Hi,
I think this might be a problem with the newest compilers: gcc 4.1+
If you like you can try a version updated for these compilers,
although they will not be the exact same code as the 3.3.7
distribution (but probably not too different).
If you want to try these sources then download them from:
http://www.fmrib.ox.ac.uk/fsldownloads/fsl-gcc4_1_0-sources.tar.gz
This will hopefully work for you.
Let me know if you have any problems.
All the best,
Mark
Michael Huang wrote:
> I am attempting to build FSL, but miscmaths fails to build, leading
> to other errors in the make. Until miscmaths, everything seems to
> compile perfectly.
>
> Making project src/miscmaths
>
> make: Warning: File
> `/fs/plum1_share6/mikefsl/fsl/config/x86_64-unknown-linux-gnu-gcc4.1.1/externallibs.mk'
> has modification time 3.5e+03 s in the future
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o miscmaths.o miscmaths.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> miscmaths.cc: In function â??NEWMAT::ReturnMatrixX
> MISCMATHS::corrcoef(const NEWMAT::Matrix&, int)â??:
> miscmaths.cc:1725: error: â??SPâ?? was not declared in this scope
> miscmaths.cc: In function â??void MISCMATHS::ols(const
> NEWMAT::Matrix&, const NEWMAT::Matrix&, const NEWMAT::Matrix&,
> NEWMAT::Matrix&, NEWMAT::Matrix&)â??:
> miscmaths.cc:1949: error: â??SPâ?? was not declared in this scope
> make: *** [miscmaths.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o optimise.o optimise.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> optimise.cc: In function â??float
> MISCMATHS::optimise(NEWMAT::ColumnVector&, int, const
> NEWMAT::ColumnVector&, float (*)(const NEWMAT::ColumnVector&), int&,
> int, const NEWMAT::ColumnVector&)â??:
> optimise.cc:337: error: â??SPâ?? was not declared in this scope
> make: *** [optimise.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o miscprob.o miscprob.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [miscprob.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o kernel.o kernel.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [kernel.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o histogram.o histogram.cc
> In file included from
> /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../include/c++/4.1.1/backward/iostream.h:31,
>
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/include.h:110,
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/newmat.h:8,
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/newmatap.h:8,
> from histogram.h:77,
> from histogram.cc:69:
> /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../include/c++/4.1.1/backward/backward_warning.h:32:2:
> warning: #warning This file includes at least one deprecated or
> antiquated header. Please consider using one of the 32 headers found
> in section 17.4.1.2 of the C++ standard. Examples include substituting
> the <X> header for the <X.h> header for C++ includes, or <iostream>
> instead of the deprecated header <iostream.h>. To disable this warning
> use -Wno-deprecated.
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [histogram.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o base2z.o base2z.cc
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o t2z.o t2z.cc
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o f2z.o f2z.cc
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o volume.o volume.cc
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o volumeseries.o
> volumeseries.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [volumeseries.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o minimize.o minimize.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> minimize.cc: In function â??void
> MISCMATHS::scg(NEWMAT::ColumnVector&, const
> MISCMATHS::gEvalFunction&, NEWMAT::ColumnVector&, float, float, int)â??:
> minimize.cc:457: error: â??SPâ?? was not declared in this scope
> make: *** [minimize.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o cspline.o cspline.cc
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [cspline.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o sparse_matrix.o
> sparse_matrix.cc
> In file included from
> /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../include/c++/4.1.1/backward/iostream.h:31,
>
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/include.h:110,
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/newmat.h:8,
> from sparse_matrix.h:73,
> from sparse_matrix.cc:76:
> /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../include/c++/4.1.1/backward/backward_warning.h:32:2:
> warning: #warning This file includes at least one deprecated or
> antiquated header. Please consider using one of the 32 headers found
> in section 17.4.1.2 of the C++ standard. Examples include substituting
> the <X> header for the <X.h> header for C++ includes, or <iostream>
> instead of the deprecated header <iostream.h>. To disable this warning
> use -Wno-deprecated.
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [sparse_matrix.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o sparsefn.o sparsefn.cc
> In file included from
> /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../include/c++/4.1.1/backward/iostream.h:31,
>
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/include.h:110,
> from
> /fs/plum1_share6/mikefsl/fsl/extras/include/newmat/newmat.h:8,
> from sparse_matrix.h:73,
> from sparsefn.cc:76:
> /usr/local/lib/gcc/x86_64-unknown-linux-gnu/4.1.1/../../../../include/c++/4.1.1/backward/backward_warning.h:32:2:
> warning: #warning This file includes at least one deprecated or
> antiquated header. Please consider using one of the 32 headers found
> in section 17.4.1.2 of the C++ standard. Examples include substituting
> the <X> header for the <X.h> header for C++ includes, or <iostream>
> instead of the deprecated header <iostream.h>. To disable this warning
> use -Wno-deprecated.
> miscmaths.h: In function â??float MISCMATHS::dot(const
> NEWMAT::ColumnVector&, const NEWMAT::ColumnVector&)â??:
> miscmaths.h:171: error: â??SPâ?? was not declared in this scope
> make: *** [sparsefn.o] Error 1
> c++ -Wall -ansi -pedantic -O3 -fexpensive-optimizations
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/newmat
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/libprob
> -I/fs/plum1_share6/mikefsl/fsl/extras/include/zlib -I.
> -I/fs/plum1_share6/mikefsl/fsl/include
> -I/fs/plum1_share6/mikefsl/fsl/include -c -o rungekutta.o
> rungekutta.cc
> make: Target `all' not remade because of errors.
> make: warning: Clock skew detected. Your build may be incomplete.
>
> =========================
> ERROR::Could not make miscmaths successfully
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