[R-SIG-Mac] compiling and loading AnalyzeFMRI
Jan de Leeuw
deleeuw at stat.ucla.edu
Thu Feb 5 19:16:39 MET 2004
You are using the Jaguar version of R-1.8.1, dynamically linked with
the Jaguar version of vecLib, and you
compile AnalyzeFMRI on Panther. That's bad. The missing symbol lsame
maybe in the
Panther and not in the Jaguar version. The dynamic linker has resolved
the symbols on Jaguar.
The rest are just warnings, they are OK.
By the way, compiling AnanalyzewFMRI on Panther, using R-1.9.0 compiled
on Panther, does not give the problem
(although SGESVD is indeed missing).
On Feb 5, 2004, at 9:39, Benjamin jacobson wrote:
> 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
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
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>
>
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical
Software
US mail: 8130 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw at stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
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