Errors running ./build

johnsmith · April 25, 2016, 5:53am

I would like to install MRtrix3 on Lubuntu 12.04.

I ran ./configure:
fred@fred:~/mrtrix3$ ./configure 

MRtrix build type requested: release

Detecting OS: linux
Checking for C++11 compliant compiler [/usr/bin/g++-4.8]: 4.8 - tested ok
Detecting pointer size: 32 bit
Detecting byte order: little-endian
Checking for variable-length array support: yes
Checking for non-POD variable-length array support: yes
Checking for zlib compression library: 1.2.3.4
checking for Eigen 3 library: 3.0.5
Checking shared library generation: yes
Checking for Qt moc: moc (version 4.8.1)
Checking for Qt qmake: qmake (version 4.8.1)
Checking for Qt rcc: rcc (version 4.8.1)
Checking for Qt: 4.8.1

writing configuration to file './release/config': ok

But when I run ./build, I get

fred@fred:~/mrtrix3$ ./build 

ERROR: (  1/412) [CC] release/cmd/tckgen.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -isystem /usr/include/eigen3 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -isystem /usr/include/eigen3 cmd/tckgen.cpp -o release/cmd/tckgen.o

failed with output

In file included from src/dwi/tractography/tracking/exec.h:25:0,
                 from cmd/tckgen.cpp:24:
src/dwi/tractography/tracking/method.h: In member function bool MR::DWI::Tractography::Tracking::MethodBase::check_seed():
src/dwi/tractography/tracking/method.h:60:24: error: Eigen::Vector3f has no member named allFinite
               if (!pos.allFinite())
                        ^
In file included from src/dwi/tractography/tracking/exec.h:29:0,
                 from cmd/tckgen.cpp:24:
src/dwi/tractography/mapping/mapper.h: In member function void MR::DWI::Tractography::Mapping::TrackMapperBase::voxelise(const MR::DWI::Tractography::Streamline<float>&, Cont&) const:
src/dwi/tractography/mapping/mapper.h:184:25: error: const class Eigen::Matrix<float, 3, 1> has no member named allFinite
                 if (dir.allFinite())
                         ^
src/dwi/tractography/mapping/mapper.h:193:23: error: const class Eigen::Matrix<float, 3, 1> has no member named allFinite
               if (dir.allFinite())
                       ^
In file included from cmd/tckgen.cpp:30:0:
src/dwi/tractography/algorithms/fact.h: In member function bool MR::DWI::Tractography::Algorithms::FACT::init():
src/dwi/tractography/algorithms/fact.h:92:25: error: const Vector3f has no member named allFinite
         if (!S.init_dir.allFinite()) {
                         ^
src/dwi/tractography/algorithms/fact.h:93:20: error: Eigen::Vector3f has no member named allFinite
           if (!dir.allFinite())
                    ^
In file included from cmd/tckgen.cpp:31:0:
src/dwi/tractography/algorithms/iFOD1.h: In member function bool MR::DWI::Tractography::Algorithms::iFOD1::init():
src/dwi/tractography/algorithms/iFOD1.h:140:25: error: const Vector3f has no member named allFinite
         if (!S.init_dir.allFinite()) {
                         ^
src/dwi/tractography/algorithms/iFOD1.h:145:28: error: const Vector3f has no member named allFinite
             dir = init_dir.allFinite() ? rand_dir (init_dir) : random_direction();
                            ^
In file included from cmd/tckgen.cpp:32:0:
src/dwi/tractography/algorithms/iFOD2.h: In member function bool MR::DWI::Tractography::Algorithms::iFOD2::init():
src/dwi/tractography/algorithms/iFOD2.h:196:31: error: const Vector3f has no member named allFinite
               if (!S.init_dir.allFinite()) {
                               ^
src/dwi/tractography/algorithms/iFOD2.h:201:34: error: const Vector3f has no member named allFinite
                   dir = init_dir.allFinite() ? rand_dir (init_dir) : random_direction();
                                  ^
In file included from cmd/tckgen.cpp:33:0:
src/dwi/tractography/algorithms/nulldist.h: In member function bool MR::DWI::Tractography::Algorithms::NullDist1::init():
src/dwi/tractography/algorithms/nulldist.h:61:26: error: const Vector3f has no member named allFinite
         dir = S.init_dir.allFinite() ? S.init_dir : random_direction();
                          ^
src/dwi/tractography/algorithms/nulldist.h: In member function bool MR::DWI::Tractography::Algorithms::NullDist2::init():
src/dwi/tractography/algorithms/nulldist.h:116:26: error: const Vector3f has no member named allFinite
         dir = S.init_dir.allFinite() ? S.init_dir : random_direction();
                          ^
In file included from cmd/tckgen.cpp:34:0:
src/dwi/tractography/algorithms/sd_stream.h: In member function bool MR::DWI::Tractography::Algorithms::SDStream::init():
src/dwi/tractography/algorithms/sd_stream.h:103:23: error: const Vector3f has no member named allFinite
       if (!S.init_dir.allFinite()) {
                       ^
src/dwi/tractography/algorithms/sd_stream.h:104:18: error: Eigen::Vector3f has no member named allFinite
         if (!dir.allFinite())
                  ^
In file included from cmd/tckgen.cpp:36:0:
src/dwi/tractography/algorithms/tensor_det.h: In member function void MR::DWI::Tractography::Algorithms::Tensor_Det::get_EV():
src/dwi/tractography/algorithms/tensor_det.h:137:13: error: class Eigen::SelfAdjointEigenSolver<Eigen::Matrix<float, 3, 3> > has no member named computeDirect
         eig.computeDirect (M);
             ^
In file included from cmd/tckgen.cpp:24:0:
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::FACT]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::FACT]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::FACT> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::FACT; std::string = std::basic_string<char>]
cmd/tckgen.cpp:181:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
                 if (!method.pos.allFinite()) {
                     ^
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::iFOD1]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::iFOD1]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::iFOD1> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::iFOD1; std::string = std::basic_string<char>]
cmd/tckgen.cpp:184:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::iFOD2]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::iFOD2]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::iFOD2> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::iFOD2; std::string = std::basic_string<char>]
cmd/tckgen.cpp:187:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::NullDist1]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::NullDist1]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::NullDist1> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::NullDist1; std::string = std::basic_string<char>]
cmd/tckgen.cpp:190:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::NullDist2]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::NullDist2]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::NullDist2> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::NullDist2; std::string = std::basic_string<char>]
cmd/tckgen.cpp:193:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::SDStream]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::SDStream]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::SDStream> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::SDStream; std::string = std::basic_string<char>]
cmd/tckgen.cpp:196:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::Seedtest]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::Seedtest]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::Seedtest> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::Seedtest; std::string = std::basic_string<char>]
cmd/tckgen.cpp:199:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::Tensor_Det]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::Tensor_Det]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::Tensor_Det> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::Tensor_Det; std::string = std::basic_string<char>]
cmd/tckgen.cpp:202:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite
src/dwi/tractography/tracking/exec.h: In instantiation of bool MR::DWI::Tractography::Tracking::Exec<Method>::gen_track(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::Tensor_Prob]:
src/dwi/tractography/tracking/exec.h:119:35:   required from bool MR::DWI::Tractography::Tracking::Exec<Method>::operator()(MR::DWI::Tractography::Tracking::GeneratedTrack&) [with Method = MR::DWI::Tractography::Algorithms::Tensor_Prob]
./lib/thread_queue.h:1049:48:   required from void MR::Thread::run_queue(Source&&, const Type&, Sink&&, size_t) [with Source = MR::Thread::{anonymous}::__Multi<MR::DWI::Tractography::Tracking::Exec<MR::DWI::Tractography::Algorithms::Tensor_Prob> >; Type = MR::Thread::{anonymous}::__Batch<MR::DWI::Tractography::Tracking::GeneratedTrack>; Sink = MR::DWI::Tractography::Tracking::WriteKernel&; size_t = unsigned int]
src/dwi/tractography/tracking/exec.h:66:122:   required from static void MR::DWI::Tractography::Tracking::Exec<Method>::run(const string&, const string&, MR::DWI::Tractography::Properties&) [with Method = MR::DWI::Tractography::Algorithms::Tensor_Prob; std::string = std::basic_string<char>]
cmd/tckgen.cpp:205:26:   required from here
src/dwi/tractography/tracking/exec.h:194:21: error: Eigen::Vector3f has no member named allFinite

