Re: [EMAN2] Error for e2speedtest.py

[Ludtke, Steven J.]

Anaconda itself sometimes has installation issues. If you find a number of dependencies aren't installed, it is possible you have a messed up Anaconda install, and should just start from scratch.

Note that given the time since the last binary release, we strongly encourage people to either use a current snapshot or (even better) build from source. 

On the Mac installing from source requires having Xcode installed, but otherwise the instructions take about the same time as a binary install, and it is MUCH easier to update/change versions if you do it that way)

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

On Jul 15, 2022, at 1:37 PM, Henry Wietfeldt <henry.w...@gmail.com> wrote:

Hi,

I installed the binary for eman2.91 on macOS Catalina, following the instructions at https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.91.  When I run e2speedtest.py, I get the following error:

(base) [xxx]:~ wietfeldthc$ e2speedtest.py
Traceback (most recent call last):
  File "/Users/wietfeldthc/eman2-sphire-sparx/bin/e2speedtest.py", line 43, in <module>
    from EMAN2 import *
  File "/Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2.py", line 49, in <module>
    from EMAN2_cppwrap import *
  File "/Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2_cppwrap.py", line 33, in <module>
    from libpyAligner2 import *
ImportError: dlopen(/Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/libpyAligner2.so, 2): Library not loaded: @rpath/libboost_python37.dylib
  Referenced from: /Users/wietfeldthc/eman2-sphire-sparx/lib/python3.7/site-packages/libpyAligner2.so
  Reason: image not found
(base) [xxx]:~ wietfeldthc$

Note that the environment variables LD_LIBRARY_PATH, DYLD_LIBRARY_PATH, PYTHONPATH and PYTHONHOME are not set and that the current conda environment is the eman2 directory.  I think this issue may have to do with the dependencies.  After installation, I first got the ModuleNotFoundError: No module named 'past' error described in the troubleshooting notes when first running e2speedtest.py.  I then manuallly installed the dependencies as suggested.  Afterwards, I got the same ModuleNotFoundError: No module named 'past' error, so I ran conda install future.  Next I ran e2speedtest.py and got the error ModuleNotFoundError: No module named 'numpy'.  Then I ran conda install numpy.  Now i get the error I'm stuck on as described above when I run any of the test commands that aren't e2version.py (which runs successfully).  When I run e2version.py, I get the following output:

(base) FNM-S106326:~ wietfeldthc$ e2version.py
EMAN 2.91 final ( GITHUB: 2021-03-08 12:05 - commit: 81caed2 )
Your EMAN2 is running on: Mac OS 10.15.7 x86_64
Your Python version is: 3.7.10
(base) FNM-S106326:~ wietfeldthc$

I believe that I'm not correctly installing the dependencies.  What do you suggest I do?  Thank you!

Henry

Henry Wietfeldt

Postbaccalaureate CRTA Fellow

Elmlund Lab| Cryo-EM

National Cancer Institute

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