fresh compilation of EMAN2.2 on Mac 10.11.6

[Valerie]

hello

e2version.py
EMAN 2.2 (GITHUB: BUILD_DATE)
Your EMAN2 is running on: Mac OS 10.11.6 x86_64
Your Python version is: 2.7.10

I just installed all libraries and compiled EMAN2 on my mac.
I installed it in /usr/local/eman2 instead of my home directory because it is cleaner.

now e2speedtest.py gives an error message:
  File "/usr/local/eman2/bin/e2speedtest.py", line 42, in <module>
    from EMAN2 import *
  File "/usr/local/eman2/libpyEM/EMAN2.py", line 44, in <module>
    from EMAN2_cppwrap import *
  File "/usr/local/eman2/libpyEM/EMAN2_cppwrap.py", line 33, in <module>
    from libpyAligner2 import *
ImportError: No module named libpyAligner2

the gui does not start either.

here are files with libpyAligner2 string in their names in the /usr/local/eman2 path:
./lib/libpyAligner2.dylib
./libpyEM/CMakeFiles/pyAligner2.dir/libpyAligner2.o
./libpyEM/libpyAligner2.cpp

Thanks for any suggestion
best regards,

Valérie Biou       
Laboratoire de Biologie Physico-Chimique des Protéines Membranaires
UMR 7099 CNRS/Univ. Paris Diderot P7
Institut de Biologie Physico-Chimique
13 rue Pierre et Marie Curie
75005 Paris - France

[Steve Ludtke]

Were you following the new instructions?:

http://blake.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_MAC_OS_X

or doing something else. At the very least it sounds like your PYTHONPATH and perhaps EMAN2DIR may not be set properly.

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----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Valerie]

Hello

I did follow the instructions. Make had problems and I made links for freetype.h and ft2build.h to /opt/X11/
then building proceeded ok.
My variables are set as follows
EMAN2DIR=/usr/local/eman2
PYTHONPATH=.:/usr/local/eman2/lib:/usr/local/eman2/libpyEM
I am using csh.

Valerie

[Steve Ludtke]

Hi. 

No, you shouldn't be pulling anything from /opt/X11!  Freetype should be available in anaconda once you've installed the listed packages on the website.

Are you sure your PYTHONPATH is set in the shell where you are trying to run, and are you sure your PATH is including anaconda2/bin before anything else?

which python

There is also something very funny going on in your installation. You should not have a libpyEM folder in eman2. To be clear, the eman2/ folder you download from GitHub is where you compile EMAN2. When you do a 'make install' it creates (normally) a ~/EMAN2 folder containing the runtime environment. I'm a bit concerned that you have somehow tried to fold the build environment together with the executable, or perhaps you compiled, but never did a 'make install' ? 

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[Valerie]

Hello

I have reinstalled everything in my home dir. ccmake had more differences than listed in your example and I corrected them all. make  worked fine in spite of warnings.
make all created an EMAN2 directory in my home dir.
running the test/rt/rt.py issued a number of failures (I attach the log file)
The gui starts and ctf estimation is ok.
however the particle picking generates errors and the images don't get displayed well (first time the image showed up but I could not zoom out and now the window stays black).
I get GL messages:

File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__
    typ.__module__, type.__name__, repr(value)[:50]
TypeError: No array-type handler for type numpy.type (value: 1) registered
Traceback (most recent call last):
  File "/Users/biou/EMAN2/lib/emimage2d.py", line 214, in paintGL
    self.render()
  File "/Users/biou/EMAN2/lib/emimage2d.py", line 1032, in render
    if self.tex_name != 0: glDeleteTextures(self.tex_name)
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__
    return self.wrapperFunction( self.baseFunction, *args, **named )
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures
    ptr = arrays.GLuintArray.asArray( size )
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray
    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__
    typ.__module__, type.__name__, repr(value)[:50]
TypeError: No array-type handler for type numpy.type (value: 1) registered
Traceback (most recent call last):
  File "/Users/biou/EMAN2/lib/emimage2d.py", line 214, in paintGL
    self.render()
  File "/Users/biou/EMAN2/lib/emimage2d.py", line 1032, in render
    if self.tex_name != 0: glDeleteTextures(self.tex_name)
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/latebind.py", line 61, in __call__
    return self.wrapperFunction( self.baseFunction, *args, **named )
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/GL/exceptional.py", line 59, in glDeleteTextures
    ptr = arrays.GLuintArray.asArray( size )
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 149, in asArray
    return cls.getHandler(value).asArray( value, typeCode or cls.typeConstant )
  File "/Users/biou/anaconda2/lib/python2.7/site-packages/OpenGL/arrays/arraydatatype.py", line 53, in __call__
    typ.__module__, type.__name__, repr(value)[:50]
TypeError: No array-type handler for type numpy.type (value: 1) registered

... sorry about all this,
Valerie

[Paul Penczek]

Yesterday Steve suggested to me rebooting the machine saying it fixed similar problems on his machine. It did not help in my case, but maybe it will help you. 

