Re: [R] compiling gap on mac os x

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri 24 Jun 2005 - 05:07:59 EST

Isn't this the age-old story of the MacOS X Fortran compiler not fully supporting compilation for dynamic libraries? Looks like the same sort of problem it has with LAPACK code. You could try rewriting the code to avoid DATA statements.

Asking MacOS-specific questions on the r-sig-mac is a better idea than using a general list.

On Thu, 23 Jun 2005, Kenny Ye wrote:

> Hi, I am having trouble compiling package gap
> http://www.hgmp.mrc.ac.uk/~jzhao/r-progs.htm on Tiger. I have installed
> XcodeTools 2.1. The binary version of gap currently available on CRAN
> has some bug and is fixed in the latest version.
>
> The message I get from R is below. Any help is greatly appreciated.
>
> best regards,
>
> Kenny Ye
>
> tar: Read 1536 bytes from -
> * Installing *source* package 'gap' ...
> ** libs
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c 2k.c -o 2k.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c 2ld.c -o 2ld.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c cline.c -o cline.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c gc.c -o gc.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c gcontrol.c -o gcontrol.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c gif.c -o gif.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c hap.c -o hap.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c hwe.hardy.c -o hwe.hardy.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c kin.morgan.c -o kin.morgan.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c makeped.c -o makeped.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c mia.c -o mia.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c muvar.c -o muvar.o
> g77 -fno-common -g -O2 -c pfc.f -o pfc.o
> g77 -fno-common -g -O2 -c pfc.sim.f -o pfc.sim.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c pgc.c -o pgc.o
> gcc-3.3 -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Resources/include
> -I/usr/local/include -fno-common -g -O2 -c whscore.c -o whscore.o
> gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
> gap.so 2k.o 2ld.o cline.o gc.o gcontrol.o gif.o hap.o hwe.hardy.o
> kin.morgan.o makeped.o mia.o muvar.o pfc.o pfc.sim.o pgc.o whscore.o
> -L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -lSystem
> -framework R
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/gap'
> npackage installation failed
> ld: warning multiple definitions of symbol _i1mach_
> pfc.sim.o definition of _i1mach_ in section (__TEXT,__text)
> /Library/Frameworks/R.framework/R(i1mach.lo) definition of _i1mach_
> ld: 2ld.o has external relocation entries in non-writable section
> (__TEXT,__text) for symbols:
> restFP
> saveFP
> make: *** [gap.so] Error 1
> ERROR: compilation failed for package 'gap'
> ** Restoring previous
> '/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/gap'
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/pathmix'
> ** Removing
> '/Library/Frameworks/R.framework/Versions/2.1.0/Resources/library/pointer'
>
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-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Received on Fri Jun 24 05:10:53 2005

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