[R-SIG-Mac] Re: Compiling Analyze FMRI
stefano iacus
stefano.iacus at unimi.it
Fri Feb 6 21:50:48 MET 2004
I have exactly the same errors.
It seems to me that the problem is the following.
The configure script does not find SGESVD inside the lapack lib
Then it switches to its own version but there, their is not lsame
(which is in R!) and I think this is causing troubles.
I've seen there is something in the windows srcs. I'll try to see (or
better, I'll ask) if a similar approach can be used under OSX.
Will be back on that.
stefano
On Feb 6, 2004, at 8:38 PM, Benjamin Jacobson wrote:
> I am still having the same issues compiling this AnalyzeFMRI library.
> I created a clean install of both the R-devel.dmg and from a
> successful build from source of the Jan312004 build of R-devel. In
> both cases similar error messages were generated when executing
> library (AnalyzeFMRI) after a successful install. Below is the output
> from one of these attempts. I am compiling on a G4 installed with
> both the most updated versions of Panther and Xtools. Thanks for your
> time.
>
>
> Ben Jacobson
>
>
> * Installing *source* package 'AnalyzeFMRI' ...
> creating cache ./config.cache
> checking for sgesdd_ in -llapack... no
> could not find SGESVD in your LAPACK library, using our routines
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -no-cpp-precomp
> -I/Library/Frameworks/R.framework/Versions/1.9.0/Resources/include
> -I/usr/local/include -Wall -pedantic -fno-common -g -O2 -c
> analyzeFMRI.c -o analyzeFMRI.o
> g77 -fno-common -g -O2 -c slapack.f -o slapack.o
> gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o
> AnalyzeFMRI.so analyzeFMRI.o slapack.o -framework vecLib
> -L/usr/local/lib -L/usr/local/lib/gcc/powerpc-apple-darwin7.0.0/3.4
> -L/usr/local/lib/gcc/powerpc-apple-darwin7.0.0/3.4/../../.. -lfrtbegin
> -lg2c -lgcc_s -lSystem -L/usr/local/lib
> -L/usr/local/lib/gcc/powerpc-apple-darwin7.0.0/3.4
> -L/usr/local/lib/gcc/powerpc-apple-darwin7.0.0/3.4/../../.. -lfrtbegin
> -lg2c -lgcc_s -lSystem -lcc_dynamic
> -L/Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin -lR
> ld: warning multiple definitions of symbol _ilaenv_
> slapack.o definition of _ilaenv_ in section (__TEXT,__text)
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
> vecLib.framework/Versions/A/libBLAS.dylib(single module) definition of
> _ilaenv_
> ld: warning multiple definitions of symbol _xerbla_
> analyzeFMRI.o 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_
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(print.lo) definition of _xerbla_
> ld: warning multiple definitions of symbol _crc32
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(crc32.o) definition of _crc32
> /usr/lib/libz.1.dylib(crc32.o) definition of _crc32
> ld: warning multiple definitions of symbol _get_crc_table
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(crc32.o) definition of _get_crc_table
> /usr/lib/libz.1.dylib(crc32.o) definition of _get_crc_table
> ld: warning multiple definitions of symbol _deflate
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflate
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflate
> ld: warning multiple definitions of symbol _deflateCopy
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateCopy
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateCopy
> ld: warning multiple definitions of symbol _deflateReset
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateReset
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateReset
> ld: warning multiple definitions of symbol _deflateSetDictionary
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateSetDictionary
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateSetDictionary
> ld: warning multiple definitions of symbol _deflateInit2_
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateInit2_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit2_
> ld: warning multiple definitions of symbol _deflateEnd
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateEnd
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateEnd
> ld: warning multiple definitions of symbol _deflateParams
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateParams
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateParams
> ld: warning multiple definitions of symbol _deflateInit_
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(deflate.o) definition of _deflateInit_
> /usr/lib/libz.1.dylib(deflate.o) definition of _deflateInit_
> ld: warning multiple definitions of symbol _zError
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(zutil.o) definition of _zError
> /usr/lib/libz.1.dylib(zutil.o) definition of _zError
> ld: warning multiple definitions of symbol _zlibVersion
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(zutil.o) definition of _zlibVersion
> /usr/lib/libz.1.dylib(zutil.o) definition of _zlibVersion
> ld: warning multiple definitions of symbol _inflateEnd
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateEnd
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateEnd
> ld: warning multiple definitions of symbol _inflateSync
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateSync
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSync
> ld: warning multiple definitions of symbol _inflateSyncPoint
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateSyncPoint
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSyncPoint
> ld: warning multiple definitions of symbol _inflate
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflate
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflate
> ld: warning multiple definitions of symbol _inflateSetDictionary
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateSetDictionary
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateSetDictionary
> ld: warning multiple definitions of symbol _inflateInit2_
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateInit2_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit2_
> ld: warning multiple definitions of symbol _inflateReset
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateReset
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateReset
> ld: warning multiple definitions of symbol _inflateInit_
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(inflate.o) definition of _inflateInit_
> /usr/lib/libz.1.dylib(inflate.o) definition of _inflateInit_
> ld: warning multiple definitions of symbol _adler32
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(adler32.o) definition of _adler32
> /usr/lib/libz.1.dylib(adler32.o) definition of _adler32
> ld: warning multiple definitions of symbol _BC
> /usr/local/lib/libreadline.4.3.dylib(terminal.so) definition of _BC
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _BC
> ld: warning multiple definitions of symbol _UP
> /usr/local/lib/libreadline.4.3.dylib(terminal.so) definition of _UP
> /usr/lib/libncurses.5.dylib(lib_termcap.o) definition of _UP
> ld: warning multiple definitions of symbol _PC
> /usr/local/lib/libreadline.4.3.dylib(terminal.so) definition of _PC
> /usr/lib/libncurses.5.dylib(lib_tputs.o) definition of _PC
> ld: warning multiple definitions of symbol _gzeof
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzeof
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzeof
> ld: warning multiple definitions of symbol _gzclose
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzclose
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzclose
> ld: warning multiple definitions of symbol _gzdopen
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzdopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzdopen
> ld: warning multiple definitions of symbol _gzerror
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzerror
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzerror
> ld: warning multiple definitions of symbol _gzflush
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzflush
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzflush
> ld: warning multiple definitions of symbol _gzgetc
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzgetc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgetc
> ld: warning multiple definitions of symbol _gzgets
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzgets
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzgets
> ld: warning multiple definitions of symbol _gzopen
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzopen
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzopen
> ld: warning multiple definitions of symbol _gzprintf
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzprintf
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzprintf
> ld: warning multiple definitions of symbol _gzputc
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzputc
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputc
> ld: warning multiple definitions of symbol _gzputs
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzputs
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzputs
> ld: warning multiple definitions of symbol _gzread
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzread
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzread
> ld: warning multiple definitions of symbol _gzrewind
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzrewind
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzrewind
> ld: warning multiple definitions of symbol _gzseek
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzseek
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzseek
> ld: warning multiple definitions of symbol _gzsetparams
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzsetparams
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzsetparams
> ld: warning multiple definitions of symbol _gztell
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gztell
> /usr/lib/libz.1.dylib(gzio.o) definition of _gztell
> ld: warning multiple definitions of symbol _gzwrite
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/
> libR.dylib(gzio.o) definition of _gzwrite
> /usr/lib/libz.1.dylib(gzio.o) definition of _gzwrite
> ** R
> ** inst
> ** help
> >>> Building/Updating help pages for package 'AnalyzeFMRI'
> Formats: text html latex example
> f.analyze.file.summary text html latex example
> f.analyzeIO.gui text html latex
> f.basic.hdr.list.create text html latex example
> f.ica.fmri text html latex
> f.ica.fmri.gui text html latex
> f.plot.ica.fmri text html latex
> f.plot.ica.fmri.jpg text html latex
> f.read.analyze.header text html latex example
> f.read.analyze.slice text html latex example
> f.read.analyze.slice.at.all.timep text html latex example
> f.read.analyze.tpt text html latex example
> f.read.analyze.ts text html latex example
> f.read.analyze.volume text html latex example
> f.spectral.summary text html latex
> f.write.analyze text html latex example
> f.write.array.to.img.2bytes text html latex
> f.write.array.to.img.8bit text html latex
> f.write.array.to.img.float text html latex
> f.write.list.to.hdr text html latex example
> * DONE (AnalyzeFMRI)
>
> Delete downloaded files (y/N)? y
>
> > library (AnalyzeFMRI)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
> unable to load shared library
> "/Library/Frameworks/R.framework/Versions/1.9.0/Resources/library/
> AnalyzeFMRI/libs/AnalyzeFMRI.so":
> dlcompat: dyld:
> /Library/Frameworks/R.framework/Versions/1.9.0/Resources/bin/R.bin
> Undefined symbols:
> _lsame_
> Error in library(AnalyzeFMRI) : .First.lib failed
>
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