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A scientific image processing software suite with a focus on CryoEM and CryoET

CMake 0.10% Python 92.32% Shell 0.01% C++ 7.17% C 0.26% Cuda 0.15% Makefile 0.01% Batchfile 0.01%

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Question regarding the requirement for OpenMPI to be compiled with --disable-dlopen

Hi,

Sorry for bothering you with that many questions.

I could now resolve almost all issues and can consistently build EMAN 2.3 from source, both, using dependencies built with CONDA and using dependencies built without CONDA.

The last missing piece is to make EMAN 2.3 using our centrally provided OpenMPI as it was compiled with support for our batch system (LSF).

Why do you have a requirement to have OpenMPI built with --disable-dlopen ? Unfortunately, our MPI is compiled with --enable-dlopen. This parameter determines, if the OpenMPI plugins are built as separate libraries (DSO) or if they are added to the main MPI library.

I don't understand how this can affect a software using OpenMPI. Shouldn't a software work independent of how OpenMPI is compiled with regards to DSO ?

Best regards and that you for the help you provided so far.

Sam

CMake Error at programs/CMakeLists.txt:28 (string)

Hi,

I would like to report an issue regarding using CMake to build eman2.

When trying to build eman 2.3 from source (using the v2.3 release tarball from github), then I receive a CMake Error caused by programs/CMakeLists.txt

CMake Error at programs/CMakeLists.txt:28 (string):
string sub-command REGEX, mode REPLACE needs at least 6 arguments total to
command.

According to

https://gitlab.kitware.com/cmake/cmake/issues/18737

this problem can be fixed by quoting the arguments of the function.

When changing programs/CMakeLists.txt:28 from

        string(REGEX REPLACE
                   "^.*-.*-g" ""
                   EMAN_GITHASH ${EMAN_GITHASH}
                   )

        string(REGEX REPLACE
                   "^.*-.*-g" ""
                   "EMAN_GITHASH" "${EMAN_GITHASH}"
                   )

then the error is no longer triggered

Definition of multiref_polar_ali_2d_delta differs between util_sparx.cpp/h and libpyUtils2.cpp

The definition in libEM/sparx/util_sparx.h says

        static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim,
                vector<float> xrng, vector<float> yrng, float step, string mode,
                vector< int >numr, float cnx, float cny, float delta_start, float delta);

while the one in libpyUtils2.cpp says

                .def("multiref_polar_ali_2d_delta", &EMAN::Util::multiref_polar_ali_2d_delta, args("image", "crefim", "xrng", "yrng", "step", "mode", "numr", "cnx", "cny"), "formerly known as apmq\nDetermine shift and rotation between image and many referenceimages (crefim, weights have to be applied) quadratic\ninterpolation")

Note the missing two arguments in the libpyUtils2 definition.

If EMAN2 isn't working for MAC, do this!

First, follow the install instructions: https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.22

Then, open terminal, and run open ~/.bash_profile

Add to that file export PATH="/Users/yourusername/EMAN2/bin:$PATH"

Save, and restart your terminal, then see if it works.

Compile didn't work

Hey guys,

I compiled your software (with the help of miniconda) and it compiled all right but when I ran make tests-verbose I got the following error:

` test 4
Start 4: progs

4: Test command: /bin/bash "/usr/local/eman2/tests/run_prog_tests.sh"
4: Test timeout computed to be: 9.99988e+06
4: basename: missing operand
4: Try 'basename --help' for more information.
4/5 Test #4: progs ............................***Failed 0.01 sec
test 5
Start 5: py-compile

5: Test command: /home/mbelouso/miniconda2/bin/python "-m" "compileall" "-q" "/usr/local/eman2"
5: Test timeout computed to be: 9.99988e+06
5/5 Test #5: py-compile ....................... Passed 0.04 sec

80% tests passed, 1 tests failed out of 5

Total Test time (real) = 12.47 sec

The following tests FAILED:
4 - progs (Failed)
Errors while running CTest
CMakeFiles/test-verbose.dir/build.make:57: recipe for target 'CMakeFiles/test-verbose' failed
make[3]: *** [CMakeFiles/test-verbose] Error 8
CMakeFiles/Makefile2:163: recipe for target 'CMakeFiles/test-verbose.dir/all' failed
make[2]: *** [CMakeFiles/test-verbose.dir/all] Error 2
CMakeFiles/Makefile2:170: recipe for target 'CMakeFiles/test-verbose.dir/rule' failed
make[1]: *** [CMakeFiles/test-verbose.dir/rule] Error 2
Makefile:214: recipe for target 'test-verbose' failed
make: *** [test-verbose] Error 2 `

And when I try and run something basic like e2display.py

File "/home/mbelouso/miniconda2/bin/e2display.py", line 2 from __future__ import print_function SyntaxError: future feature print_function is not defined

cmake didn't give any glaring errors, although when it compiled there we lots and lots of warnings about unused variables...

Thanks for your time and efforts with this project!

traceback running e2projectmanager.py

Hello.

We're having some issues with eman2 2.22 on a new system, CentOS 7.

As a user, trying to run e2projectmanager.py results in:

-bash-4.2$ e2projectmanager.py
Traceback (most recent call last):
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 572, in open_db
try : ret=JSDict(path)
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 643, in init
self.sync()
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 693, in sync
except: raise Exception("Error: Unable to open {} for writing".format(self.normpath))
Exception: Error: Unable to open /executor/info/project.json for writing

Traceback (most recent call last):
File "/opt/cryoem/EMAN2_2.22/bin/e2projectmanager.py", line 2134, in
pm = EMProjectManager()
File "/opt/cryoem/EMAN2_2.22/bin/e2projectmanager.py", line 67, in init
self.loadPMdb()
File "/opt/cryoem/EMAN2_2.22/bin/e2projectmanager.py", line 124, in loadPMdb
self.pm_projects_db = js_open_dict("info/project.json")
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 78, in js_open_dict
return JSDict.open_db(url)
File "/opt/cryoem/EMAN2_2.22/lib/python2.7/site-packages/EMAN2jsondb.py", line 577, in open_db
raise Exception("Unable to open "+path)
Exception: Unable to open info/project.json

However, I am able to run it normally as root. I have checked permissions, but can't seem to find an issue there. Any assistance is appreciated.

