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Compiling Analyze FMRI

3 messages · Benjamin Jacobson, stefano iacus

Original
Benjamin Jacobson
# 
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
stefano iacus
# 
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:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      stefano iacus
    

    

      
      #
    

  


  

      
From inside the AnalyzeFMRI package: by copying the code of LSAME from  
src/sblas.unused in the file src/slapack.f fixes the problem and R is  
happy with this.

I don't know yet a better solution.

stefano

        
On Feb 6, 2004, at 8:38 PM, Benjamin Jacobson wrote: