Installing EMAN2.3 - missing modules?

741 views
Skip to first unread message

Daphne

unread,
Jul 16, 2019, 1:45:46 AM7/16/19
to EMAN2
I am trying to install EMAN2.3 for Windows according to the installation instructions here, under "Native Win7/10 64 bit" (I am running Windows 10). However, when I run the programs listed in the last step, I get the following output:

C:\Users\Daphne>e2version.py
EMAN 2.3 final (GITHUB: 2019-04-25 14:10 - commit: 6aaac88e2 )
Your EMAN2 is running on: Windows 64bit
Your Python version is: 2.7.16

C:\Users\Daphne>e2speedtest.py
Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\Library\bin\e2speedtest.py", line 36, in <module>
    from past.utils import old_div
ImportError: No module named past.utils

C:\Users\Daphne>e2display.py
Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\Library\bin\e2display.py", line 36, in <module>
    from builtins import range
ImportError: No module named builtins

C:\Users\Daphne>e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24
Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\Library\bin\e2proc2d.py", line 35, in <module>
    from past.utils import old_div
ImportError: No module named past.utils

Steve Ludtke

unread,
Jul 16, 2019, 8:09:07 AM7/16/19
to em...@googlegroups.com
Hi,
this has been discussed in the past. It isn't completely clear why it happens sometimes, but the solution is usually to simply run:

conda install future -c defaults

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)



--
--
----------------------------------------------------------------------------------------------
You received this message because you are subscribed to the Google
Groups "EMAN2" group.
To post to this group, send email to em...@googlegroups.com
To unsubscribe from this group, send email to eman2+un...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/eman2

---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eman2+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/a7b85f1d-29fd-4fd3-8a1b-f99b18074fca%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Daphne

unread,
Jul 16, 2019, 11:51:02 AM7/16/19
to EMAN2
Hi Steve,

It still doesn't seem to be working. Here is what I got after running conda install future -c defaults :

C:\Users\Daphne>e2version.py
EMAN 2.3 final (GITHUB: 2019-04-25 14:10 - commit: 6aaac88e2 )
Your EMAN2 is running on: Windows 64bit
Your Python version is: 2.7.16

C:\Users\Daphne>e2speedtest.py
Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\Library\bin\e2speedtest.py", line 44, in <module>
    from numpy import array
ImportError: No module named numpy


C:\Users\Daphne>e2display.py
Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\Library\bin\e2display.py", line 37, in <module>
    from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser
  File "C:\Users\Daphne\EMAN2\lib\site-packages\EMAN2.py", line 51, in <module>
    from EMAN2_cppwrap import *
  File "C:\Users\Daphne\EMAN2\lib\site-packages\EMAN2_cppwrap.py", line 35, in <module>
    from libpyAligner2 import *
ImportError: DLL load failed: The specified module could not be found.


C:\Users\Daphne>e2proc2d.py :64:64:1 test.hdf --process mask.sharp:outer_radius=24
Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\Library\bin\e2proc2d.py", line 37, in <module>
    from EMAN2 import *
  File "C:\Users\Daphne\EMAN2\lib\site-packages\EMAN2.py", line 51, in <module>
    from EMAN2_cppwrap import *
  File "C:\Users\Daphne\EMAN2\lib\site-packages\EMAN2_cppwrap.py", line 35, in <module>
    from libpyAligner2 import *
ImportError: DLL load failed: The specified module could not be found.
To unsubscribe from this group, send email to em...@googlegroups.com

For more options, visit this group at
http://groups.google.com/group/eman2

---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to em...@googlegroups.com.

Steve Ludtke

unread,
Jul 16, 2019, 12:15:58 PM7/16/19
to em...@googlegroups.com
Tunay theorized that some portion of the installer script failed while it was running, and suggested the logs would be useful, but he will need to ask for what he wants specifically.

Unfortunately, Windows machines can be very tricky. This looks to me more like a conflict with some other installed software package. One of the common problems people have on windows is when another software package they have installed also installs Python on their computer, and that other Python gets used in preference to the Python provided with EMAN2.

Tunay, any advice?

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)


To unsubscribe from this group, send email to eman2+un...@googlegroups.com

For more options, visit this group at
http://groups.google.com/group/eman2

---
You received this message because you are subscribed to the Google Groups "EMAN2" group.
To unsubscribe from this group and stop receiving emails from it, send an email to eman2+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/f00716ed-2260-4ba2-a7b5-ac9cf1bc006e%40googlegroups.com.

shadow walker

unread,
Jul 16, 2019, 1:47:44 PM7/16/19
to em...@googlegroups.com
In install_logs/ in the installation folder there should be three log files. If the installation did not complete some of the files might be missing. Can you send those files, please? Those files will have some information about your computer environment, so if you are concerned about privacy, you can send them privately.

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/8BD11818-4EDD-4853-9F61-8041277F9A4B%40gmail.com.

For more options, visit https://groups.google.com/d/optout.


--
shadow_walker

Daphne

unread,
Jul 16, 2019, 2:35:31 PM7/16/19
to em...@googlegroups.com
Okay thanks, I will email them to you privately.

You received this message because you are subscribed to a topic in the Google Groups "EMAN2" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/eman2/rRV1mMWIBE0/unsubscribe.
To unsubscribe from this group and all its topics, send an email to eman2+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAMkj2Emx%3DoHeHW1v9GTVpAD62kaEdduQ7r6yDg2T%3DKhUDL_Z7g%40mail.gmail.com.

shadow walker

unread,
Jul 16, 2019, 2:53:35 PM7/16/19
to em...@googlegroups.com
Looking at the logs, I can't see that the installation completed successfully. It could be that some part of the installation was not logged, but I think it is unlikely. Can you try to complete the installation manually with this command?

conda.exe install -v eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2B_wX9j9EtiAb%2B7TfaWbk8vVaFtW-HweUGk5FUhbikdVdxAPiA%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.


--
shadow_walker

Daphne

unread,
Jul 17, 2019, 12:48:18 AM7/17/19
to em...@googlegroups.com
Now I'm getting this:


To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAMkj2E%3DPtiV61D6bEtfTyaW_P_rEnMbBPn33R%3Dz7iN262cEdcg%40mail.gmail.com.

Daphne

unread,
Jul 17, 2019, 12:48:38 AM7/17/19
to em...@googlegroups.com
Sorry, pressed send too early. I got this:

C:\Users\Daphne>conda.exe install -v eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
'conda.exe' is not recognized as an internal or external command,
operable program or batch file.

shadow walker

unread,
Jul 17, 2019, 11:59:01 AM7/17/19
to em...@googlegroups.com
Under your Start menu there should be a new folder, "Anaconda2 (64-bit)". Click it to expand and then, click "Anaconda Prompt". Run the command in this terminal. If that folder is missing, you need to setup your PATH as described in the instructions, items 3., 4. and 5.

  • Start a command prompt by clicking Start menu and typing cmd.exe in the dialog at the bottom.

  • On the command prompt, type 

    setx path "%path%;c:\<path to EMAN2 directory>\Library\bin"
  • Close the command prompt and open a new one.


To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2B_wX9gE2mZTusLox0UXpU%2ByoB0%2BKknEeR-hO201SQpbAXEi6A%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.


--
shadow_walker

Daphne

unread,
Jul 17, 2019, 8:47:19 PM7/17/19
to em...@googlegroups.com
Here is what I got after running the command in the Anaconda terminal:

C:\Users\Daphne>conda.exe install -v eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
Conda is constrained to only using the old .tar.bz2 file format because you have conda-build installed, and it is <3.18.3.  Update or remove conda-build to get smaller downloads and faster extractions.

Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed

Traceback (most recent call last):
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\exceptions.py", line 1043, in __call__
    return func(*args, **kwargs)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\cli\main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\cli\conda_argparse.py", line 82, in do_call
    exit_code = getattr(module, func_name)(args, parser)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\cli\main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\cli\install.py", line 280, in install
    force_reinstall=context.force_reinstall or context.force,
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\core\solve.py", line 112, in solve_for_transaction
    force_remove, force_reinstall)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\core\solve.py", line 150, in solve_for_diff
    force_remove)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\core\solve.py", line 249, in solve_final_state
    ssc = self._run_sat(ssc)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\common\io.py", line 88, in decorated
    return f(*args, **kwds)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\core\solve.py", line 684, in _run_sat
    history_specs=ssc.specs_from_history_map)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\common\io.py", line 88, in decorated
    return f(*args, **kwds)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\resolve.py", line 1189, in solve
    self.find_conflicts(specs, specs_to_add, history_specs)
  File "C:\Users\Daphne\EMAN2\lib\site-packages\conda\resolve.py", line 449, in find_conflicts
    raise UnsatisfiableError(bad_deps, strict=strict_channel_priority)
UnsatisfiableError: The following specifications were found to be incompatible with each other:

  - eman-deps=14.1 -> conda==4.6.14 -> conda-build[version='>=3']
  - pkgs/main/win-64::conda-build==3.15.1=py27_0
  - pkgs/main/win-64::pip==19.0.3=py27_0 -> python[version='>=2.7,<2.8.0a0']

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAMkj2Ekt7NUfM8TN8yTEHoJKNZZ1oibhuA8CdWbG3n_nC2w4jA%40mail.gmail.com.

shadow walker

unread,
Jul 17, 2019, 9:05:00 PM7/17/19
to em...@googlegroups.com
Can you try the following commands?

conda config --set auto_update_conda False
conda install -v conda=4.6.14 conda-build=3.17.8 eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y


To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2B_wX9iT7X5XBh9ZMZjSFfFsAYe5_ecHxKeddpE%2BL4%2B%3DibdKfg%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.


--
shadow_walker

Daphne

unread,
Jul 17, 2019, 11:13:57 PM7/17/19
to em...@googlegroups.com
I'm getting this now:

(base) C:\Users\Daphne>conda config --set auto_update_conda False

(base) C:\Users\Daphne>conda install -v conda=4.6.14 conda-build=3.17.8 eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
  - pkgs/main/win-64::pip==19.0.3=py27_0 -> python[version='>=2.7,<2.8.0a0']
To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAMkj2E%3DJ68h52cZsKv%2BBX3bCv%2BZy36NRfLcxgov_CisWS3Ce8w%40mail.gmail.com.

shadow walker

unread,
Jul 18, 2019, 12:04:34 AM7/18/19
to em...@googlegroups.com
Sorry for going back and forth with this. I think recent changes to conda are causing problems here. If the original problem was a temporary problem, trying the whole install from scratch might be easier. To do that, first, uninstall eman2 using the uninstaller in your installation. The file name should be something like Uninstall-EMAN2.exe.

I am trying to come up with a solution to fix installations and I will post them here or update our wiki instructions once I have something.


To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CA%2B_wX9jKzinsAN6tB2u1Q1QuD5iR7%3Dqxe_S1rr-DChMDUTrSJA%40mail.gmail.com.

For more options, visit https://groups.google.com/d/optout.


--
shadow_walker

Reply all
Reply to author
Forward
0 new messages