GPU too old

Hello. I have installed the binary version of EMAN2 on a rather old linux workstation and when we tried to run e2tomoseg_convnet.py we got the error of:
tensorflow.python.framework.errors_impl.InternalError: Failed to create session

i suspect that it is because the GPU is too old, because it works fine on newer workstations. And I am thinking about trying to compile EMAN2 against our GPU. However, I got stuck in the middle of compiling (even though I followed EMAN2 instructions) as I cannot let cmake recognize my conda path even though I ran cmake within conda environment.

Now at this stage, I have 3 questions:

Is it possible to just reconfigure GPU for the working version of EMAN2?
If I have to compile EMAN2 myself, how to properly configure the environment such that cmake is able to recognize miniconda?
How to specify GPU architecture when I compile EMAN2?

Thanks a lot for any inputs!

No module named past.utils

Upon installing Eman2 on Ubuntu16.04, when I tried running e2projectmanager.py, this came up:

(eman-env) root@thlab:~/.conda/envs/eman-env/bin# e2projectmanager.py Traceback (most recent call last): File "/home/thlab/.conda/envs/eman-env/bin/e2projectmanager.py", line 35, in <module> from past.utils import old_div ImportError: No module named past.utils
Future is already installed using pip.

CMake Error set_property can not be used on an ALIAS target

Hi,

I am using CMake 3.12.4 to build eman2 from source (I also tested with CMake 3.14.4 and got the same error) and got the following error:

 CMake Error at /cluster/apps/gcc-4.8.5/cmake-3.14.4-2yckzriatk5ei7cuqncwz5il26gb63oz/share/cmake-3.14/Modules/FindFreetype.cmake:178
 (set_property):
   set_property can not be used on an ALIAS target.
 Call Stack (most recent call first):
   cmake/Freetype.cmake:1 (find_package)
   cmake/FindFTGL.cmake:27 (include)
   libEM/CMakeLists.txt:180 (find_package)

Is this a known problem ?

What version of CMake do you recommend to build eman2 ?

Any help is appreciated.

Revert 6af3d53e11c34ad0c255b053b8ad09e94a30ba2e to enable openmpi tests

mergetomoseg.py command not found in EMAN2

I am using the latest version of EMAN2.2 and I am trying to segment a tomogram using the CNN protocol in EMAN. Annotation works quite fine for most of the features however, in some cases microtubules are being picked as single membrane feature, even after extensive training. In the online instruction it has been suggested to train the neuronal network separately on the features that cause ambiguity and then run annotations against each other using mergetomoseg.py <annotation #1> <annotation #2> <...> --output . However, when I run mergetomoseg.py, I get the error message that the command not found. I am wondering if you have any suggestion for this issue? Is there any replacement for this command in EMAN2.2?

Thanks very much for your help in advance.

Useless code in libEM/emdata_transform.cpp

This is libEM/emdata_transform.cpp:1242-1245:

				float k2 = (float)(kx*kx+ky*ky);
				if (k2==0) { continue;}
				float phiK =0;
				if (k2>0) phiK= jxjyatan2[ (ky+Mid-1)*End + kx+Mid-1];  phiK= atan2((float)ky,(float)kx);

I observe first that unless the computation of k2 overflows, it never produces a negative value, and that if it produces exactly zero then the last two lines are not reached.

In that case, it is not necessary to check explicitly at line 1245 whether k2 exceeds 0. More significantly, however, the value copied into phiK from jxjyatan2 is always immediately overwritten by the result of calling atan2(). This probably constitutes only a trivial performance problem as long as the computed index into jxjyatan2 is a valid one, but it begs the question of whether something else was intended here.

An analogous computation of phiQ appears deeper in the same loop nest, at lines 1255-1258. Comments analogous to the above apply to it.

Incorrect convolution processing under some circumstances

This is libEM/processor.cpp:13695-13697:

		EMData* selem = params["selem"];
		float *sd = selem->get_data();
		kernel = vector<float>(sd, sd + sizeof sd / sizeof sd[0]);

The intent appears to be to construct a vector<float> representation of the data referenced by selem->get_data(), but it does not actually do that. The problem is that sizeof sd evaluates to the size of a pointer, probably 8 bytes on most current machines, whereas what is needed for computing the number of elements that way is the size of the whole array to which sd points.

It looks like changing the last of those lines to

		kernel = vector<float>(sd, sd + selem->get_size());

might produce the wanted result.

Fix e2pdbviewer.py

Traceback (most recent call last):
  File "/Users/shadow_walker/eman2/bin/e2pdbviewer.py", line 34, in <module>
    from emdataitem3d import EMStructureItem3D
ImportError: cannot import name EMStructureItem3D

Bogus method wrappers

It seems to be standard practice in this codebase to insert cast operators into the declarations of Boost.Python method wrappers, such as in this example from line 612 of libpyEM/libpyAligner2.cpp:

        .def("compute_1d_fromimage", (std::vector<float,std::allocator<float> > (EMAN::EMAN2Ctf::*)(int, float, EMAN::EMData*) )&EMAN::EMAN2Ctf::compute_1d, (std::vector<float,std::allocator<float> > (EMAN_EMAN2Ctf_Wrapper::*)(int, float, EMAN::EMData*))&EMAN_EMAN2Ctf_Wrapper::default_compute_1d_fromimage)

I guess this is to match overloads. Such casts should be fine, provided that the target type of the cast is compatible with the type of the function. If it isn't compatible, however, as in the case of the above example, then undefined behavior ensues when the function is called via the wrapper. In practice, it looks like the mismatches of this type appearing in the codebase are likely to produce genuine misbehavior.

The issue with the above example is that EMAN2Ctf::compute_1d takes four arguments (one with a default value), not three, and the type of the third is EMAN::Ctf::CtfType, not EMAN::EMData *.

Several other occurrences of such issues appear in libpyEM/libpyTransform2.cpp:

at line 228 (Vec4f.set_value)
at line 254 (Vec3f.set_value)
at line 305 (Vec3i.set_value)
at line 352 (Vec2f.set_value)
at line 578(Transform.translate_newbasis overload)

The problem in all the vector cases is that the relevant set_value() methods in the vector templates declare their arguments to be const references, whereas the casts specify that they are ordinary passed-by-value built-in types. The problem in the Transform case appears to be that the wrong method is being wrapped -- from the signature and a comparison to the order of method declarations in libEM/transform.h, it appears that the intention was to wrap the fourth form of Transform.translate(), not a second form of Transform.translate_newBasis() (which does not exist).

