glib2 and glib2-dev (which brings in glib2-shlibs)
Nope, that didn't work. I am really just mucking around here - I am not even sure what sort of functionality util.h is going to provide to the gcc.
Cheers,
JP
On Friday, Oct 17, 2003, at 04:08 Europe/Madrid, Alexander Hansen wrote:
That looks really odd to me, because on my system pthread.h and util.h are both in /usr/include . Check and see if you have /usr/include/util.h .
It also could be looking for a util.h that was installed via R. You may want to set your environment up as per
http://fink.sourceforge.net/faq/usage-general.php#compile-myself
On Thursday, October 16, 2003, at 10:18 AM, JP Glutting wrote:
Hi Again,
I am trying to compile the R/SPlus extensions for the R package that is installed with fink. I have downloaded the package, and as the instructions indicate, run this command:
R INSTALL --clean RSPython (RSPython is adirectory).
I get this error:
* Installing *source* package 'RSPython' ...
checking for python... /sw/bin/python
Using threads
checking for gcc... gcc
checking for C compiler default output... configure: error: C compiler cannot create executables
check `config.log' for details.
ERROR: configuration failed for package 'RSPython'
when checking the config.log file, I see this:
configure:1666: $? = 0
configure:1668: gcc -v </dev/null >&5
Reading specs from /usr/libexec/gcc/darwin/ppc/3.1/specs
Thread model: posix
Apple Computer, Inc. GCC version 1175, based on gcc version 3.1 20020420 (prerelease)
configure:1671: $? = 0
configure:1673: gcc -V </dev/null >&5
gcc: argument to `-V' is missing
configure:1676: $? = 1
configure:1696: checking for C compiler default output
configure:1699: gcc conftest.c -lpthread -lutil >&5
ld: can't locate file for: -lutil
configure:1702: $? = 1
configure: failed program was:
#line 1679 "configure"
#include "confdefs.h"
int main () {
; return 0; } configure:1729: error: C compiler cannot create executables check `config.log' for details.
So it looks like the gcc can't find the "util" library. Has anyone had this problem? Does anyone know what the util library does, where it is, and if there are OS X libraries that need to be included in the path to compile correctly (or R libraries that need to be included).
This is the first real thing I have tried to compile on the Mac. I did compile "Hello World" just to make sure that the compiler was installed and working.
Thanks for any help.
Cheers,
JP
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