What should I do?

ThijsDhollander · April 25, 2016, 6:10am

I’m not 100% sure, but it looks like your version of the Eigen library is probably a quite old one… The errors that you’re getting are definitely about a member from an Eigen Class missing; which I guess might be due to an outdated version.

So I’d say: try and update your version of the Eigen library, and try ./configure and ./build again after that.

rsmith · April 25, 2016, 6:27am

Yep. Don’t let the length fool you, there’s actually only a grand total of two unique errors:

error: Eigen::Vector3f has no member named allFinite
error: class Eigen::SelfAdjointEigenSolver has no member named computeDirect

That distribution is 4 years old, and I’m guessing the Eigen version you’ve installed is a snapshot of Eigen at that point in time. Grabbing the latest version of Eigen should fix it.

Though it may be necessary to uninstall it through your package manager, download the latest version manually, and manually point the MRtrix3 configure script to the location of the manual install using the EIGEN_CFLAGS environment variable (the configure script should provide instructions if it is unable to find Eigen).

jdtournier · April 25, 2016, 7:43am

I just came across that exact same issue just a few days ago. Grabbing a fresh version of Eigen fixed it for me. Make sure you don’t use their current master branch, grab the latest release snapshot - otherwise you’ll get other types of errors (I’ll have to look into that when I have a minute, I’m hoping it’s a temporary glitch in Eigen’s development branch).

In more detail:

download the latest release version of Eigen
put the file in your MRtrix3 folder
extract it in place:
```
  $ tar xvzf eigen-eigen-*.tar.gz
```
run configure with the right flags to tell it where to find your local Eigen installation:
```
 $ EIGEN_CFLAGS="-isystem \"$(pwd)/eigen-eigen-07105f7124f9\"" ./configure
```
Note that you may need to amend the location for Eigen, although the line above should work as-is…
assuming that step works, try building again:
```
 $ ./build
```

johnsmith · April 28, 2016, 12:35am

Thanks for all the replies. I tried again - how can I fix the new errors?

fred@fred:~/mrtrix3$ export CXX=/usr/bin/g++-4.8fred@fred:~/mrtrix3$ ./configure 

MRtrix build type requested: release

Detecting OS: linux
Checking for C++11 compliant compiler [/usr/bin/g++-4.8]: 4.8 - tested ok
Detecting pointer size: 32 bit
Detecting byte order: little-endian
Checking for variable-length array support: yes
Checking for non-POD variable-length array support: yes
Checking for zlib compression library: 1.2.3.4
checking for Eigen 3 library: 3.2.8
Checking shared library generation: yes
Checking for Qt moc: moc (version 4.8.1)
Checking for Qt qmake: qmake (version 4.8.1)
Checking for Qt rcc: rcc (version 4.8.1)
Checking for Qt: 4.8.1

writing configuration to file './release/config': ok

fred@fred:~/mrtrix3$ ./build 
(  1/412) [CC] release/cmd/tckgen.o
(  2/412) [CC] release/cmd/dirmerge.o
(  3/412) [CC] release/lib/formats/pipe.o
(  4/412) [CC] release/src/dwi/tractography/mapping/gaussian/mapper.o
(  5/412) [CC] release/src/dwi/tractography/seeding/gmwmi.o
(  6/412) [CC] release/src/gui/opengl/shader.o
(  7/412) [CC] release/cmd/tsfdivide.o
(  8/412) [CC] release/cmd/mesh2pve.o
(  9/412) [CC] release/cmd/meshfilter.o
( 10/412) [CC] release/src/gui/opengl/gl_core_3_3.o
( 11/412) [CC] release/src/gui/mrview/tool/connectome/file_data_vector.o
( 12/412) [MOC] release/src/gui/mrview/tool/tractography/tractogram_moc.cpp
( 13/412) [CC] release/src/dwi/directions/mask.o
( 14/412) [CC] release/cmd/tcknormalise.o
( 15/412) [CC] release/lib/adapter/reslice.o
( 16/412) [CC] release/src/gui/mrview/tool/connectome/selection.o
( 17/412) [CC] release/src/dwi/tractography/GT/externalenergy.o
( 18/412) [CC] release/cmd/fod2dec.o
( 19/412) [CC] release/lib/image_io/base.o
( 20/412) [CC] release/cmd/tsfinfo.o
( 21/412) [CC] release/lib/exception.o
( 22/412) [CC] release/src/dwi/tractography/mapping/mapping.o
( 23/412) [CC] release/lib/image_io/sparse.o
( 24/412) [CC] release/cmd/mrmesh.o
( 25/412) [MOC] release/src/gui/mrview/spin_box_moc.cpp
( 26/412) [MOC] release/src/gui/mrview/tool/view_moc.cpp
( 27/412) [CC] release/src/gui/mrview/tool/connectome/connectome.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -pipe -O2 -Wall -W -D_REENTRANT -DQT_WEBKIT -DQT_NO_DEBUG -DQT_SVG_LIB -DQT_OPENGL_LIB -DQT_GUI_LIB -DQT_CORE_LIB -DQT_SHARED -isystem /usr/share/qt4/mkspecs/linux-g++ -isystem /usr/include/qt4/QtCore -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtOpenGL -isystem /usr/include/qt4/QtSvg -isystem /usr/include/qt4 -isystem /usr/X11R6/include src/gui/mrview/tool/connectome/connectome.cpp -o release/src/gui/mrview/tool/connectome/connectome.o:

src/gui/mrview/tool/connectome/connectome.cpp: In member function bool MR::GUI::MRView::Tool::Connectome::import_vector_file(MR::GUI::MRView::Tool::FileDataVector&, const string&):
src/gui/mrview/tool/connectome/connectome.cpp:2758:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (data.size() != num_nodes()) {
                                          ^


( 28/412) [MOC] release/src/gui/lighting_dock_moc.cpp
( 29/412) [CC] release/lib/mrtrix.o
( 30/412) [CC] release/cmd/dwi2tensor.o
( 31/412) [CC] release/src/connectome/connectome.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 src/connectome/connectome.cpp -o release/src/connectome/connectome.o:

src/connectome/connectome.cpp: In function void MR::Connectome::verify_matrix(MR::Connectome::matrix_type&, MR::Connectome::node_t):
src/connectome/connectome.cpp:32:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if (in.rows() != num_nodes)
                    ^


( 32/412) [CC] release/cmd/mrcalc.o
( 33/412) [CC] release/lib/file/dicom/image.o
( 34/412) [CC] release/cmd/mrpad.o
( 35/412) [CC] release/cmd/fixeldivide.o
( 36/412) [CC] release/lib/formats/mrtrix_utils.o
( 37/412) [CC] release/src/gui/mrview/mode/base.o
( 38/412) [CC] release/src/dwi/tractography/properties.o
( 39/412) [MOC] release/src/gui/mrview/colourmap_button_moc.cpp
( 40/412) [CC] release/src/gui/opengl/font.o
( 41/412) [CC] release/cmd/tck2connectome.o
( 42/412) [CC] release/src/gui/lighting_dock.o
( 43/412) [CC] release/src/dwi/tractography/mapping/writer.o
( 44/412) [CC] release/src/dwi/tractography/rng.o
( 45/412) [CC] release/src/gui/dialog/opengl.o
( 46/412) [CC] release/src/gui/gui.o
( 47/412) [CC] release/src/gui/dwi/render_frame.o
( 48/412) [CC] release/lib/formats/analyse.o
( 49/412) [CC] release/src/gui/mrview/tool/fixel.o
( 50/412) [CC] release/src/gui/dialog/dicom.o
( 51/412) [CC] release/cmd/tcksample.o
( 52/412) [MOC] release/src/gui/mrview/combo_box_error_moc.cpp
( 53/412) [CC] release/src/dwi/tractography/seeding/dynamic.o
( 54/412) [CC] release/src/gui/mrview/tool/screen_capture.o
( 55/412) [CC] release/src/gui/mrview/tool/connectome/colourmap_observers.o
( 56/412) [CC] release/src/gui/mrview/mode/ortho.o
( 57/412) [CC] release/cmd/mrthreshold.o
( 58/412) [CC] release/lib/file/dicom/dict.o
( 59/412) [CC] release/src/dwi/tractography/mapping/mapper_plugins.o
( 60/412) [CC] release/src/gui/mrview/tool/view_moc.o
( 61/412) [CC] release/cmd/5tt2vis.o
( 62/412) [CC] release/src/gui/mrview/tool/base.o
( 63/412) [CC] release/lib/formats/list.o
( 64/412) [CC] release/lib/image_io/pipe.o
( 65/412) [CC] release/cmd/afdconnectivity.o
( 66/412) [CC] release/src/gui/mrview/tool/roi_editor/model.o
( 67/412) [CC] release/src/gui/shview/render_window.o
( 68/412) [CC] release/src/dwi/tractography/SIFT/track_contribution.o
( 69/412) [CC] release/src/dwi/directions/set.o
( 70/412) [CC] release/src/gui/dialog/report_exception.o
( 71/412) [CC] release/src/dwi/fmls.o
( 72/412) [CC] release/cmd/dcminfo.o
( 73/412) [CC] release/src/dwi/sdeconv/constrained.o
( 74/412) [CC] release/cmd/meshconvert.o
( 75/412) [CC] release/src/gui/mrview/tool/connectome/edge.o
( 76/412) [CC] release/cmd/dwi2mask.o
( 77/412) [CC] release/cmd/mrfilter.o
( 78/412) [CC] release/src/dwi/tractography/SIFT/gradient_sort.o
( 79/412) [CC] release/lib/formats/mri.o
( 80/412) [MOC] release/src/gui/mrview/tool/odf/preview_moc.cpp
( 81/412) [CC] release/src/gui/mrview/tool/tractography/tractogram_moc.o
( 82/412) [CC] release/src/gui/mrview/combo_box_error_moc.o
( 83/412) [MOC] release/src/gui/mrview/tool/roi_editor/roi_moc.cpp
( 84/412) [CC] release/lib/file/dicom/tree.o
( 85/412) [CC] release/src/dwi/tractography/ACT/gmwmi.o
( 86/412) [CC] release/src/gui/dialog/progress.o
( 87/412) [CC] release/src/gui/shapes/sphere.o
( 88/412) [CC] release/cmd/tsfmult.o
( 89/412) [CC] release/src/gui/mrview/tool/vector.o
( 90/412) [CC] release/src/gui/mrview/tool/tractography/track_scalar_file.o
( 91/412) [CC] release/lib/formats/mrtrix.o
( 92/412) [CC] release/src/gui/dwi/renderer.o
( 93/412) [CC] release/lib/image_io/scratch.o
( 94/412) [MOC] release/src/gui/mrview/tool/connectome/node_list_moc.cpp
( 95/412) [CC] release/src/gui/mrview/tool/connectome/node_list_moc.o
( 96/412) [CC] release/cmd/labelconfig.o
( 97/412) [CC] release/src/dwi/tractography/tracking/write_kernel.o
( 98/412) [CC] release/lib/formats/ram.o
( 99/412) [CC] release/src/gui/mrview/mode/volume.o
(100/412) [CC] release/src/dwi/tractography/resample.o
(101/412) [CC] release/cmd/sh2response.o
(102/412) [CC] release/src/connectome/mat2vec.o
(103/412) [CC] release/lib/formats/nifti1.o
(104/412) [CC] release/lib/file/key_value.o
(105/412) [CC] release/src/gui/mrview/tool/connectome/matrix_list.o
(106/412) [MOC] release/src/gui/mrview/tool/odf/odf_moc.cpp
(107/412) [CC] release/cmd/warpcorrect.o
(108/412) [CC] release/src/dwi/tractography/GT/particlegrid.o
(109/412) [CC] release/cmd/tcksift.o
(110/412) [CC] release/cmd/mrtransform.o
(111/412) [CC] release/src/dwi/tractography/SIFT/track_index_range.o
(112/412) [CC] release/cmd/dwiextract.o
(113/412) [CC] release/cmd/mrcat.o
(114/412) [CC] release/cmd/warpinit.o
(115/412) [CC] release/src/dwi/tractography/SIFT2/tckfactor.o
(116/412) [CC] release/lib/file/ofstream.o
(117/412) [CC] release/src/gui/mrview/colourmap_button.o
(118/412) [CC] release/src/dwi/shells.o
(119/412) [CC] release/lib/app.o
(120/412) [CC] release/cmd/mrview.o
(121/412) [MOC] release/src/gui/dwi/render_frame_moc.cpp
(122/412) [CC] release/cmd/fod2fixel.o
(123/412) [CC] release/cmd/mrinfo.o
(124/412) [CC] release/cmd/tsfthreshold.o
(125/412) [CC] release/src/gui/shapes/cube.o
(126/412) [CC] release/lib/file/dicom/mapper.o
(127/412) [CC] release/src/gui/mrview/tool/connectome/node.o
(128/412) [CC] release/src/dwi/tractography/seeding/basic.o
(129/412) [CC] release/cmd/tckmap.o
(130/412) [CC] release/src/gui/mrview/tool/tractography/tractogram.o
(131/412) [CC] release/cmd/shview.o
(132/412) [CC] release/lib/header.o
(133/412) [CC] release/src/gui/mrview/tool/odf/item.o
(134/412) [CC] release/lib/image_io/fetch_store.o
(135/412) [MOC] release/src/gui/opengl/lighting_moc.cpp
(136/412) [CC] release/src/gui/opengl/lighting_moc.o
(137/412) [CC] release/src/dwi/tractography/connectome/matrix.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 src/dwi/tractography/connectome/matrix.cpp -o release/src/dwi/tractography/connectome/matrix.o:

src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::scale_by_streamline_count():
src/dwi/tractography/connectome/matrix.cpp:111:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (node_t i = 0; i != counts.rows(); ++i) {
                                       ^
src/dwi/tractography/connectome/matrix.cpp:112:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t j = i; j != counts.cols(); ++j) {
                                         ^
src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::remove_unassigned():
src/dwi/tractography/connectome/matrix.cpp:126:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t i = 0; i != data.cols() - 1; ++i) {
                                           ^
src/dwi/tractography/connectome/matrix.cpp:133:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t i = 0; i != data.rows() - 1; ++i) {
                                           ^
src/dwi/tractography/connectome/matrix.cpp:134:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (node_t j = i; j != data.cols() - 1; ++j) {
                                             ^
src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::zero_diagonal():
src/dwi/tractography/connectome/matrix.cpp:149:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (node_t i = 0; i != data.rows(); ++i)
                                     ^
src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::error_check(const std::set<unsigned int>&):
src/dwi/tractography/connectome/matrix.cpp:158:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (node_t i = 0; i != counts.rows(); ++i) {
                                       ^
src/dwi/tractography/connectome/matrix.cpp:159:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t j = i; j != counts.cols(); ++j) {
                                         ^


(138/412) [CC] release/src/dwi/tractography/seeding/list.o
(139/412) [CC] release/lib/bitset.o
(140/412) [CC] release/src/dwi/tractography/GT/internalenergy.o
(141/412) [CC] release/lib/file/dicom/quick_scan.o
(142/412) [CC] release/cmd/dcmedit.o
(143/412) [CC] release/cmd/shbasis.o
(144/412) [CC] release/src/gui/lighting_dock_moc.o
(145/412) [CC] release/cmd/sh2power.o
(146/412) [MOC] release/src/gui/shview/render_window_moc.cpp
(147/412) [CC] release/src/gui/shview/render_window_moc.o
(148/412) [MOC] release/src/gui/mrview/tool/screen_capture_moc.cpp
(149/412) [CC] release/src/dwi/tractography/connectome/exemplar.o
(150/412) [CC] release/src/gui/cursor.o
(151/412) [CC] release/src/mesh/mesh.o
(152/412) [CC] release/cmd/tsfsmooth.o
(153/412) [CC] release/src/dwi/tractography/file_base.o
(154/412) [RCC] src/gui/mrview/icons.cpp
(155/412) [CC] release/src/gui/mrview/icons.o
(156/412) [MOC] release/src/gui/mrview/tool/connectome/connectome_moc.cpp
(157/412) [CC] release/src/gui/mrview/tool/connectome/connectome_moc.o
(158/412) [CC] release/src/dwi/tractography/SIFT2/reg_calculator.o
(159/412) [CC] release/cmd/shconv.o
(160/412) [CC] release/lib/formats/dicom.o
(161/412) [MOC] release/src/gui/dialog/image_properties_moc.cpp
(162/412) [CC] release/src/gui/mrview/adjust_button.o
(163/412) [CC] release/src/dwi/tractography/SIFT/sifter.o
(164/412) [CC] release/cmd/fixel2sh.o
(165/412) [CC] release/src/gui/projection.o
(166/412) [CC] release/cmd/msdwi2fod.o
(167/412) [CC] release/lib/stride.o
(168/412) [CC] release/cmd/dwinormalise.o
(169/412) [CC] release/cmd/mrmath.o
ERROR: (169/412) [CC] release/cmd/mrmath.o

ERROR: (169/412) [CC] release/cmd/mrmath.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 cmd/mrmath.cpp -o release/cmd/mrmath.o

failed with output

g++-4.8: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-4.8/README.Bugs> for instructions.

Dave · April 28, 2016, 12:57am

Hi John,
What are the specs of the system you are building on? It’s possible you are running out of RAM during the build.

You might want to monitor your RAM usage during the build to see.

If this is an issue, you could try to restrict the number of processors used during the build by setting the number of processors to 1.

@jdtournier, we may want to add this in as a build script option again. I needed to use it the other day too, but saw it had been removed.

Cheers,
Dave

johnsmith · April 28, 2016, 4:12am

I was building on 0.75 GB RAM. I increased it to 1.5 GB RAM. Thanks so much, everyone!

