Package Details: fsl 6.0.3-1

Git Clone URL: https://aur.archlinux.org/fsl.git (read-only, click to copy)
Package Base: fsl
Description: A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
Upstream URL: http://www.fmrib.ox.ac.uk/fsl/
Licenses: custom
Submitter: fishburn
Maintainer: tobac
Last Packager: tobac
Votes: 11
Popularity: 0.40
First Submitted: 2012-07-02 23:36
Last Updated: 2020-01-03 19:33

Latest Comments

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Feakster commented on 2020-03-06 20:49

Not sure whether it helps or not, but the errors seem to start at around line 3999 in my build.log, in the section for building fslsurface. All other errors seem to propagate downstream from the resulting missing fslsurface/fslsurfaceio.h file. The relevant section of output is below:

Making project src/fslsurface

Building dependency file depend.mk
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
/bin/rm -f /tmp/fslgrot fslsurfacemaths 
Building dependency file depend.mk
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -D_FORTIFY_SOURCE=2  -c -o fslsurfacefns.o fslsurfacefns.cc
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -D_FORTIFY_SOURCE=2  -c -o fslsurfaceio.o fslsurfaceio.cc
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -D_FORTIFY_SOURCE=2  -c -o fslsurface.o fslsurface.cc
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -D_FORTIFY_SOURCE=2  -c -o fslsurface_first.o fslsurface_first.cc
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -D_FORTIFY_SOURCE=2  -c -o fslsurface_dataconv.o fslsurface_dataconv.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -D_FORTIFY_SOURCE=2  -c -o fslsurfacemaths.o fslsurfacemaths.cpp
fslsurfacefns.cc: In instantiation of ‘void fslsurface_name::conn2dist(fslsurface_name::fslSurface<T, T2>&, const T2&, std::__cxx11::list<std::pair<T2, T2> >&, std::vector<std::__cxx11::list<std::pair<T2, T> > >&) [with T = float; T2 = unsigned int]’:
fslsurfacefns.cc:702:46:   required from ‘void fslsurface_name::sc_smooth_gaussian_geodesic(fslsurface_name::fslSurface<T, T2>&, const unsigned int&, const T&, const T&, bool) [with T = float; T2 = unsigned int]’
fslsurfacefns.cc:945:173:   required from here
fslsurfacefns.cc:510:22: warning: variable ‘notFoundDup’ set but not used [-Wunused-but-set-variable]
  510 |                 bool notFoundDup=true;
      |                      ^~~~~~~~~~~
ar -r libfslsurface.a  fslsurfacefns.o fslsurfaceio.o fslsurface.o
ar: creating libfslsurface.a
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11     -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/libprob -I/usr/include  -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -Wl,-rpath,'$ORIGIN/../lib' -L/usr/lib -llapack -lopenblas  -L/home/benjamin/.cache/yay/fsl/src/fsl/extras/lib -L/usr/lib -L. -L/home/benjamin/.cache/yay/fsl/src/fsl/lib -L/home/benjamin/.cache/yay/fsl/src/fsl/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o fslsurfacemaths fslsurfacemaths.o fslsurfaceio.o fslsurfacefns.o fslsurface_first.o fslsurface.o -lgiftiio -lexpat -lfirst_lib -lmeshclass -lshapeModel -lfslvtkio -lmeshclass -lnewimage -lmiscmaths -lNewNifti -lznz -lnewmat -lutils -lprob -lz -lGL -lGLU
In file included from /usr/include/string.h:495,
                 from /usr/include/c++/9.2.1/cstring:42,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap/armadillo:24,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap/armawrap.hpp:13,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap/newmat.h:8,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap/newmatap.h:4,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimage.h:80,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimageall.h:72,
                 from /home/benjamin/.cache/yay/fsl/src/fsl/include/shapeModel/shapeModel.h:73,
                 from ./fslsurface_first.h:71,
                 from fslsurface_first.cc:64:
In function ‘char* strncpy(char*, const char*, size_t)’,
    inlined from ‘void NEWIMAGE::volume<T>::setAuxFile(std::string) [with T = short int]’ at /home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimage.h:361:53,
    inlined from ‘void NEWIMAGE::copybasicproperties(const NEWIMAGE::volume<T>&, NEWIMAGE::volume<U>&) [with S = short int; D = short int]’ at /home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimage.h:927:5,
    inlined from ‘void NEWIMAGE::copyconvert(const NEWIMAGE::volume<T>&, NEWIMAGE::volume<U>&, bool) [with S = short int; D = short int]’ at /home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimage.h:938:24:
/usr/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ specified bound 24 equals destination size [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/ld: fslsurfacemaths.o: in function `main':
/home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:330: undefined reference to `fslsurface_name::getFSLtoNIFTIxfm(NEWIMAGE::volume<float> const&)'
/usr/bin/ld: /home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:355: undefined reference to `fslsurface_name::meshRegLeastSq(fslsurface_name::fslSurface<float, unsigned int> const&, fslsurface_name::fslSurface<float, unsigned int> const&, unsigned int const&)'
/usr/bin/ld: /home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:609: undefined reference to `fslsurface_name::reconSurface_from_bvars(fslsurface_name::fslSurface<float, unsigned int>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/usr/bin/ld: /home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:638: undefined reference to `fslsurface_name::FtoP(std::vector<float, std::allocator<float> > const&, int const&, int const&)'
/usr/bin/ld: /home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:647: undefined reference to `fslsurface_name::vertexMVglm(fslsurface_name::fslSurface<float, unsigned int>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
/usr/bin/ld: /home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:625: undefined reference to `fslsurface_name::reconAllSurfacesAndSave(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/usr/bin/ld: /home/benjamin/.cache/yay/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:695: undefined reference to `NEWIMAGE::volume<short> fslsurface_name::fillMesh<float, unsigned int>(fslsurface_name::fslSurface<float, unsigned int> const&, NEWIMAGE::volume<short> const&, int const&)'
collect2: error: ld returned 1 exit status
make: *** [Makefile:61: fslsurfacemaths] Error 1
ar -r libfslsurface_backcompat.a fslsurface_first.o fslsurface_dataconv.o
ar: creating libfslsurface_backcompat.a
make: Target 'all' not remade because of errors.

