janelia-flyem / buildem Goto Github PK

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CMake and other scripts to help build process of FlyEM software

License: Other

CMake 91.74% Python 6.28% Shell 1.98%

buildem's People

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stuarteberg mstump jensnrad fblumenthal yu818 pombredanne chaubold ukoethe azizanajeeb nathanfrench externalrepositories

buildem's Issues

The lemon-1.2.3 library fails to build on Mac 10.7.5

The lemon-1.2.3 library fails to build on Mac 10.7.5 genrating this error message:

In file included from /Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:34:
In file included from /Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:40:
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/bits/bezier.h:162:17: warning: 
      unused variable 'f' [-Wunused-variable]
    const Point f=(d+e)/2;
                ^
In file included from /Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:34:
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:85:3: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>'
      requested here
  graphToEps(g,"graph_to_eps_demo_out_1_pure.eps").
  ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:93:5: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>::CoordsTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<lemon::dim2::Point<int>>>>'
      requested here
    coords(coords).
    ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:110:5: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>::NodeColorsTraits<lemon::ComposeMap<lemon::Palette,
      lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<int>>>>' requested
      here
    nodeColors(composeMap(palette,colors)).
    ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:137:5: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>::NodeShapesTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<int>>>'
      requested here
    nodeShapes(shapes).
    ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:152:18: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>::NodeSizesTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<double>>>'
      requested here
    nodeScale(2).nodeSizes(sizes).
                 ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:170:5: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::GraphToEps<lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>::NodeSizesTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<double>>>::CoordsTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<lemon::dim2::Point<int>>>>'
      requested here
    coords(coords).
    ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:225:12: error: 
      dependent using declaration resolved to type without 'typename'
  using T::NodeTextColorType;
           ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/demo/graph_to_eps_demo.cc:201:5: note: 
      in instantiation of template class
      'lemon::GraphToEps<lemon::GraphToEps<lemon::GraphToEps<lemon::DefaultGraphToEpsTraits<lemon::ListDigraph>>::CoordsTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<lemon::dim2::Point<int>>>>::NodeTextsTraits<lemon::DigraphExtender<lemon::ListDigraphBase>::NodeMap<int>>>'
      requested here
    nodeTexts(hcolors).nodeTextSize(.6).
    ^
/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3/lemon/graph_to_eps.h:127:8: note: 
      target of using declaration
  enum NodeTextColorType
       ^
1 warning and 7 errors generated.
make[5]: *** [demo/CMakeFiles/graph_to_eps_demo.dir/graph_to_eps_demo.cc.o] Error 1
make[4]: *** [demo/CMakeFiles/graph_to_eps_demo.dir/all] Error 2
make[3]: *** [all] Error 2
make[2]: *** [/Volumes/SSD/ilastik/buildem/src/lemon-1.2.3-stamp/lemon-1.2.3-build] Error 2
make[1]: *** [CMakeFiles/lemon-1.2.3.dir/all] Error 2
make: *** [all] Error 2

Allow specification of packages built outside of flyem-build

Although the purpose of flyem-build is to have a consistent, version-controlled build of FlyEM apps, we can permit knowledgeable developers to point to outside packages instead of always building everything from scratch.

This can be done via a command-line option, similar to the current -D USE_PROJECT_DOWNLOAD method. Manual modules will be obtained through standard CMake find package commands.

Unset cflags and cxxflags before building?

When building ilastik with buildem, one can run into the problem that NumPy does not compile and complains about several Python Symbols not being found for the respective architecture. It took us quite a while to find out that this was caused by some CFLAGS being set, that overwrote the default numpy settings. (found here)

Experienced this on OSX Mavericks 10.9, with CFLAGS="-march=core2" set.