SyntaxError: invalid syntax

This was mentioned in #204. Tracking here as any other PRs will be failing until this is addressed.

Error:

Compiling ./examples/e2ddd_external.py ...
  File "./examples/e2ddd_external.py", line 165
    if options.patch != 1 1: cmd += " -Patch {} ".format(options.patch)
                          ^
SyntaxError: invalid syntax

Suspect it is caused by this,

eman2/examples/e2ddd_external.py

Line 165 in 98bea25

if options.patch != 1 1: cmd += " -Patch {} ".format(options.patch)

ImportError: No module named past.utils

I have installed EMAN2 following this page: https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda/2.22

I'm working on my PC, the system is Ubuntu 16.04.

When I'm trying to test, the python e2version.py works fine. Here's the output:

EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )
Your EMAN2 is running on: Linux-4.8.0-36-generic-x86_64-with-debian-stretch-sid 4.8.0-36-generic
Your Python version is: 2.7.15

And when running e2speedtest.py, the above error occurred:

ImportError: No module named past.utils

Could you give me some advice?

Thank you so much!!!

GUI: text field too small in e2projectmanager

In e2projectmanager, we cannot run e2initialmodel.py jobs because the "symmetry number" field is too small to enter a valid number (it's only a few pixels wide). As a workaround, we have been running e2initialmodel.py in the shell.

This is on:

EMAN 2.22 final (GITHUB: 2018-08-20 20:33 - commit: f4f3952 )
Your EMAN2 is running on: Mac OS 10.14.1 x86_64
Your Python version is: 2.7.14

NameError: global name 'EMANVERSION' is not defined

Hi specialists,

I am trying install EMAN2.2 (centos6 or centos7 version). But when I ran e2display.py and failed with a error as following.

$ e2display.py
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2display.py", line 34, in
from EMAN2 import EMANVERSION, E2init, E2end, EMData, base_name, file_exists, EMArgumentParser
ImportError: cannot import name EMANVERSION

I tried other programmes. e2proc3d.py is ok for both versions, but e2proc2d.py or e2reliontoeman.py didn't work for neither versions.

$ e2reliontoeman.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 157, in
main()
File "/home/jianhaoc/s/EMAN22centos7/bin/e2reliontoeman.py", line 56, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined

$ e2proc2d.py --help
Traceback (most recent call last):
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 1171, in
main()
File "/home/jianhaoc/s/EMAN22centos6/bin/e2proc2d.py", line 174, in main
parser = EMArgumentParser(usage=usage,version=EMANVERSION)
NameError: global name 'EMANVERSION' is not defined

Am I missing something? Thank you!

Regards,
Jianhao

Tkinter issue with binary installation

When using e2projectmanager.py, python has an issue with its tk support. I am using EMAN2.2alpha binary installation in CentOS 7.

The error is the following:

import _tkinter # If this fails your Python may not be configured for Tk
ImportError: No module named _tkinter

Other version I have for python do not have this issue.

Cheers,

Bug/needs improvement: emimagemx

Steps to reproduce:

python -m eman2_gui.emimagemx
Click outside of the image stack

Traceback (most recent call last):
  File "/miniconda/lib/python2.7/site-packages/eman2_gui/emimagemx.py", line 1968, in mouseReleaseEvent
    self.__app_mode_mouse_up(event)
  File "/miniconda/lib/python2.7/site-packages/eman2_gui/emimagemx.py", line 1729, in __app_mode_mouse_up
    self.mx_mouseup.emit(event, lc)
TypeError: EMImageMXWidget.mx_mouseup[QMouseEvent, tuple].emit(): argument 2 has unexpected type 'NoneType'

Cannot install EMAN2 2.3 on Ubuntu 18.04

I'm having difficulty installing EMAN2 2.3 on an Ubuntu 18.04 machine.

Following instructions, I run

bash eman2.3.linux64.sh

Installation proceeds for a while, but eventually this error is printed

wcwidth-0.1.7        | 25 KB     | ########## | 100%
blas-1.0             | 6 KB      | ########## | 100%
openmpi-2.0.2        | 2.6 MB    | ########## | 100%
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... ERROR conda.core.link:_execute_post_link_actions(658): An error occurred while installing package 'conda-forge::pyopengl-3.1.0-py27_0'.
LinkError: post-link script failed for package conda-forge::pyopengl-3.1.0-py27_0
running your command again with `-v` will provide additional information
location of failed script: /home/ubuntu/EMAN2/bin/.pyopengl-post-link.sh
==> script messages <==
<None>

Attempting to roll back.


failed
ERROR conda.core.link:_execute(568): An error occurred while installing package 'conda-forge::pyopengl-3.1.0-py27_0'.
LinkError: post-link script failed for package conda-forge::pyopengl-3.1.0-py27_0
running your command again with `-v` will provide additional information
location of failed script: /home/ubuntu/EMAN2/bin/.pyopengl-post-link.sh
==> script messages <==
<None>

Attempting to roll back.

Rolling back transaction: ...working... done

CondaMultiError: LinkError: post-link script failed for package conda-forge::pyopengl-3.1.0-py27_0
running your command again with `-v` will provide additional information
location of failed script: /home/ubuntu/EMAN2/bin/.pyopengl-post-link.sh
==> script messages <==
<None>


+ cat

INSTALLATION IS NOW COMPLETE

Afterwards, I cannot get EMAN2 binaries to work, with the following error:

ubuntu@ip-172-31-12-165:~$ e2proc3d.py
Traceback (most recent call last):
  File "/home/ubuntu/EMAN2/bin/e2proc3d.py", line 37, in <module>
    from past.utils import old_div
ImportError: No module named past.utils

Any help is appreciated! A similar error occurred when I tried to install the previous version 2.22

The machine is a relatively fresh EC2 instance - I did have an existing Anaconda3 install, but I removed it from .bashrc and my environment prior to installing EMAN2.