 ========================= 
ERROR::Could not make fslsurface successfully

tobac commented on 2020-02-24 10:23

The thing is, my initial efforts to reproduce this (apparently quite common) error were unsuccessful. I hope I can work on it later this week.

Anyway, if you contact me by e-mail (see PKGBUILD), we can usually find a solution on a one-by-one basis.

Fjalar commented on 2020-02-24 09:55

Got the exact same error as Feakster and jpeter, have provided build.log

tobac commented on 2020-01-08 10:24

@jpeter Sure. You can find a valid address in the PKGBUILD file.

jpeter commented on 2020-01-08 10:20

@tobac The build.log is very large. Email?

tobac commented on 2020-01-08 10:08

@jpeter Fair enough, but I still don't have a build.log :). Feakster didn't get back to me. Could you email/pastebin me yours?

jpeter commented on 2020-01-08 09:31

Same build error as Feakster commented on 2020-01-05 09:54

tobac commented on 2020-01-06 08:11

@keiichilownsu12 I'm indeed subscribed, so sure, go ahead :)

Wrt cloning their online wiki, I don't think they provide an official means. Using wget --mirror was not successful either.

keiichiiownsu12 commented on 2020-01-06 08:03

@tobac also, are you perhaps subscribed to the fsl-support mailing list? I could raise the issue there and forward you the response (if I get any), if you are interested (i.e. the outdated documentation)

keiichiiownsu12 commented on 2020-01-06 07:59

@tobac do you know if they provide a means to clone their offline wiki?