...
( 32/412) [CC] release/cmd/mrcalc.o
( 33/412) [CC] release/lib/file/dicom/image.o
( 34/412) [CC] release/cmd/mrpad.o
( 35/412) [CC] release/cmd/fixeldivide.o
( 36/412) [CC] release/lib/formats/mrtrix_utils.o
( 37/412) [CC] release/src/gui/mrview/mode/base.o
( 38/412) [CC] release/src/dwi/tractography/properties.o
( 39/412) [MOC] release/src/gui/mrview/colourmap_button_moc.cpp
( 40/412) [CC] release/src/gui/opengl/font.o
( 41/412) [CC] release/cmd/tck2connectome.o
( 42/412) [CC] release/src/gui/lighting_dock.o
( 43/412) [CC] release/src/dwi/tractography/mapping/writer.o
( 44/412) [CC] release/src/dwi/tractography/rng.o
( 45/412) [CC] release/src/gui/dialog/opengl.o
( 46/412) [CC] release/src/gui/gui.o
( 47/412) [CC] release/src/gui/dwi/render_frame.o
( 48/412) [CC] release/lib/formats/analyse.o
( 49/412) [CC] release/src/gui/mrview/tool/fixel.o
( 50/412) [CC] release/src/gui/dialog/dicom.o
( 51/412) [CC] release/cmd/tcksample.o
( 52/412) [MOC] release/src/gui/mrview/combo_box_error_moc.cpp
( 53/412) [CC] release/src/dwi/tractography/seeding/dynamic.o
( 54/412) [CC] release/src/gui/mrview/tool/screen_capture.o
( 55/412) [CC] release/src/gui/mrview/tool/connectome/colourmap_observers.o
( 56/412) [CC] release/src/gui/mrview/mode/ortho.o
( 57/412) [CC] release/cmd/mrthreshold.o
( 58/412) [CC] release/lib/file/dicom/dict.o
( 59/412) [CC] release/src/dwi/tractography/mapping/mapper_plugins.o
( 60/412) [CC] release/src/gui/mrview/tool/view_moc.o
( 61/412) [CC] release/cmd/5tt2vis.o
( 62/412) [CC] release/src/gui/mrview/tool/base.o
( 63/412) [CC] release/lib/formats/list.o
( 64/412) [CC] release/lib/image_io/pipe.o
( 65/412) [CC] release/cmd/afdconnectivity.o
( 66/412) [CC] release/src/gui/mrview/tool/roi_editor/model.o
( 67/412) [CC] release/src/gui/shview/render_window.o
( 68/412) [CC] release/src/dwi/tractography/SIFT/track_contribution.o
( 69/412) [CC] release/src/dwi/directions/set.o
( 70/412) [CC] release/src/gui/dialog/report_exception.o
( 71/412) [CC] release/src/dwi/fmls.o
( 72/412) [CC] release/cmd/dcminfo.o
( 73/412) [CC] release/src/dwi/sdeconv/constrained.o
( 74/412) [CC] release/cmd/meshconvert.o
( 75/412) [CC] release/src/gui/mrview/tool/connectome/edge.o
( 76/412) [CC] release/cmd/dwi2mask.o
( 77/412) [CC] release/cmd/mrfilter.o
( 78/412) [CC] release/src/dwi/tractography/SIFT/gradient_sort.o
( 79/412) [CC] release/lib/formats/mri.o
( 80/412) [MOC] release/src/gui/mrview/tool/odf/preview_moc.cpp
( 81/412) [CC] release/src/gui/mrview/tool/tractography/tractogram_moc.o
( 82/412) [CC] release/src/gui/mrview/combo_box_error_moc.o
( 83/412) [MOC] release/src/gui/mrview/tool/roi_editor/roi_moc.cpp
( 84/412) [CC] release/lib/file/dicom/tree.o
( 85/412) [CC] release/src/dwi/tractography/ACT/gmwmi.o
( 86/412) [CC] release/src/gui/dialog/progress.o
( 87/412) [CC] release/src/gui/shapes/sphere.o
( 88/412) [CC] release/cmd/tsfmult.o
( 89/412) [CC] release/src/gui/mrview/tool/vector.o
( 90/412) [CC] release/src/gui/mrview/tool/tractography/track_scalar_file.o
( 91/412) [CC] release/lib/formats/mrtrix.o
( 92/412) [CC] release/src/gui/dwi/renderer.o
( 93/412) [CC] release/lib/image_io/scratch.o
( 94/412) [MOC] release/src/gui/mrview/tool/connectome/node_list_moc.cpp
( 95/412) [CC] release/src/gui/mrview/tool/connectome/node_list_moc.o
( 96/412) [CC] release/cmd/labelconfig.o
( 97/412) [CC] release/src/dwi/tractography/tracking/write_kernel.o
( 98/412) [CC] release/lib/formats/ram.o
( 99/412) [CC] release/src/gui/mrview/mode/volume.o
(100/412) [CC] release/src/dwi/tractography/resample.o
(101/412) [CC] release/cmd/sh2response.o
(102/412) [CC] release/src/connectome/mat2vec.o
(103/412) [CC] release/lib/formats/nifti1.o
(104/412) [CC] release/lib/file/key_value.o
(105/412) [CC] release/src/gui/mrview/tool/connectome/matrix_list.o
(106/412) [MOC] release/src/gui/mrview/tool/odf/odf_moc.cpp
(107/412) [CC] release/cmd/warpcorrect.o
(108/412) [CC] release/src/dwi/tractography/GT/particlegrid.o
(109/412) [CC] release/cmd/tcksift.o
(110/412) [CC] release/cmd/mrtransform.o
(111/412) [CC] release/src/dwi/tractography/SIFT/track_index_range.o
(112/412) [CC] release/cmd/dwiextract.o
(113/412) [CC] release/cmd/mrcat.o
(114/412) [CC] release/cmd/warpinit.o
(115/412) [CC] release/src/dwi/tractography/SIFT2/tckfactor.o
(116/412) [CC] release/lib/file/ofstream.o
(117/412) [CC] release/src/gui/mrview/colourmap_button.o
(118/412) [CC] release/src/dwi/shells.o
(119/412) [CC] release/lib/app.o
(120/412) [CC] release/cmd/mrview.o
(121/412) [MOC] release/src/gui/dwi/render_frame_moc.cpp
(122/412) [CC] release/cmd/fod2fixel.o
(123/412) [CC] release/cmd/mrinfo.o
(124/412) [CC] release/cmd/tsfthreshold.o
(125/412) [CC] release/src/gui/shapes/cube.o
(126/412) [CC] release/lib/file/dicom/mapper.o
(127/412) [CC] release/src/gui/mrview/tool/connectome/node.o
(128/412) [CC] release/src/dwi/tractography/seeding/basic.o
(129/412) [CC] release/cmd/tckmap.o
(130/412) [CC] release/src/gui/mrview/tool/tractography/tractogram.o
(131/412) [CC] release/cmd/shview.o
(132/412) [CC] release/lib/header.o
(133/412) [CC] release/src/gui/mrview/tool/odf/item.o
(134/412) [CC] release/lib/image_io/fetch_store.o
(135/412) [MOC] release/src/gui/opengl/lighting_moc.cpp
(136/412) [CC] release/src/gui/opengl/lighting_moc.o
(137/412) [CC] release/src/dwi/tractography/connectome/matrix.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 src/dwi/tractography/connectome/matrix.cpp -o release/src/dwi/tractography/connectome/matrix.o:

src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::scale_by_streamline_count():
src/dwi/tractography/connectome/matrix.cpp:111:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (node_t i = 0; i != counts.rows(); ++i) {
                                       ^
src/dwi/tractography/connectome/matrix.cpp:112:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t j = i; j != counts.cols(); ++j) {
                                         ^
src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::remove_unassigned():
src/dwi/tractography/connectome/matrix.cpp:126:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t i = 0; i != data.cols() - 1; ++i) {
                                           ^
src/dwi/tractography/connectome/matrix.cpp:133:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t i = 0; i != data.rows() - 1; ++i) {
                                           ^
src/dwi/tractography/connectome/matrix.cpp:134:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (node_t j = i; j != data.cols() - 1; ++j) {
                                             ^
src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::zero_diagonal():
src/dwi/tractography/connectome/matrix.cpp:149:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (node_t i = 0; i != data.rows(); ++i)
                                     ^
src/dwi/tractography/connectome/matrix.cpp: In member function void MR::DWI::Tractography::Connectome::Matrix::error_check(const std::set<unsigned int>&):
src/dwi/tractography/connectome/matrix.cpp:158:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (node_t i = 0; i != counts.rows(); ++i) {
                                       ^
src/dwi/tractography/connectome/matrix.cpp:159:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (node_t j = i; j != counts.cols(); ++j) {
                                         ^


