Package Details: fsl 6.0.4-2

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: 0.018760
First Submitted: 2012-07-02 23:36
Last Updated: 2020-08-26 10:02

Latest Comments

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keiichiiownsu12 commented on 2020-09-14 22:34

@liamtimms you should email either @tobac or @adkipnis for a binary package, if you need to update.

liamtimms commented on 2020-08-28 15:35

Getting this:

!!ERROR in BUILD!!
  Could not make the following projects successfully:
    fdt ptx2

in the build log on the new update. Haven't had time to investigate further.

tobac commented on 2020-08-26 10:01

FSL 6.0.4. Good luck.

tobac commented on 2020-07-26 20:45

@adkipnis Sent you an email.

adkipnis commented on 2020-07-26 12:01

@tobac I'd like to compare the two binaries in practice. How may I access your version? :)

tobac commented on 2020-07-19 07:51

Or just write me an email and I'll provide you with a binary Arch package :)

adkipnis commented on 2020-07-18 19:36

If you NEED to use fsl on your Arch install but cannot build it from source: I have dual booted Ubuntu with Arch and installed fsl there instead, then copied the contents of /opt/fsl to Arch, edited .bashrc to include

export FSLDIR=/opt/fsl/
export PATH=${FSLDIR}/bin:$PATH
source $FSLDIR/etc/fslconf/fsl.sh

and source .bashrc (cf. the FSL wiki on the general setup procedure).

Had to additionally edit /opt/fsl/tcl/fslstart.tcl to change the line set HOSTNAME "the-hostname-of-my-arch-install".

And now fsl seems to run properly. Will give updates if I encounter bugs.

Feakster commented on 2020-06-05 11:09

With the newer version of GCC, I still can't successfully build the package. However, this time the errors start a bit sooner in the build process on line 3358 of the build.log, in the section for building the meshclass project. Output below:

Making project src/meshclass

Building dependency file depend.mk
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
/bin/rm -f /tmp/fslgrot drawmesh selfintersection 
Building dependency file depend.mk
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 point.o point.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 mpoint.o mpoint.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 triangle.o triangle.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 mesh.o mesh.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 pt_special.o pt_special.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 profile.o profile.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 drawmesh.o drawmesh.cpp
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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 selfintersection.o selfintersection.cpp
triangle.cpp: In member function ‘const bool mesh::Triangle::intersect(const mesh::Triangle&) const’:
triangle.cpp:203:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  203 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |        ~~~~~~~~~~^~~
triangle.cpp:203:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  203 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                        ~~~~~~~~~~^~~
triangle.cpp:203:68: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  203 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                          ~~~~~~~~~~^~~
triangle.cpp:203:100: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  203 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                                                          ~~~~~~~~~~^~~
triangle.cpp:235:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  235 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |        ~~~~~~~~~~^~~
triangle.cpp:235:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  235 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                        ~~~~~~~~~~^~~
triangle.cpp:235:68: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  235 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                          ~~~~~~~~~~^~~
triangle.cpp:235:100: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  235 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                                                          ~~~~~~~~~~^~~
triangle.cpp:269:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  269 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |        ~~~~~~~~~~^~~
triangle.cpp:269:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  269 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                        ~~~~~~~~~~^~~
triangle.cpp:269:68: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  269 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                          ~~~~~~~~~~^~~
triangle.cpp:269:100: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  269 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                                                          ~~~~~~~~~~^~~
triangle.cpp:300:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  300 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |        ~~~~~~~~~~^~~
triangle.cpp:300:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  300 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                        ~~~~~~~~~~^~~
triangle.cpp:300:68: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  300 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                          ~~~~~~~~~~^~~
triangle.cpp:300:100: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  300 |   if (((n1 | n3) > 0 & (n2 | n3) > 0 & (n1 | n2) > 0) | ((n1 | n3) < 0 & (n2 | n3) < 0 & (n1 | n2) < 0) )
      |                                                                                          ~~~~~~~~~~^~~
In file included from drawmesh.cpp:72:
/home/benjamin/.cache/yay/fsl/src/fsl/include/utils/options.h:606:7: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  606 |       throw(X_OptionError);
      |       ^~~~~
In file included from /usr/include/string.h:495,
                 from /usr/include/c++/10.1.0/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 drawmesh.cpp:73:
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 = double; D = short int]’ at /home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimage.h:927:20:
/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));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ar -r libmeshclass.a point.o mpoint.o triangle.o mesh.o pt_special.o profile.o 
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -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/usr/include -I/usr/include/boost -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,'$ORIGIN/../lib' -L/usr/lib -llapack -lopenblas  -L/usr/lib -L. -L/home/benjamin/.cache/yay/fsl/src/fsl/lib -L/home/benjamin/.cache/yay/fsl/src/fsl/lib -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now -o drawmesh drawmesh.o mpoint.o triangle.o mesh.o point.o pt_special.o -lnewimage -lmiscmaths -lNewNifti -lznz -lnewmat -lutils -lz 
c++ -Wall -ansi -pedantic -Wno-long-long -std=c++11  -g   -m64 -g -O3 -fexpensive-optimizations -m64 -I/usr/include/boost -I/home/benjamin/.cache/yay/fsl/src/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/usr/include -I/usr/include/boost -I. -I/home/benjamin/.cache/yay/fsl/src/fsl/include -I/home/benjamin/.cache/yay/fsl/src/fsl/include -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -fno-plt -Wl,-rpath,'$ORIGIN/../lib' -L/usr/lib -llapack -lopenblas  -L/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 selfintersection selfintersection.o mpoint.o triangle.o mesh.o point.o pt_special.o -lnewimage -lmiscmaths -lNewNifti -lznz -lnewmat -lutils -lz 
ar: creating libmeshclass.a
/usr/bin/ld: drawmesh.o: in function `int NEWIMAGE::read_volumeROI<double>(NEWIMAGE::volume<double>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, short&, long, long, long, long, long, long, long, long, bool, bool)':
/home/benjamin/.cache/yay/fsl/src/fsl/include/newimage/newimageio.h:127: undefined reference to `int NEWIMAGE::readGeneralVolume<double>(NEWIMAGE::volume<double>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, short&, bool, long, long, long, long, long, long, long, long, long, long, long, long, long, long, bool)'
collect2: error: ld returned 1 exit status
make: *** [Makefile:25: drawmesh] Error 1
make: Target 'all' not remade because of errors.

 ========================= 
ERROR::Could not make meshclass successfully

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.