Also, e2version.py appears to work:

ubuntu@ip-172-31-12-165:~$ e2version.py
EMAN 2.3 final (GITHUB: 2019-04-25 14:05 - commit: 6aaac88 )
Your EMAN2 is running on: Linux-4.15.0-1045-aws-x86_64-with-debian-buster-sid 4.15.0-1045-aws
Your Python version is: 2.7.16

Fix e2refinetorelion2d.py

$ e2refinetorelion2d.py -h
Running e2refinetorelion2d.py
Traceback (most recent call last):
  File "/Users/shadow_walker/eman2/bin/e2refinetorelion2d.py", line 79, in <module>
    (options, args) = parser.parse_args()
  File "/Users/shadow_walker/EMAN2/lib/EMAN2.py", line 506, in parse_args
    parsedargs = argparse.ArgumentParser.parse_args(self)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1701, in parse_args
    args, argv = self.parse_known_args(args, namespace)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1733, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1939, in _parse_known_args
    start_index = consume_optional(start_index)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1879, in consume_optional
    take_action(action, args, option_string)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 1807, in take_action
    action(self, namespace, argument_values, option_string)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 996, in __call__
    parser.print_help()
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 2340, in print_help
    self._print_message(self.format_help(), file)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 2314, in format_help
    return formatter.format_help()
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 281, in format_help
    help = self._root_section.format_help()
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 211, in format_help
    func(*args)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 211, in format_help
    func(*args)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 517, in _format_action
    help_text = self._expand_help(action)
  File "/Users/shadow_walker/anaconda/envs/eman/lib/python2.7/argparse.py", line 603, in _expand_help
    return self._get_help_string(action) % params
ValueError: unsupported format character '=' (0x3d) at index 41

Incorrect gauss initialization in e2pdb2em.py

e2pdb2em.py:212-216
Also, can you provide a reference for constants (Table 1)?

ImportError: No module named global_def

When I run this code on my local HPC cluster, I receive this error when running the refine.py script for multi-reference refinement:

Traceback (most recent call last):
  File "/opt/qb3/eman2-2.05/contrib/nogales/refine.py", line 35, in <module>
    import global_def
ImportError: No module named global_def
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.

Fix e2ctf

$ e2ctf.py --gui micrographs/BGal_000232.hdf &
[2] 95971
$ Using A/pix from header
Traceback (most recent call last):
  File "/anaconda/bin/e2ctf.py", line 2912, in newSet
    else : self.guirealim.set_data([EMData()])
  File "/anaconda/lib/python2.7/site-packages/emimage2d.py", line 463, in set_data
    self.auto_contrast(inspector_update=False,display_update=False)
  File "/anaconda/lib/python2.7/site-packages/emimage2d.py", line 530, in auto_contrast
    mean=self.data.get_attr("mean")
RuntimeError: NotExistingObjectException at /<some-path>/eman2/libEM/emdata_metadata.cpp:1148: error with 'mean': 'The requested key does not exist' caught

More recent runs:

$ e2ctf.py --gui micrographs/BGal_000232.hdf &
[1] 78530
$ Using A/pix from header
Traceback (most recent call last):
  File "/minicondas/bin/e2ctf.py", line 2917, in newSet
    else : self.guirealim.set_data([EMData()])
  File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 463, in set_data
    self.auto_contrast(inspector_update=False,display_update=False)
  File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 530, in auto_contrast
    mean=self.data.get_attr("mean")
RuntimeError

$ e2ctf.py --gui micrographs/BGal_000232.hdf
Using A/pix from header
Traceback (most recent call last):
  File "/minicondas/bin/e2ctf.py", line 2917, in newSet
    else : self.guirealim.set_data([EMData()])
  File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 463, in set_data
    self.auto_contrast(inspector_update=False,display_update=False)
  File "/minicondas/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 530, in auto_contrast
    mean=self.data.get_attr("mean")
RuntimeError: NotExistingObjectException at /<some-path>/eman2/libEM/emdata_metadata.cpp:1148: error with 'mean': 'The requested key does not exist' caught

Wrong python being installed in conda environment?

I have been trying to install EMAN 2.22 and 2.3 on linux and get the same errors about not being able to import: from past.utils import old_div

As far as I can tell, this is backwards-compat shim, but the python installed by the eman2 installer is not python 3... so this is not needed?

Bug: emimage2d

Steps to reproduce:

python -m eman2_gui.emimage2d
Shift + scroll mouse wheel

Traceback (most recent call last):
  File "/miniconda/lib/python2.7/site-packages/eman2_gui/emimage2d.py", line 1748, in wheelEvent
    self.mousewheel.emit(event)
TypeError: EMImage2DWidget.mousewheel[QMouseEvent].emit(): argument 1 has unexpected type 'QWheelEvent'

Bug in emplot2d

Data file to plot:

Steps to reproduce:

Run e2display.py
Select file to plot
Click Plot 2D
Click one of the data points

$ Traceback (most recent call last):
  File "/minicondas/envs/eman-deps-11-gui/lib/python2.7/site-packages/eman2_gui/emplot2d.py", line 861, in mousePressEvent
    self.update_selected((event.x(),event.y()),lc)
  File "/miniconda/envs/eman-deps-11-gui/lib/python2.7/site-packages/eman2_gui/emplot2d.py", line 780, in update_selected
    if r[srt[i]]<3 : self.selected.append(srt[i])
IndexError: index 4 is out of bounds for axis 0 with size 4

Could NOT find OpenGL

I was following the instructions on the EMAN wiki to build from source, but I'm stuck at the cmake step. Here is the error output:

BEGIN ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h

HDF5_INCLUDE_PATH: /home/xguan/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /home/xguan/anaconda2/envs/eman-env/lib/libhdf5.so
Searching in /home/xguan/anaconda2/envs/eman-env/include for hdf5.h and ...
FIND_LIBRARY: HDF5_LIBRARY NAMES hdf5 PATHS /lib /home/xguan/anaconda2/envs/eman-env/lib

END ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h

HDF5_INCLUDE_PATH: /home/xguan/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /home/xguan/anaconda2/envs/eman-env/lib/libhdf5.so
HDF5_LIBRARY: /home/xguan/anaconda2/envs/eman-env/lib/libhdf5.so
PNG_LIBRARIES: /home/xguan/anaconda2/envs/eman-env/lib/libpng.so;/home/xguan/anaconda2/envs/eman-env/lib/libz.so
CMake Error at /home/xguan/anaconda2/envs/eman-env/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find OpenGL (missing: OPENGL_gl_LIBRARY OPENGL_INCLUDE_DIR)
Call Stack (most recent call first):
/home/xguan/anaconda2/envs/eman-env/share/cmake-3.8/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
/home/xguan/anaconda2/envs/eman-env/share/cmake-3.8/Modules/FindOpenGL.cmake:170 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
cmake/OpenGL.cmake:1 (find_package)
libEM/CMakeLists.txt:175 (include)

Thanks for your help!

libEM/sparx/util_sparx.cpp does not compile on CentOS6 6.7 ?