Regards,

Pawel

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<tests.log>

[Steve Ludtke]

You should not try to run the rt module. We have used that for development purposes occasionally over time. It does not have updated tests at the moment.

Could you post your CMakeCache file and your complete set of environment variables in the shell where you are experiencing this error (just type 'set')?  

You can try rebooting, but I seem to recall this particular problem may have been something else...

On Feb 14, 2017, at 5:01 AM, Valerie <plump...@gmail.com> wrote:

No array-type handler for type numpy.type 

[Valerie]

 here are the files you asked for.
thanks

[Steve Ludtke]

No obvious problems in the cmake parameters, but your PATH doesn't include $HOME/anaconda2/bin, and your PYTHONPATH doesn't include $EMAN2DIR/bin. $HOME/anaconda2/bin must be the first item in your path (possibly after '.') for reliable operation.  With those changes and a reboot of the machine, see if the problem persists...

On Feb 14, 2017, at 7:56 AM, Valerie <plump...@gmail.com> wrote:

 here are the files you asked for.
thanks

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<CMakeCache.txt><env.log>

[Valerie]

Hello Steve,

Sorry I was busy working on the Linux version that works :)

I have changed the PATH and PYTHONPATH on the mac and rebooted, but particle picking shows a broken image as shown on the attached screen shot.

 echo $PATH
.:/Users/biou/anaconda2/bin:/Users/biou/EMAN2/bin:/Users/biou/prog/tcoffee/Version_11.00.8cbe486/bin:/usr/local/xtal/validation-v8.061-prod-bin-darwin/bin:/opt/X11/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/X11R6/bin:/usr/X11R6/bin:/sw/bin:/sw/sbin:/usr/local/bin:/Users/biou/prog:/Users/biou/prog/fasta-35.4.11/bin:/Users/biou/util:/usr/local/phaser/phaser-macosx-1.2:/opt/local/bin:/usr/local/xdsme-0.5.0.2/bin/noarch/:/usr/local/xplor-nih-2.29/bin:/Users/biou/prog/pdb2pqr-1.8:/usr/local/XDS-OSX_64:/usr/local/xdsme-master/bin/noarch
 echo $PYTHONPATH
/Users/biou/EMAN2/bin:/Users/biou/EMAN2/lib

Best,

Valerie

[Paul Penczek]

This is still better than what I got, which was set of greenish spots. 

Do you get any warnings when you display an image?

Regards,

Pawel

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<Capture d’écran 2017-02-16 à 11.13.50.png>

[Steve Ludtke]

Huh...  Do the rest of the GUI displays (widgets, etc.) look ok?   This seems like an OpenGL issue, maybe an issue with Texture rendering.  Could you run a 

conda info, and cross check the versions with the versions posted on the installation instructions troubleshooting section?

[Valerie]

the troubleshooting page does not talk about conda info. do you mean conda list?
if yes, my config shows a few differences with yours  and in particular pyopengl: your version is 3.0.2 and mine is 3.1.1a1
Should I downgrade my pyopengl? if it is the case, can you please explain how to do this?
thanks
Valerie

[Steve Ludtke]

Oops, yes, I did mean conda list.  Yes,  try

conda install pyopengl=3.0.2

and see if that helps. That statement struck a chord in my memory as well. I think I may have done that myself during install, but failed to note it...  If that doesn't fully resolve the problem, and there are other differences, you might try a similar syntax to change the version of those as well.

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[Valerie]

it works! thanks a lot for your help.
Valerie

[Valerie]

sorry Pawel,

I rebooted the Mac before I saw your message so I have lost the warnings. now you talk about it, I do have warnings from Matplotlib that I didn't use to have: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
but they don't seem to be in connection with my image display problem.
it was indeed the pyopengl version that was different as seen from conda list. Hope this helps you solve your problem.

Valerie

[Steve Ludtke]

Excellent! Wonder what the issue is with the newer PyOpenGL. I'm updating the Wiki now. Thanks!

On Feb 16, 2017, at 10:00 AM, Valerie <plump...@gmail.com> wrote:

it works! thanks a lot for your help.
Valerie

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