[R-SIG-Mac] restFP and saveFP errors installing R and R libraries

[J-C. Marioni]

Hello Mac R wizards,


We have been trying to install the following R libraries "rmutil" and 
"repeated" from Jim Lindsey's web page. 
http://popgen.unimaas.nl/~jlindsey/rcode.html These libraries are required 
for the aCGH package in BioConductor (http://www.bioconductor.org/) We got 
errors during their installation..... ld: dist.o has external relocation 
entries in non-writable section (_TEXT,_text) for symbols: restFP saveFP


>From the R-help mail list we got a reply suggesting that we might avoid the 
problem by installing R from source. We attempted to do this, but got 
similar errors relating to restFP and saveFP in the make step. Brian Ripley 
suggested that this has something to do with the fact that the Fortran 
compiler on mac is compiled using FSF rather than with on the apple system.

see http://www.astro.gla.ac.uk/users/norman/note/2004/restFP/

"The DarwinPorts and Fink g77 builds use the Free Software Foundation (FSF) 
GCC, while the Apple compilers use a GCC variant with OSX-specific 
modifications which have not, or not yet, been integrated with the FSF 
mainline. That means that the GCC back-ends -- that is, the parts which 
generate the object code which is linked to make libraries and executables 
-- produce object code which is slightly different, sometimes to the point 
of being incompatible. This incompatibility is a problem if and only if you 
are using both back-ends, that is, if you are mixing Fortran (from FSF g77) 
with code produced by Apple GCC."

So....we tried
% env LDFLAGS=-lcc_dynamic ./configure
and got the following error

$ env LDFLAGS=-lcc_dynamic ./configure --with-blas='-framework vecLib' 
--with-lapack --with-aqua checking build system type... 
powerpc-apple-darwin8.1.0 checking host system type... 
powerpc-apple-darwin8.1.0 loading site script './config.site' loading build 
specific script './config.site' checking for pwd... /bin/pwd checking 
whether builddir is srcdir... yes checking for working aclocal... found 
checking for working autoconf... found checking for working automake... 
found checking for working autoheader... found checking for working 
makeinfo... found checking for gawk... no checking for mawk... no checking 
for nawk... no checking for awk... awk checking for egrep... grep -E 
checking whether ln -s works... yes checking for ranlib... ranlib checking 
for bison... bison -y checking for ar... ar checking for a BSD-compatible 
install... /usr/bin/install -c checking for javac... /usr/bin/javac 
checking for sed... /usr/bin/sed checking for less... /usr/bin/less 
checking for perl... /usr/bin/perl checking whether perl version is at 
least 5.004... yes checking for dvips... 
/usr/local/teTeX/bin/powerpc-apple-darwin-current/dvips checking for tex... 
/usr/local/teTeX/bin/powerpc-apple-darwin-current/tex checking for latex... 
/usr/local/teTeX/bin/powerpc-apple-darwin-current/latex checking for 
makeindex... /usr/local/teTeX/bin/powerpc-apple-darwin-current/makeindex 
checking for pdftex... 
/usr/local/teTeX/bin/powerpc-apple-darwin-current/pdftex checking for 
pdflatex... /usr/local/teTeX/bin/powerpc-apple-darwin-current/pdflatex 
checking for makeinfo... /usr/bin/makeinfo checking for unzip... 
/usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... 
/usr/bin/gzip checking for firefox... no checking for mozilla... no 
checking for netscape... no checking for galeon... no checking for 
kfmclient... no checking for opera... no checking for gnome-moz-remote... 
no checking for open... /usr/bin/open using default browser ... 
/usr/bin/open checking for acroread... no checking for acroread4... no 
checking for xpdf... no checking for gv... no checking for gnome-gv... no 
checking for ggv... no checking for kghostview... no checking for open... 
/usr/bin/open checking for gcc... gcc checking for C compiler default 
output file name... configure: error: C compiler cannot create executables 
See `config.log' for more details.



So then we went to
http://www.swarm.org/wiki/Swarm:_MacOS_X_binaries#Notes_on_packages
installed the following for Tiger

2004-02-04/gsed.pkg.sit
2004-02-04/libpng.pkg.sit
2005-02-05/tcl8.4.7.pkg.sit
2004-02-04/hdf5_1.6.1.pkg.sit
2005-02-05/swarmx2.2.pkg.sit

and
gcc-4-swarm.dmg

The idea for doing this was to get an apple compiled fortran compiler.

Then we re ran the ./configure using
./configure --with-blas='-framework vecLib' --with-lapack --with-aqua

with no apparent errors
but the make gave the following error output shown below

st12:~/Desktop/R-2.1.1 jcm68$ make make[1]: Nothing to be done for `R'. 
make[1]: Nothing to be done for `R'. make[2]: Nothing to be done for `R'. 
creating src/scripts/R.fe config.status: creating src/include/config.h 
config.status: src/include/config.h is unchanged Rmath.h is unchanged 
make[3]: Nothing to be done for `R'. make[4]: `libbz2.a' is up to date. 
make[4]: `libpcre.a' is up to date. make[4]: `libz.a' is up to date. 
../../../src/include/libintl.h is unchanged ../../../include/libintl.h is 
unchanged make[4]: `localecharset.h' is up to date. make[4]: `libintl.a' is 
up to date. make[3]: `stamp-lo' is up to date. make[3]: `stamp-lo' is up to 
date. make[3]: `stamp-lo' is up to date. gcc -dynamiclib -L/usr/local/lib 
-dynamiclib -install_name libR.dylib -compatibility_version 2.1.0 
-current_version 2.1.1 -headerpad_max_install_names -o libR.dylib 
Rembedded.lo CConverters.lo CommandLineArgs.lo Rdynload.lo Renviron.lo 
RNG.lo apply.lo arithmetic.lo apse.lo array.lo attrib.lo base.lo bind.lo 
builtin.lo character.lo coerce.lo colors.lo complex.lo connections.lo 
context.lo cov.lo cum.lo dcf.lo datetime.lo debug.lo deparse.lo deriv.lo 
dotcode.lo dounzip.lo dstruct.lo duplicate.lo engine.lo envir.lo errors.lo 
eval.lo format.lo fourier.lo gevents.lo gram.lo gram-ex.lo graphics.lo 
identical.lo internet.lo iosupport.lo lapack.lo list.lo logic.lo main.lo 
mapply.lo match.lo memory.lo model.lo names.lo objects.lo optim.lo 
optimize.lo options.lo par.lo paste.lo pcre.lo platform.lo plot.lo 
plot3d.lo plotmath.lo print.lo printarray.lo printvector.lo printutils.lo 
qsort.lo random.lo regex.lo registration.lo relop.lo saveload.lo scan.lo 
seq.lo serialize.lo size.lo sort.lo source.lo split.lo sprintf.lo 
startup.lo subassign.lo subscript.lo subset.lo summary.lo sysutils.lo 
unique.lo util.lo version.lo vfonts.lo xxxpr.lo `ls ../appl/*.lo 
../nmath/*.lo ../unix/*.lo 2>/dev/null` -framework vecLib 
-L/usr/local/lib/gcc/powerpc-apple-darwin6.8/3.4.2 -lg2c -lSystem 
../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a 
../extra/intl/libintl.a -lreadline -lm -liconv ld: warning multiple 
definitions of symbol _xerbla_ print.lo definition of _xerbla_ in section 
(__TEXT,__text) 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib(single 
module) definition of _xerbla_ ld: warning multiple definitions of symbol 
_signgam ../nmath/lgamma.lo definition of _signgam in section 
(__DATA,__common) 
/usr/lib/gcc/powerpc-apple-darwin8/4.0.0/../../../libSystem.dylib(gamma9.o) 
definition of _signgam ld: Undefined symbols: restFP saveFP 
/usr/bin/libtool: internal link edit command failed make[3]: *** 
[libR.dylib] Error 1 make[2]: *** [R] Error 2 make[1]: *** [R] Error 1 
make: *** [R] Error 1


Another suggestion on this website 
(http://www.astro.gla.ac.uk/users/norman/note/2004/restFP/) is to do the 
following????

"The restFP and saveFP functions are defined in Apple's libgcc, and so the 
fix is simply to include this library in your link line. The best way of 
doing this is to include the option

-lcc_dynamic
in your link line."

But we don't really understand what this means?


Any help would be much appreciated.

Thanks,

John