(138/412) [CC] release/src/dwi/tractography/seeding/list.o
(139/412) [CC] release/lib/bitset.o
(140/412) [CC] release/src/dwi/tractography/GT/internalenergy.o
(141/412) [CC] release/lib/file/dicom/quick_scan.o
(142/412) [CC] release/cmd/dcmedit.o
(143/412) [CC] release/cmd/shbasis.o
(144/412) [CC] release/src/gui/lighting_dock_moc.o
(145/412) [CC] release/cmd/sh2power.o
(146/412) [MOC] release/src/gui/shview/render_window_moc.cpp
(147/412) [CC] release/src/gui/shview/render_window_moc.o
(148/412) [MOC] release/src/gui/mrview/tool/screen_capture_moc.cpp
(149/412) [CC] release/src/dwi/tractography/connectome/exemplar.o
(150/412) [CC] release/src/gui/cursor.o
(151/412) [CC] release/src/mesh/mesh.o
(152/412) [CC] release/cmd/tsfsmooth.o
(153/412) [CC] release/src/dwi/tractography/file_base.o
(154/412) [RCC] src/gui/mrview/icons.cpp
(155/412) [CC] release/src/gui/mrview/icons.o
(156/412) [MOC] release/src/gui/mrview/tool/connectome/connectome_moc.cpp
(157/412) [CC] release/src/gui/mrview/tool/connectome/connectome_moc.o
(158/412) [CC] release/src/dwi/tractography/SIFT2/reg_calculator.o
(159/412) [CC] release/cmd/shconv.o
(160/412) [CC] release/lib/formats/dicom.o
(161/412) [MOC] release/src/gui/dialog/image_properties_moc.cpp
(162/412) [CC] release/src/gui/mrview/adjust_button.o
(163/412) [CC] release/src/dwi/tractography/SIFT/sifter.o
(164/412) [CC] release/cmd/fixel2sh.o
(165/412) [CC] release/src/gui/projection.o
(166/412) [CC] release/cmd/msdwi2fod.o
(167/412) [CC] release/lib/stride.o
(168/412) [CC] release/cmd/dwinormalise.o
(169/412) [CC] release/cmd/mrmath.o
(170/412) [CC] release/src/dwi/tractography/mapping/twi_stats.o
(171/412) [MOC] release/src/gui/mrview/tool/tractography/track_scalar_file_moc.cpp
(172/412) [CC] release/cmd/dirgen.o
(173/412) [CC] release/cmd/peaks2amp.o
(174/412) [CC] release/src/connectome/config/config.o
(175/412) [CC] release/cmd/tckedit.o
(176/412) [CC] release/src/gui/mrview/tool/odf/preview.o
(177/412) [CC] release/cmd/mrstats.o
(178/412) [CC] release/src/gui/shapes/cylinder.o
(179/412) [CC] release/cmd/dirsplit.o
(180/412) [CC] release/lib/math/bessel.o
(181/412) [MOC] release/src/gui/color_button_moc.cpp
(182/412) [CC] release/src/gui/color_button_moc.o
(183/412) [CC] release/src/dwi/tractography/SIFT2/streamline_stats.o
(184/412) [CC] release/cmd/dirflip.o
(185/412) [CC] release/src/dwi/tractography/tracking/tractography.o
(186/412) [CC] release/cmd/tckglobal.o
(187/412) [CC] release/lib/stats.o
(188/412) [MOC] release/src/gui/mrview/adjust_button_moc.cpp
(189/412) [CC] release/src/gui/mrview/adjust_button_moc.o
(190/412) [CC] release/src/dwi/tractography/roi.o
(191/412) [CC] release/src/gui/mrview/tool/overlay.o
(192/412) [CC] release/src/dwi/tractography/GT/particle.o
(193/412) [CC] release/cmd/label2mesh.o
(194/412) [CC] release/src/gui/mrview/tool/odf/odf_moc.o
(195/412) [CC] release/lib/image_io/gz.o
(196/412) [CC] release/src/gui/dialog/image_properties_moc.o
(197/412) [CC] release/src/gui/mrview/tool/roi_editor/roi.o
(198/412) [CC] release/src/gui/mrview/spin_box_moc.o
(199/412) [CC] release/cmd/fixelcfestats.o
(200/412) [CC] release/src/gui/mrview/tool/connectome/shaders.o
(201/412) [CC] release/src/dwi/tractography/SIFT/sift.o
(202/412) [MOC] release/src/gui/mrview/tool/vector_moc.cpp
(203/412) [CC] release/src/gui/mrview/tool/vector_moc.o
(204/412) [CC] release/cmd/sh2peaks.o
(205/412) [CC] release/src/dwi/tractography/seeding/seeding.o
(206/412) [CC] release/lib/formats/mrtrix_gz.o
(207/412) [MOC] release/src/gui/mrview/tool/overlay_moc.cpp
(208/412) [CC] release/src/gui/mrview/tool/overlay_moc.o
(209/412) [CC] release/src/gui/mrview/tool/odf/model.o
(210/412) [CC] release/lib/formats/nifti1_gz.o
(211/412) [CC] release/src/gui/mrview/window.o
(212/412) [CC] release/lib/file/config.o
(213/412) [CC] release/src/gui/mrview/tool/tractography/track_scalar_file_moc.o
(214/412) [CC] release/src/dwi/tractography/connectome/extract.o
(215/412) [MOC] release/src/gui/mrview/displayable_moc.cpp
(216/412) [CC] release/src/gui/mrview/displayable_moc.o
(217/412) [MOC] release/src/gui/mrview/mode/ortho_moc.cpp
(218/412) [CC] release/cmd/transformcalc.o
(219/412) [CC] release/src/gui/mrview/tool/roi_editor/roi_moc.o
(220/412) [CC] release/cmd/dwi2adc.o
(221/412) [CC] release/src/gui/mrview/volume.o
(222/412) [CC] release/src/gui/dwi/render_frame_moc.o
(223/412) [CC] release/src/gui/mrview/tool/roi_editor/item.o
(224/412) [CC] release/src/dwi/gradient.o
(225/412) [CC] release/src/gui/mrview/displayable.o
(226/412) [CC] release/src/dwi/tractography/ACT/act.o
(227/412) [CC] release/src/dwi/tractography/mapping/mapper.o
(228/412) [CC] release/lib/image_io/ram.o
(229/412) [CC] release/lib/file/dicom/select_cmdline.o
(230/412) [CC] release/lib/formats/mgz.o
(231/412) [CC] release/cmd/fixelcorrespondence.o
(232/412) [CC] release/src/gui/mrview/colourmap_button_moc.o
(233/412) [CC] release/lib/image_io/mosaic.o
(234/412) [RCC] src/gui/shview/icons.cpp
(235/412) [CC] release/src/gui/shview/icons.o
(236/412) [CC] release/cmd/fixelthreshold.o
(237/412) [CC] release/cmd/mrresize.o
(238/412) [CC] release/src/gui/mrview/mode/ortho_moc.o
(239/412) [CC] release/src/gui/dialog/image_properties.o
(240/412) [CC] release/src/gui/mrview/tool/tractography/tractography.o
(241/412) [CC] release/lib/file/dicom/patient.o
(242/412) [CC] release/cmd/dwi2noise.o
(243/412) [CC] release/src/dwi/directions/predefined.o
(244/412) [CC] release/cmd/dwi2fod.o
(245/412) [CC] release/lib/file/dicom/study.o
(246/412) [CC] release/src/dwi/tractography/editing/worker.o
(247/412) [CC] release/src/dwi/tractography/editing/receiver.o
(248/412) [CC] release/cmd/5tt2gmwmi.o
(249/412) [CC] release/cmd/tcksift2.o
(250/412) [CC] release/src/gui/color_button.o
(251/412) [CC] release/cmd/mrconvert.o
(252/412) [CC] release/lib/file/name_parser.o
(253/412) [CC] release/cmd/amp2sh.o
(254/412) [CC] release/src/dwi/tractography/SIFT2/coeff_optimiser.o
(255/412) [CC] release/cmd/tckinfo.o
(256/412) [CC] release/src/connectome/lut.o
(257/412) [CC] release/src/gui/mrview/tool/connectome/node_overlay.o
(258/412) [CC] release/src/gui/mrview/tool/odf/preview_moc.o
(259/412) [CC] release/cmd/mrclusterstats.o
(260/412) [CC] release/src/gui/mrview/mode/slice.o
(261/412) [CC] release/lib/thread.o
(262/412) [CC] release/lib/formats/mrtrix_sparse.o
(263/412) [CC] release/src/dwi/tractography/SIFT/proc_mask.o
(264/412) [CC] release/src/gui/mrview/tool/view.o
(265/412) [CC] release/src/gui/mrview/mode/lightbox.o
(266/412) [CC] release/cmd/5ttedit.o
(267/412) [CC] release/src/gui/shapes/halfsphere.o
(268/412) [CC] release/src/dwi/tractography/connectome/tck2nodes.o
(269/412) [CC] release/src/dwi/tractography/mapping/voxel.o
(270/412) [CC] release/src/gui/mrview/tool/odf/odf.o
(271/412) [CC] release/cmd/fixelstats.o
(272/412) [CC] release/cmd/fixel2tsf.o
(273/412) [CC] release/lib/formats/mgh.o
(274/412) [MOC] release/src/gui/gui_moc.cpp
(275/412) [CC] release/src/gui/gui_moc.o
(276/412) [CC] release/lib/image_io/default.o
(277/412) [CC] release/cmd/tckstats.o
(278/412) [CC] release/src/dwi/tractography/SIFT2/line_search.o
(279/412) [CC] release/lib/datatype.o
(280/412) [CC] release/src/dwi/tractography/SIFT2/fixel_updater.o
(281/412) [CC] release/src/gui/mrview/gui_image.o
(282/412) [CC] release/lib/file/dicom/element.o
(283/412) [CC] release/src/gui/mrview/tool/screen_capture_moc.o
(284/412) [CC] release/cmd/voxel2fixel.o
(285/412) [CC] release/src/gui/dialog/list.o
(286/412) [CC] release/src/gui/dialog/file.o
(287/412) [CC] release/src/gui/mrview/combo_box_error.o
(288/412) [MOC] release/src/gui/mrview/mode/lightbox_moc.cpp
(289/412) [CC] release/src/gui/mrview/mode/lightbox_moc.o
(290/412) [CC] release/lib/file/dicom/series.o
(291/412) [CC] release/lib/file/mgh_utils.o
(292/412) [CC] release/src/gui/mrview/tool/connectome/node_list.o
(293/412) [CC] release/src/dwi/tractography/editing/editing.o
(294/412) [CC] release/cmd/tckconvert.o
(295/412) [CC] release/cmd/mrcrop.o
(296/412) [CC] release/src/dwi/tractography/mapping/fixel_td_map.o
(297/412) [CC] release/lib/version.o
(298/412) [CC] release/cmd/label2colour.o
(299/412) [CC] release/cmd/connectome2tck.o
(300/412) [CC] release/src/dwi/tractography/GT/mhsampler.o
(301/412) [CC] release/cmd/maskfilter.o
(302/412) [CC] release/lib/progressbar.o
(303/412) [CC] release/src/dwi/tractography/GT/gt.o
(304/412) [CC] release/lib/math/SH.o
(305/412) [CC] release/cmd/tensor2metric.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 cmd/tensor2metric.cpp -o release/cmd/tensor2metric.o:

