Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Compiling problems under Ubuntu #4

Open
hmattern opened this issue Feb 15, 2016 · 5 comments
Open

Compiling problems under Ubuntu #4

hmattern opened this issue Feb 15, 2016 · 5 comments

Comments

@hmattern
Copy link

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:

  • export ST_BIN_DIR=/software/st4/bin
  • export CHAINLINK_DIR=/home/magland/chainlink2
  • qmake
  • make

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
Copy link
Author

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

  • comment out the following line in src/st4.pro:
    SUBDIRS += VS
    with a "#"

@hmattern
Copy link
Author

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
Copy link
Collaborator

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 [email protected] 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
#4 (comment)
.

Regards!

Cheng Li
Email: [email protected]

@hmattern
Copy link
Author

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?

@magland
Copy link
Owner

magland commented Feb 17, 2016

Yes, I can send that to you.
Jeremy

On Wed, Feb 17, 2016 at 5:01 AM, hmattern [email protected] 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
#4 (comment)
.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@magland @licheng2002 @hmattern