[R-SIG-Mac] compiling and loading AnalyzeFMRI

[Benjamin jacobson]

I have had the opportunity to play with installing the AnalyzeFMRI  
package and have a better idea of what is going wrong.  Was hoping that  
somebody on the list will be able to help.


I am currently running the R-Aqua version 1.8 for Jaguar.  Below is the  
output from building and trying to load the package.


* 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/Applications/StartR.app/RAqua.app/Contents/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-darwin6.6/3.4  
-L/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../.. -lfrtbegin  
-lg2c -lSystem  -L/usr/local/lib  
-L/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4  
-L/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../.. -lfrtbegin  
-lg2c -lSystem -lcc_dynamic
ld: warning -L: directory name  
(/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4) does not exist
ld: warning -L: directory name  
(/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../..) does not  
exist
ld: warning -L: directory name  
(/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4) does not exist
ld: warning -L: directory name  
(/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../..) does not  
exist
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_
** 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  
"/Applications/StartR.app/RAqua.app/Contents/library/AnalyzeFMRI/libs/ 
AnalyzeFMRI.so":
   dlcompat: dyld:  
/Applications/StartR.app/RAqua.app/Contents/MacOS/RAqua Undefined  
symbols:
_lsame_
Error in library(AnalyzeFMRI) : .First.lib failed


It looks as though, the problem lies in incompatibility between  
Panther's Linear Algebra libraries (LAPACK, and BLAS), and the  
libraries that come prepackaged with AnalyzeFMRI (As I know lsame is  
part of LAPACK).

Anybody have any suggestions.  Can I force the library to build solely  
against Panther linear algebra tools, do I need to adjust the library  
search path.  Not sure where to proceed from here, and could really use  
some help as I depend on the AnalyzeFMRI library quite a bit for the  
code I have written.  Hope this description of the problem is more  
explicit than what I posted before.


thanks for your time.


Ben Jacobson

------------------------------------------------------------------------ 
-

Benjamin Jacobson
Department of Psychology - University of Colorado at Boulder
Medical Scholars Program - University of Illinois, Urbana-Champaign
Muenzinger E-022
Boulder, CO 80309
303-735-5802
jacobson at psych.colorado.edu