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

stefano iacus jago at mclink.it
Thu Jul 14 21:58:47 CEST 2005 

It seems you navigate through lots of web pages but probably not read  
the R for Mac OS X Faq.
You are not even telling us R version, os x version and tools  
installed (i.e. gcc, g77 etc).
My suggestion is to read the R for OS X FAQ and consult both http:// 
wiki.urbanek.info/ and http://www.economia.unimi.it/R

stefano



On 14/lug/05, at 19:32, J-C. Marioni wrote:

>
> 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
>
> _______________________________________________
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> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>

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