In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h: In member function void Processor::operator()(MR::Image<float>&):
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +24) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +24) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +40) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +40) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +64) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +64) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +48) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +48) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +32) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +32) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: es may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: es was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +56) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +56) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +16) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +16) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/fred/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +8) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +8) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^


(306/412) [CC] release/lib/formats/xds.o
(307/412) [CC] release/cmd/fixel2voxel.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 cmd/fixel2voxel.cpp -o release/cmd/fixel2voxel.o:

cmd/fixel2voxel.cpp: In member function virtual bool SplitSize::operator()(OpBase::in_type&, OpBase::out_type&):
cmd/fixel2voxel.cpp:576:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (out.index(3) < in.value().size())
                                            ^
cmd/fixel2voxel.cpp: In member function virtual bool SplitValue::operator()(OpBase::in_type&, OpBase::out_type&):
cmd/fixel2voxel.cpp:599:44: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (out.index(3) < in.value().size())
                                            ^


(308/412) [CC] release/lib/file/mmap.o

/usr/bin/g++-4.8 -c -std=c++11 -pthread -fPIC -march=native -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/fred/mrtrix3/eigen-eigen-07105f7124f9 lib/file/mmap.cpp -o release/lib/file/mmap.o:

lib/file/mmap.cpp: In constructor MR::File::MMap::MMap(const MR::File::Entry&, bool, bool, int64_t):
lib/file/mmap.cpp:113:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (fsbuf.f_type == 0xff534d42 /* CIFS */|| fsbuf.f_type == 0x6969 /* NFS */ || 
                             ^