I see the following error when trying to build with gcc on CentOS 6.7,

libEM/sparx/util_sparx.cpp:26532: error: ‘fftwf_alloc_real’ was not declared in this scope

.... and the source file lists,

26529 #ifdef _WIN32
26530 float _cvv = (float *) malloc(2_size_sizeof(float));
26531 #else
26532 float *cvv = fftwf_alloc_real(2_size);
26533 #endif //_WIN32
26534

There is no other instance of "fftwf_alloc_real" in this file. I'm building with libfftw3f.so.3.3.2. I have not built the source in a few months, but this configuration used to work.

SyntaxError: keyword argument repeated

This error comes up when compiled with py3.

eman2/examples/e2ddd_external.py

Lines 87 to 88 in 98bea25

 parser.add_argument("--dark", default = None, type=str, help="Use this dark reference.",guitype='filebox', browser="EMMovieDataTable(withmodal=True,multiselect=True)", row=2, col=0,rowspan=1, colspan=2, mode="align",mode="movie") 

 parser.add_argument("--gain", default = None, type=str, help="Use this gain reference.",guitype='filebox', browser="EMMovieDataTable(withmodal=True,multiselect=True)", row=3, col=0,rowspan=1, colspan=2, mode="align",mode="movie")

*** Error compiling './examples/e2ddd_external.py'...
  File "./examples/e2ddd_external.py", line 89
    parser.add_argument("--dark",  default = None, type=str, help="Use this dark reference.", guitype='filebox',  browser="EMMovieDataTable(withmodal=True,multiselect=True)",  row=2, col=0, rowspan=1, colspan=2, mode="align", mode="movie")
                                                                                                                                                                                                                                 ^
SyntaxError: keyword argument repeated

[TODO] Re-enable write jpeg test on mac jenkins

test_write_jpeg started failing on Mac Jenkins, but not on TravisCI, and has been disabled in 29ee455, until it is sorted out.

Error in sxcompute_isac_avg.py", line 114, in compute_average_noctf frc = fsc(fft(sumavg), fft(sumctf2)) UnboundLocalError: local variable 'sumavg' referenced before assignment

I've looked at the code and this seems to be a bug. I'm coping complete Traceback below. Please let me know if you have questions or need more information. Thank you.

mpirun -np 12 sxcompute_isac_avg.py --stack='start.hdf' --isac_dir='Class2D4' --output_dir='Class2D4/beautify2d_s' --radius=62 --noctf --pixel_size=1.62
2018-02-23_11:27:01 => Postprocessing ISAC 2D averages starts
2018-02-23_11:27:01 => Executed successfully: mkdir Class2D4/beautify2d_s
Class2D4
we don't get pixel size value
Traceback (most recent call last):
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 114, in compute_average_noctf
frc = fsc(fft(sumavg), fft(sumctf2))
UnboundLocalError: local variable 'sumavg' referenced before assignment

Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.

Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
Shutdown complete, exiting
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 110, in compute_average_noctf
tmp = cosinemask(rot_shift2D(mlist[im], alpha, sx, sy, mr), radius)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 1011, in rot_shift2D
if mirror: img.process_inplace("xform.mirror", {"axis":'x'})
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 111, in compute_average_noctf
tmp = fft(tmp)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 416, in fft
return e.do_fft()
Traceback (most recent call last):
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 114, in compute_average_noctf
frc = fsc(fft(sumavg), fft(sumctf2))
UnboundLocalError: local variable 'sumavg' referenced before assignment
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 110, in compute_average_noctf
tmp = cosinemask(rot_shift2D(mlist[im], alpha, sx, sy, mr), radius)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 1010, in rot_shift2D
img = img.rot_scale_trans2D_background(angle, sx, sy, scale)
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 110, in compute_average_noctf
tmp = cosinemask(rot_shift2D(mlist[im], alpha, sx, sy, mr), radius)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/morphology.py", line 1364, in cosinemask
return Util.cosinemask(im, radius, cosine_width, bckg, s)
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 110, in compute_average_noctf
tmp = cosinemask(rot_shift2D(mlist[im], alpha, sx, sy, mr), radius)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 1010, in rot_shift2D
img = img.rot_scale_trans2D_background(angle, sx, sy, scale)
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 110, in compute_average_noctf
tmp = cosinemask(rot_shift2D(mlist[im], alpha, sx, sy, mr), radius)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/morphology.py", line 1364, in cosinemask
return Util.cosinemask(im, radius, cosine_width, bckg, s)
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 111, in compute_average_noctf
tmp = fft(tmp)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 416, in fft
return e.do_fft()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 111, in compute_average_noctf
tmp = fft(tmp)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 416, in fft
return e.do_fft()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 111, in compute_average_noctf
tmp = fft(tmp)
File "/usr/local/EMAN2-SPHIRE/lib/python2.7/site-packages/fundamentals.py", line 416, in fft
return e.do_fft()
Traceback (most recent call last):
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 550, in
main()
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 447, in main
if Tracker["constants"]["noctf"]: ini_avg, frc = compute_average_noctf(mlist, Tracker["constants"]["radius"])
File "/usr/local/EMAN2-SPHIRE/bin/sxcompute_isac_avg.py", line 114, in compute_average_noctf
frc = fsc(fft(sumavg), fft(sumctf2))
UnboundLocalError: local variable 'sumavg' referenced before assignment

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[3037,1],3]
Exit code: 1

Failing branch: add_tests_sphire1_3

@lucalusn , the commits on branch add_tests_sphire1_3 seem to be always failing. If the tests are not important for you, can you skip tests by including "[ci skip]" in your commit messages or move your branch from cryoem/eman2 to your own fork.

Move parts of e2ctf and e2eulerxplor that are used in other places to libpyEM

Some code in e2ctf and e2eulerxplor is called from some places in libpyEM. This prevents those modules to be run as programs which is useful for testing.

To be addressed after the release.

