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magland / sequencetree4

SequenceTree version 4
GNU General Public License v2.0
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Compiling problems under Ubuntu #4

Open hmattern opened 8 years ago

hmattern commented 8 years ago

Unfortunately, I could not install SeqTree properly. Here is what I did so far:

I set up a virtual machine with Ubuntu (on a Win7 PC). Installed Qt5, downloaded SeqTree 4 from GitHub and extracted it to ~/sequencetree4. I opened a terminal in ~/sequencetree4/src. Here I tried “sudo ./install.x” which basically does:

Unfortunately, I get the following error from the “make” command:

/usr/bin/ld: cannot find -lgsl /usr/bin/ld: cannot find -lgslcblas collect2: error: ld returned 1 exit status Makefile:291: recipe for target '../../bin/VS' failed make[1]: * [../../bin/VS] Error 1 make[1]: Leaving directory '/home/seqtree/sequencetree4/src/VS' Makefile:70: recipe for target 'sub-VS-make_first' failed make: * [sub-VS-make_first] Error 2

Thanks in advance, Hendrik

hmattern commented 8 years ago

As Jeremy suggested via mail I had to do the following:

hmattern commented 8 years ago

Now I get the following error:

cd gui/ && ( test -e Makefile || /usr/lib/x86_64-linux-gnu/qt5/bin/qmake /home/seqtree/sequencetree4/src/gui/gui.pro -o Makefile ) && make -f Makefile 
make[1]: Entering directory '/home/seqtree/sequencetree4/src/gui'
make[1]: Nothing to be done for 'first'.
make[1]: Leaving directory '/home/seqtree/sequencetree4/src/gui'
cd results_viewer/ && ( test -e Makefile || /usr/lib/x86_64-linux-gnu/qt5/bin/qmake /home/seqtree/sequencetree4/src/results_viewer/results_viewer.pro -o Makefile ) && make -f Makefile 
make[1]: Entering directory '/home/seqtree/sequencetree4/src/results_viewer'
g++ -m64 -Wl,-O1 -o ../../bin/results_viewer build/rvmain.o build/rvmainwindow.o build/rvfileview.o build/mda.o build/complex.o build/viewmdamodel.o build/viewmdawidget2d.o build/viewmdawidget1d.o build/viewmdawidget.o build/brightnesstool.o build/fftw_library.o build/apply_fft.o build/export_to_imagej.o build/qrc_st4.o build/moc_rvmainwindow.o build/moc_rvfileview.o build/moc_viewmdamodel.o build/moc_viewmdawidget2d.o build/moc_viewmdawidget1d.o build/moc_viewmdawidget.o build/moc_brightnesstool.o   -L/usr/X11R6/lib64 -L../../bin -lfftw3 -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread 
/usr/bin/ld: cannot find -lfftw3
collect2: error: ld returned 1 exit status
Makefile:200: recipe for target '../../bin/results_viewer' failed
make[1]: *** [../../bin/results_viewer] Error 1
make[1]: Leaving directory '/home/seqtree/sequencetree4/src/results_viewer'
Makefile:69: recipe for target 'sub-results_viewer-make_first' failed
make: *** [sub-results_viewer-make_first] Error 2
licheng2002 commented 8 years ago

It seems that you need fftw is missing. Could you please install fftw first. Download here: http://www.fftw.org/

Then do the following steps:

  1. git clone https://github.com/magland/sequencetree4.git
  2. cd sequence4/src
  3. qmake
  4. make
  5. cd ../
  6. mkdir tmp
  7. cd bin
  8. ./st4

Thanks!

On Mon, Feb 15, 2016 at 9:33 AM, hmattern notifications@github.com wrote:

Now I get the following error:

cd gui/ && ( test -e Makefile || /usr/lib/x86_64-linux-gnu/qt5/bin/qmake /home/seqtree/sequencetree4/src/gui/gui.pro -o Makefile ) && make -f Makefile make[1]: Entering directory '/home/seqtree/sequencetree4/src/gui' make[1]: Nothing to be done for 'first'. make[1]: Leaving directory '/home/seqtree/sequencetree4/src/gui' cd results_viewer/ && ( test -e Makefile || /usr/lib/x86_64-linux-gnu/qt5/bin/qmake /home/seqtree/sequencetree4/src/results_viewer/results_viewer.pro -o Makefile ) && make -f Makefile make[1]: Entering directory '/home/seqtree/sequencetree4/src/results_viewer' g++ -m64 -Wl,-O1 -o ../../bin/results_viewer build/rvmain.o build/rvmainwindow.o build/rvfileview.o build/mda.o build/complex.o build/viewmdamodel.o build/viewmdawidget2d.o build/viewmdawidget1d.o build/viewmdawidget.o build/brightnesstool.o build/fftw_library.o build/apply_fft.o build/export_to_imagej.o build/qrc_st4.o build/moc_rvmainwindow.o build/moc_rvfileview.o build/moc_viewmdamodel.o build/moc_viewmdawidget2d.o build/moc_viewmdawidget1d.o build/moc_viewmdawidget.o build/moc_brightnesstool.o -L/usr/X11R6/lib64 -L../../bin -lfftw3 -lQt5Widgets -lQt5Gui -lQt5Core -lGL -lpthread /usr/bin/ld: cannot find -lfftw3 collect2: error: ld returned 1 exit status Makefile:200: recipe for target '../../bin/results_viewer' failed make[1]: * [../../bin/results_viewer] Error 1 make[1]: Leaving directory '/home/seqtree/sequencetree4/src/results_viewer' Makefile:69: recipe for target 'sub-results_viewer-make_first' failed make: * [sub-results_viewer-make_first] Error 2

— Reply to this email directly or view it on GitHub https://github.com/magland/sequencetree4/issues/4#issuecomment-184231175 .

Regards!

Cheng Li Email: licheng2002@gmail.com

hmattern commented 8 years ago

Hi you were right the fftw was missing. Also gsl was missing. I did the following to set up my virtual machine with SetTree4 in case anybody is interested:

I have one remaining question: What do I have to do to export the sequences to e.g. a Siemens scanner? Do I need a special library?

magland commented 8 years ago

Yes, I can send that to you. Jeremy

On Wed, Feb 17, 2016 at 5:01 AM, hmattern notifications@github.com wrote:

Hi you were right the fftw was missing. Also gsl was missing. I did the following to set up my virtual machine with SetTree4 in case anybody is interested:

  • Download here: http://www.fftw.org/
  • extract to folder you like
  • cd to fftw folder
  • ./ configure
  • make
  • sudo make install
  • Download here: ftp://ftp.gnu.org/gnu/gsl/
  • extract to folder you like
  • cd to fftw folder
  • ./ configure
  • make
  • sudo make install
  • sudo apt-get install git
  • sudo apt-get install qt5-default
  • git clone https://github.com/magland/sequencetree4.git
  • cd sequence4/src
  • qmake
  • make
  • cd ..
  • mkdir tmp
  • cd bin
  • ../st4

I have one remaining question: What do I have to do to export the sequences to e.g. a Siemens scanner? Do I need a special library?

— Reply to this email directly or view it on GitHub https://github.com/magland/sequencetree4/issues/4#issuecomment-185131619 .