(309/412) [CC] release/src/gui/opengl/lighting.o
(310/412) [MOC] release/src/gui/mrview/window_moc.cpp
(311/412) [CC] release/src/gui/mrview/window_moc.o
(312/412) [MOC] release/src/gui/mrview/tool/connectome/selection_moc.cpp
(313/412) [CC] release/src/gui/mrview/tool/connectome/selection_moc.o
(314/412) [CC] release/lib/file/nifti1_utils.o
(315/412) [LD] release/lib/libmrtrix-0.3.14.so
(316/412) [LB] release/bin/tsfmult
(317/412) [LB] release/bin/tcksample
(318/412) [LB] release/bin/dcminfo
(319/412) [LB] release/bin/fod2dec
(320/412) [LB] release/bin/fixelstats
(321/412) [LB] release/bin/meshfilter
(322/412) [LB] release/bin/mrconvert
(323/412) [LB] release/bin/label2mesh
(324/412) [LB] release/bin/dwi2adc
(325/412) [LB] release/bin/warpinit
(326/412) [LB] release/bin/shconv
(327/412) [LB] release/bin/fixelcorrespondence
(328/412) [LB] release/bin/mrmesh
(329/412) [LB] release/bin/tckgen
(330/412) [LB] release/bin/mrthreshold
(331/412) [LB] release/bin/sh2response
(332/412) [LB] release/bin/dwi2fod
(333/412) [LB] release/bin/fod2fixel
(334/412) [LB] release/bin/dwi2tensor
(335/412) [LB] release/bin/afdconnectivity
(336/412) [LB] release/bin/msdwi2fod
(337/412) [LB] release/bin/maskfilter
(338/412) [LB] release/bin/sh2power
(339/412) [LB] release/bin/mrtransform
(340/412) [LB] release/bin/dwinormalise
(341/412) [LB] release/bin/tensor2metric
(342/412) [LB] release/bin/transformcalc
(343/412) [LB] release/bin/tsfthreshold
(344/412) [LB] release/bin/mrfilter
(345/412) [LB] release/bin/5ttedit
(346/412) [LB] release/bin/mrpad
(347/412) [LB] release/bin/tcknormalise
(348/412) [LB] release/bin/5tt2vis
(349/412) [LB] release/bin/amp2sh
(350/412) [LB] release/bin/dwi2mask
(351/412) [LB] release/bin/dcmedit
(352/412) [LB] release/bin/tckconvert
(353/412) [LB] release/bin/fixel2voxel
(354/412) [LB] release/bin/dwi2noise
(355/412) [LB] release/bin/mrinfo
(356/412) [LB] release/bin/meshconvert
(357/412) [LB] release/bin/fixeldivide
(358/412) [LB] release/bin/label2colour
(359/412) [LB] release/bin/tsfsmooth
(360/412) [LB] release/bin/dwiextract
(361/412) [LB] release/bin/shbasis
(362/412) [LB] release/bin/mrcalc
(363/412) [LB] release/bin/tcksift2
(364/412) [LB] release/bin/peaks2amp
(365/412) [LB] release/bin/tckglobal
(366/412) [LB] release/bin/fixel2sh
(367/412) [LB] release/bin/5tt2gmwmi
(368/412) [LB] release/bin/fixel2tsf
(369/412) [LB] release/bin/fixelcfestats
(370/412) [LB] release/bin/mrresize
(371/412) [LB] release/bin/voxel2fixel
(372/412) [LB] release/bin/tckinfo
(373/412) [LB] release/bin/labelconfig
(374/412) [LB] release/bin/mrclusterstats
(375/412) [LB] release/bin/mesh2pve
(376/412) [LB] release/bin/mrcrop
(377/412) [LB] release/bin/tsfdivide
(378/412) [LB] release/bin/warpcorrect
(379/412) [LB] release/bin/mrcat
(380/412) [LB] release/bin/fixelthreshold
(381/412) [LB] release/bin/mrmath
(382/412) [LB] release/bin/sh2peaks
(383/412) [CC] release/src/gui/mrview/tool/roi_editor/undoentry.o
(384/412) [CC] release/src/gui/mrview/colourmap.o
(385/412) [CC] release/src/gui/opengl/gl.o
(386/412) [LB] release/bin/shview
(387/412) [LB] release/bin/tcksift
(388/412) [CC] release/src/dwi/tractography/connectome/connectome.o
(389/412) [MOC] release/src/gui/mrview/tool/tractography/tractography_moc.cpp
(390/412) [CC] release/src/gui/mrview/tool/tractography/tractography_moc.o
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(392/412) [CC] release/cmd/dirstat.o
(393/412) [LB] release/bin/mrstats
(394/412) [CC] release/cmd/fixelmult.o
(395/412) [LB] release/bin/fixelmult
(396/412) [LB] release/bin/tsfinfo
(397/412) [CC] release/src/dwi/directions/file.o
(398/412) [LB] release/bin/dirgen
(399/412) [LB] release/bin/dirmerge
(400/412) [LB] release/bin/dirsplit
(401/412) [LB] release/bin/dirstat
(402/412) [LB] release/bin/dirflip
(403/412) [CC] release/src/dwi/tractography/weights.o
(404/412) [LB] release/bin/tck2connectome
(405/412) [LB] release/bin/tckedit
(406/412) [LB] release/bin/connectome2tck
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(409/412) [CC] release/cmd/sh2amp.o
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jdtournier · April 28, 2016, 7:44am

I don’t think there ever was an option as such… I added the environment variable a while back to deal with building on low RAM / high core count systems, but that’s as far as it went… Not against the idea of adding this as an explicit option though.

Other possibility is to see whether we can detect out of RAM problems and dynamically reduce the thread count (pretty simple really, just leave the failing thread idle, carry on with the others). We’d just need to push the failed job back onto the todo list… Worth investigating? Maybe after ISMRM though…

egarza · July 14, 2016, 3:43pm

Thanks, got the same error and this fix helped. I just got some warnings in the build, hopefully nothing important.

g++-4.9 -c -std=c++11 -pthread -fPIC -march=native -DMRTRIX_WORD64 -I/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9 -Wall -O2 -DNDEBUG -Isrc -Icmd -I./lib -Icmd -I/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9 cmd/tensor2metric.cpp -o release/cmd/tensor2metric.o:

In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h: In member function void Processor::operator()(MR::Image<float>&):
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +8) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +8) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +24) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +24) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +40) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +40) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +56) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +56) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +16) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +16) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +32) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +32) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +48) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +48) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: *((void*)& es +64) may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: *((void*)& es +64) was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^
In file included from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Core:277:0,
                 from /home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/Geometry:4,
                 from ./lib/types.h:29,
                 from ./lib/mrtrix.h:38,
                 from ./lib/cmdline_option.h:28,
                 from ./lib/app.h:28,
                 from ./lib/command.h:22,
                 from cmd/tensor2metric.cpp:17:
/home/egarza/MRI/apps/mrtrix3/eigen-eigen-07105f7124f9/Eigen/src/Core/DenseCoeffsBase.h:495:7: warning: es may be used uninitialized in this function [-Wmaybe-uninitialized]
       derived().coeffRef(index) = other.derived().coeff(index);
       ^
cmd/tensor2metric.cpp:159:54: note: es was declared here
       Eigen::SelfAdjointEigenSolver<Eigen::Matrix3d> es;
                                                      ^


(339/442) [CC] release/src/gui/opengl/gl.o

jdtournier · July 14, 2016, 6:45pm

Good to hear. About the warnings: I don’t think there’s anything to worry about, they relate to the internal workings of the Eigen library. Not much we can do about it. You should be able to suppress them by modifying your EIGEN_CFLAGS before invoking ./configure. I assume you must have used:

export EIGEN_CFLAGS="-I$(pwd)/eigen-eigen-07105f7124f9"

If you’d used instead:

export EIGEN_CFLAGS="-isystem \"$(pwd)/eigen-eigen-07105f7124f9\""

followed by:

export CXX=/usr/bin/g++-4.9
./configure 
./build

I’m pretty sure you wouldn’t have seen any such warnings.

No point in doing this now, by the way, the end result will be the same. I’m just mentioning it here for completeness in case others are interested in suppressing these warnings…

egarza · July 15, 2016, 7:28pm

Excellent. I have say I’m using Ubuntu 12.04 because I’m to lazy to change to 14.04, but I will have to do so at some point.

Thanks again,

Eduardo

dp93 · August 8, 2018, 7:47pm

This worked for me as well. Thank you!