Should we unset the cflags and cxxflags for building with buildem? Or at least tell the user to do so.

windows support

buildem looks amazing to me but i think i am blocked because of OS specific command line functions in each projects .rule file in visual studio

'env' is not recognized as an internal or external command, operable program or batch file.

i believe we use 'set'...

i tried to set some of the variables in the BuildSupport.cmake without luck. @line 57...
set (BUILDEM_PLATFORM_SPECIFIC_ENV "set")

i also tried to replace 'env' with 'set' @line 64 without luck.

ideas?

buildem broke gdb on fedora

gdb returns the following error

gdb: symbol lookup error: gdb: undefined symbol: PyUnicodeUCS4_FromEncodedObject

after buildem/lib added to the LD_LIBRARY_PATH. The problem might be related to incompatible python build in buildem.

PyQt4 fails to build on (my) ubuntu

Hi,

I am trying to use buildem to compile ilastik on ubuntu 12.04.02. I used the provided example CMakesList.txt and added the following includes:

include (qt4)
include (pyqt4)
include (vigra)
include (qimage2ndarray)
include (h5py)
include (ilastik)
include (ilastik-gui)

I get the following error

[ 44%] Performing patch step for 'pyqt4-4.9.5'
env: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: Permission denied
make[2]: *** [/home/dummy/junk/buildem/src/pyqt4-4.9.5-stamp/pyqt4-4.9.5-patch] Error 126
make[1]: *** [CMakeFiles/pyqt4-4.9.5.dir/all] Error 2
make: *** [all] Error 2

using sudo make results in the same error.
I checked the permissions of pyqt4-4.9.5/configure.py:
-rw-r--r--
However, changing them (chmod +wx) is not a good idea:

import: unable to grab mouse `': Resource temporarily unavailable @ error/xwindow.c/XSelectWindow/9052.
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 36: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: pyqt_version: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 37: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: pyqt_version_str: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 39: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: sip_min_version: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 41: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_version: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 42: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_edition: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 43: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_licensee: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 44: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_dir: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 45: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_incdir: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 46: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_libdir: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 47: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_bindir: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 48: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_datadir: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 49: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_pluginsdir: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 50: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_xfeatures: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 51: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_shared: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 52: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_framework: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 56: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_macx_spec: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 58: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: qt_sip_flags: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 60: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: pyqt_modules: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 61: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: pyqt_modroot: not found
/home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: 62: /home/dummy/junk/buildem//src/pyqt4-4.9.5/configure.py: Syntax error: "(" unexpected
make[2]: *** [/home/dummy/junk/buildem/src/pyqt4-4.9.5-stamp/pyqt4-4.9.5-patch] Error 2
make[1]: *** [CMakeFiles/pyqt4-4.9.5.dir/all] Error 2
make: *** [all] Error 2

Any ideas?
Thanks,
Jens

libtiff 4.0.3 does not build on Mac

The preprocessor macro HAVE_APPLE_OPENGL_FRAMEWORK is not set during configure and tool/tiffgt.c fails to compile. When setting HAVE_APPLE_OPENGL_FRAMEWORK to 1 it works. Perhaps that file should be patched?

python.cmake: Disable openssl support by default

OpenSSL has a license that is incompatible with the GPL. Hence, some projects may need to exclude openssl from their python builds. python.cmake should exclude openssl by default, but provide a CMake switch to include it.

Packages dependencies should only be specified once.

At present, a cmake script mystuff.cmake has to specify a dependency twice, once via include(dependency) and then again in DEPENDS ${dependency_NAME}. The second spec is easily forgotten, which can lead to bad behavior of a fresh buildem checkout. Unfortunately, the omission is not easily noticed by the developer of mystuff.cmake because dependency is usually already present in his build. Is it possible to remove the redundancy, e.g. by something like DEPENDS ${all_includes} which automatically makes all includes a dependency?

janelia-flyem / buildem Goto Github PK

buildem's People

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buildem's Issues

The lemon-1.2.3 library fails to build on Mac 10.7.5

Allow specification of packages built outside of flyem-build

Unset cflags and cxxflags before building?

windows support

buildem broke gdb on fedora

PyQt4 fails to build on (my) ubuntu

libtiff 4.0.3 does not build on Mac

python.cmake: Disable openssl support by default

Packages dependencies should only be specified once.

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