Revert 6dd50f7d3da7026fb2bd1b1dfe58c6a0b3556f5b to enable pickle tests

Please provide a list of EMAN2 dependencies

Hi,

Neither on https://blake.bcm.edu/emanwiki/EMAN2 nor on github the list of required dependencies for EMAN2 is available.

Install dependencies

conda install cmake=3.9 -c defaults
conda install eman-deps=14 -c cryoem -c defaults -c conda-forge

Not everybody uses conda. On many HPC clusters, conda is not available. On our HPC cluster, we do not support conda. Therefore could you please provide a list of dependencies required for EMAN2 ?

Best regards

Sam

Failed to build from source

Dear developer:

I am trying to build from source according to the webpage.

However when I execute the cmake line I encounter the following error:

(eman-env) user@ubuntu16:~/EMANSRC/eman2-src$ sudo cmake ../eman2
CMake Deprecation Warning at CMakeLists.txt:9 (cmake_policy):
  The OLD behavior for policy CMP0002 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.


# conda environments:
#
                         /home/user/EMAN2
base                  *  /usr/local/anaconda2
eman-env                 /usr/local/anaconda2/envs/eman-env
py36                     /usr/local/anaconda2/envs/py36

CMAKE_PREFIX_PATH: /usr/local/anaconda2/envs/eman-env;/usr/local/anaconda2/envs/eman-env/..
PYTHON_EXECUTABLE:   /usr/local/anaconda2/envs/eman-env/bin/python
PYTHON_LIBRARIES:    /usr/local/anaconda2/envs/eman-env/lib/libpython2.7.so
PYTHON_INCLUDE_DIRS: /usr/local/anaconda2/envs/eman-env/include/python2.7
PYTHON_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include/python2.7
PYTHON_INCLUDE_DIR:  /usr/local/anaconda2/envs/eman-env/include/python2.7
NUMPY_INCLUDE_DIR: /usr/local/anaconda2/envs/eman-env/lib/python2.7/site-packages/numpy/core/include
Python site-packages: /usr/local/anaconda2/envs/eman-env/lib/python2.7/site-packages

### BEGIN ### CHECK_REQUIRED_LIB FFTW3F fftw3f fftw3.h libfftw3f-3
FFTW3F_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3F_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3f.so
Searching in /usr/local/anaconda2/envs/eman-env/include for fftw3.h and  ...
FIND_LIBRARY: FFTW3F_LIBRARY NAMES fftw3f libfftw3f-3 PATHS /lib /usr/local/anaconda2/envs/eman-env/lib
### END ### CHECK_REQUIRED_LIB FFTW3F fftw3f fftw3.h libfftw3f-3
FFTW3F_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3F_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3f.so

### BEGIN ### CHECK_REQUIRED_LIB FFTW3D fftw3 fftw3.h libfftw3-3
FFTW3D_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3D_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3.so
Searching in /usr/local/anaconda2/envs/eman-env/include for fftw3.h and  ...
FIND_LIBRARY: FFTW3D_LIBRARY NAMES fftw3 libfftw3-3 PATHS /lib /usr/local/anaconda2/envs/eman-env/lib
### END ### CHECK_REQUIRED_LIB FFTW3D fftw3 fftw3.h libfftw3-3
FFTW3D_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
FFTW3D_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libfftw3.so
TIFF_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libtiff.so
JPEG_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libjpeg.so

### BEGIN ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h
HDF5_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libhdf5.so
Searching in /usr/local/anaconda2/envs/eman-env/include for hdf5.h and  ...
FIND_LIBRARY: HDF5_LIBRARY NAMES hdf5  PATHS /lib /usr/local/anaconda2/envs/eman-env/lib
### END ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h
HDF5_INCLUDE_PATH: /usr/local/anaconda2/envs/eman-env/include
HDF5_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libhdf5.so
HDF5_LIBRARY: /usr/local/anaconda2/envs/eman-env/lib/libhdf5.so
PNG_LIBRARIES: /usr/local/anaconda2/envs/eman-env/lib/libpng.so;/usr/local/anaconda2/envs/eman-env/lib/libz.so
CMake Error at /usr/local/anaconda2/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find OpenGL (missing: OPENGL_gl_LIBRARY)
Call Stack (most recent call first):
  /usr/local/anaconda2/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
  /usr/local/anaconda2/share/cmake-3.9/Modules/FindOpenGL.cmake:170 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  cmake/OpenGL.cmake:1 (find_package)
  libEM/CMakeLists.txt:175 (include)


-- Configuring incomplete, errors occurred!
See also "/home/user/EMANSRC/eman2-src/CMakeFiles/CMakeOutput.log".
See also "/home/user/EMANSRC/eman2-src/CMakeFiles/CMakeError.log".

But I think I have already installed opengl

(eman-env) user@ubuntu16:~/EMANSRC/eman2-src$ locate libGL.so
/home/users/user/MATLAB/R2017b/sys/opengl/lib/glnxa64/libGL.so.1
/home/users/user/MATLAB/R2017b/sys/opengl/lib/glnxa64/libGL.so.1.6.0
/usr/lib/i386-linux-gnu/mesa/libGL.so.1
/usr/lib/i386-linux-gnu/mesa/libGL.so.1.2.0
/usr/lib/nvidia-387/libGL.so
/usr/lib/nvidia-387/libGL.so.1
/usr/lib/nvidia-387/libGL.so.1.0.0
/usr/lib/x86_64-linux-gnu/libGL.so
/usr/lib/x86_64-linux-gnu/mesa/libGL.so
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1
/usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0
/usr/lib32/nvidia-387/libGL.so
/usr/lib32/nvidia-387/libGL.so.1
/usr/lib32/nvidia-387/libGL.so.1.0.0

Any suggestions will be appreciated!

Thanks!

lacks a type converter from python utf string or bytes to std::string

diff --git libpyEM/libpyTypeConverter2.cpp libpyEM/libpyTypeConverter2.cpp
index c9c4461fa..5aa4ff983 100644
--- libpyEM/libpyTypeConverter2.cpp
+++ libpyEM/libpyTypeConverter2.cpp
@@ -112,6 +112,7 @@ BOOST_PYTHON_MODULE(libpyTypeConverter2)
EMAN::EMObject_to_python();
EMAN::Dict_to_python();
EMAN::String_to_python();

EMAN::String_from_python();
EMAN::Dict_from_python();

EMAN::tuple3_to_pythonEMAN::IntPoint();
diff --git libpyEM/typeconverter.h libpyEM/typeconverter.h
index ace5ab315..34b474b55 100644
--- libpyEM/typeconverter.h
+++ libpyEM/typeconverter.h
@@ -915,6 +916,51 @@ namespace EMAN {

};
struct String_from_python {
```
  String_from_python() {
```

  	boost::python::converter::registry::push_back(

```
  		&convertible,
```
```
  		&construct,
```

  		boost::python::type_id<std::string>());

```
  }
```

  // Determine if obj_ptr can be converted in a std::string

  static void* convertible(PyObject* obj_ptr) {

  	if (!PyUnicode_Check(obj_ptr) && !PyBytes_Check(obj_ptr)) {

```
  		return 0;
```
```
  	}
```
```
  	return obj_ptr;
```
```
  }
```

  // Convert obj_ptr into a std::string

```
  static void construct(
```
```
  	PyObject* obj_ptr,
```

  	boost::python::converter::rvalue_from_python_stage1_data* data)	{

```
  	const char* value(nullptr);
```

  	boost::python::object temp_bytes_obj;

```
  	if (PyUnicode_Check(obj_ptr)) {
```

  		PyObject * temp_bytes(PyUnicode_AsEncodedString(obj_ptr, "UTF-8", "strict")); // Owned reference

```
  		if (temp_bytes != nullptr) {
```

  			// Take over lifetime management of temp_bytes

  			temp_bytes_obj = boost::python::object(boost::python::handle<>(temp_bytes));

  			value = PyBytes_AS_STRING(temp_bytes);

```
  		} else {
```

  			boost::python::throw_error_already_set();

```
  		}
```

  	} else if (PyBytes_Check(obj_ptr)) {

  		value = PyBytes_AS_STRING(obj_ptr);

```
  	} else {
```

  		boost::python::throw_error_already_set();

```
  	}
```

  	if (value == nullptr) boost::python::throw_error_already_set();

```
  	void* storage = (
```

  		(boost::python::converter::rvalue_from_python_storage<std::string>*)

```
  		data)->storage.bytes;
```
```
  	new (storage) std::string(value);
```
```
  	data->convertible = storage;		
```
```
	}
```
};

}

Fix e2cmpxplor.py

Traceback (most recent call last):
  File "/Users/shadow_walker/eman2/bin/e2cmpxplor.py", line 36, in <module>
    from e2eulerxplor import InputEventsManager
ImportError: cannot import name InputEventsManager

[TODO] Re-enable disabled tests during python 3 transition

2.3 install issues

We have several researchers clamoring for this new and improved version of EMAN2, but I am having a heck of a time getting it to run. To troubleshoot, I have started my install attempts in a docker container. The install feels like it could use some work. I can try to run parts of EMAN2 after an install and figure out which things are missing here and there, but that feels inefficient if there are folks who have this running for them.

I'm hopeful that someone more familiar with what is needed could give it a once-over and update things so all needed packages are properly installed (preferably once?). It would also be really nice if the site that the installer points to for documentation (https://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda) had some. If there is some way in which I can contribute I am open to suggestions.

Here is the dockerfile:

FROM ubuntu:18.04

RUN apt-get update && \
    apt-get -y install build-essential \
                       libgl1-mesa-dev \
                       libglu1-mesa \
                       libglu1-mesa-dev \
                       libsm-dev \
                       libxrender-dev \
                       mesa-common-dev \
                       mesa-utils \
                       wget

RUN cd /tmp && \
    wget --quiet https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh && \
    bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2

ENV PATH="/opt/EMAN2/bin:$PATH"

And the log from a build attempt:

$ docker build -t eman2:2.3-testing .
Sending build context to Docker daemon   2.56kB
Step 1/4 : FROM ubuntu:18.04
 ---> d131e0fa2585
Step 2/4 : RUN apt-get update &&     apt-get -y install build-essential                        libgl1-mesa-dev                        libglu1-mesa                        libglu1-mesa-dev                        libsm-dev                        libxrender-dev                        mesa-common-dev                        mesa-utils                        wget
 ---> Running in b96d2a72e160
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Fetched 16.1 MB in 3s (5257 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu ca-certificates cpp cpp-7
  dirmngr dpkg-dev fakeroot g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gnupg
  gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client gpg-wks-server gpgconf
  gpgsm libalgorithm-diff-perl libalgorithm-diff-xs-perl
  libalgorithm-merge-perl libasan4 libasn1-8-heimdal libassuan0 libatomic1
  libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libdpkg-perl
  libdrm-amdgpu1 libdrm-common libdrm-dev libdrm-intel1 libdrm-nouveau2
  libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libexpat1
  libfakeroot libfile-fcntllock-perl libgbm1 libgcc-7-dev libgcc1
  libgdbm-compat4 libgdbm5 libgl1 libgl1-mesa-dri libglapi-mesa libgles1
  libgles2 libglvnd-core-dev libglvnd-dev libglvnd0 libglx-mesa0 libglx0
  libgomp1 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libisl19 libitm1
  libkrb5-26-heimdal libksba8 libldap-2.4-2 libldap-common libllvm7
  liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libmpx2 libnpth0 libopengl0
  libpciaccess0 libperl5.26 libpsl5 libpthread-stubs0-dev libquadmath0
  libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules
  libsasl2-modules-db libsensors4 libsm6 libsqlite3-0 libssl1.1
  libstdc++-7-dev libstdc++6 libtsan0 libubsan0 libwayland-client0
  libwayland-server0 libwind0-heimdal libx11-6 libx11-data libx11-dev
  libx11-doc libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0
  libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev
  libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev
  libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev
  libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1
  libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev
  libxext6 libxfixes-dev libxfixes3 libxrender1 libxshmfence-dev libxshmfence1
  libxxf86vm-dev libxxf86vm1 linux-libc-dev make manpages manpages-dev
  multiarch-support netbase openssl patch perl perl-modules-5.26
  pinentry-curses publicsuffix readline-common x11-common x11proto-core-dev
  x11proto-damage-dev x11proto-dev x11proto-fixes-dev x11proto-xext-dev
  x11proto-xf86vidmode-dev xorg-sgml-doctools xtrans-dev xz-utils
Suggested packages:
  binutils-doc cpp-doc gcc-7-locales dbus-user-session libpam-systemd
  pinentry-gnome3 tor debian-keyring g++-multilib g++-7-multilib gcc-7-doc
  libstdc++6-7-dbg gcc-multilib autoconf automake libtool flex bison gdb
  gcc-doc gcc-7-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
  libasan4-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg
  libmpx2-dbg libquadmath0-dbg parcimonie xloadimage scdaemon glibc-doc git
  bzr gdbm-l10n libice-doc pciutils libsasl2-modules-gssapi-mit
  | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp
  libsasl2-modules-sql lm-sensors libsm-doc libstdc++-7-doc libxcb-doc
  libxext-doc make-doc man-browser ed diffutils-doc perl-doc
  libterm-readline-gnu-perl | libterm-readline-perl-perl pinentry-doc
  readline-doc
The following NEW packages will be installed:
  binutils binutils-common binutils-x86-64-linux-gnu build-essential
  ca-certificates cpp cpp-7 dirmngr dpkg-dev fakeroot g++ g++-7 gcc gcc-7
  gcc-7-base gnupg gnupg-l10n gnupg-utils gpg gpg-agent gpg-wks-client
  gpg-wks-server gpgconf gpgsm libalgorithm-diff-perl
  libalgorithm-diff-xs-perl libalgorithm-merge-perl libasan4 libasn1-8-heimdal
  libassuan0 libatomic1 libbinutils libbsd0 libc-dev-bin libc6-dev libcc1-0
  libcilkrts5 libdpkg-perl libdrm-amdgpu1 libdrm-common libdrm-dev
  libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0
  libegl1 libelf1 libexpat1 libfakeroot libfile-fcntllock-perl libgbm1
  libgcc-7-dev libgdbm-compat4 libgdbm5 libgl1 libgl1-mesa-dev libgl1-mesa-dri
  libglapi-mesa libgles1 libgles2 libglu1-mesa libglu1-mesa-dev
  libglvnd-core-dev libglvnd-dev libglvnd0 libglx-mesa0 libglx0 libgomp1
  libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal
  libheimntlm0-heimdal libhx509-5-heimdal libice-dev libice6 libisl19 libitm1
  libkrb5-26-heimdal libksba8 libldap-2.4-2 libldap-common libllvm7
  liblocale-gettext-perl liblsan0 libmpc3 libmpfr6 libmpx2 libnpth0 libopengl0
  libpciaccess0 libperl5.26 libpsl5 libpthread-stubs0-dev libquadmath0
  libreadline7 libroken18-heimdal libsasl2-2 libsasl2-modules
  libsasl2-modules-db libsensors4 libsm-dev libsm6 libsqlite3-0 libssl1.1
  libstdc++-7-dev libtsan0 libubsan0 libwayland-client0 libwayland-server0
  libwind0-heimdal libx11-6 libx11-data libx11-dev libx11-doc libx11-xcb-dev
  libx11-xcb1 libxau-dev libxau6 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0
  libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev
  libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0
  libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev
  libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev
  libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6
  libxfixes-dev libxfixes3 libxrender-dev libxrender1 libxshmfence-dev
  libxshmfence1 libxxf86vm-dev libxxf86vm1 linux-libc-dev make manpages
  manpages-dev mesa-common-dev mesa-utils multiarch-support netbase openssl
  patch perl perl-modules-5.26 pinentry-curses publicsuffix readline-common
  wget x11-common x11proto-core-dev x11proto-damage-dev x11proto-dev
  x11proto-fixes-dev x11proto-xext-dev x11proto-xf86vidmode-dev
  xorg-sgml-doctools xtrans-dev xz-utils
The following packages will be upgraded:
  gcc-8-base libgcc1 libstdc++6
3 upgraded, 180 newly installed, 0 to remove and 2 not upgraded.
Need to get 81.0 MB of archives.
After this operation, 471 MB of additional disk space will be used.
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Get:93 http://archive.ubuntu.com/ubuntu bionic/main amd64 fakeroot amd64 1.22-2ubuntu1 [62.3 kB]
Get:94 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg-l10n all 2.2.4-1ubuntu1.2 [49.6 kB]
Get:95 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg-utils amd64 2.2.4-1ubuntu1.2 [127 kB]
Get:96 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg amd64 2.2.4-1ubuntu1.2 [467 kB]
Get:97 http://archive.ubuntu.com/ubuntu bionic/main amd64 pinentry-curses amd64 1.1.0-1 [35.8 kB]
Get:98 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-agent amd64 2.2.4-1ubuntu1.2 [227 kB]
Get:99 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-wks-client amd64 2.2.4-1ubuntu1.2 [91.9 kB]
Get:100 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpg-wks-server amd64 2.2.4-1ubuntu1.2 [84.9 kB]
Get:101 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gpgsm amd64 2.2.4-1ubuntu1.2 [215 kB]
Get:102 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 gnupg amd64 2.2.4-1ubuntu1.2 [249 kB]
Get:103 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-diff-perl all 1.19.03-1 [47.6 kB]
Get:104 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-diff-xs-perl amd64 0.04-5 [11.1 kB]
Get:105 http://archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]
Get:106 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-amdgpu1 amd64 2.4.95-1~18.04.1 [17.4 kB]
Get:107 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpciaccess0 amd64 0.14-1 [17.9 kB]
Get:108 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-intel1 amd64 2.4.95-1~18.04.1 [59.9 kB]
Get:109 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-radeon1 amd64 2.4.95-1~18.04.1 [21.7 kB]
Get:110 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-nouveau2 amd64 2.4.95-1~18.04.1 [16.5 kB]
Get:111 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libdrm-dev amd64 2.4.95-1~18.04.1 [121 kB]
Get:112 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libwayland-server0 amd64 1.16.0-1ubuntu1.1~18.04.1 [29.8 kB]
Get:113 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgbm1 amd64 18.2.8-0ubuntu0~18.04.2 [24.2 kB]
Get:114 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglapi-mesa amd64 18.2.8-0ubuntu0~18.04.2 [23.4 kB]
Get:115 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libwayland-client0 amd64 1.16.0-1ubuntu1.1~18.04.1 [23.8 kB]
Get:116 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb1 amd64 2:1.6.4-3ubuntu0.2 [9376 B]
Get:117 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri2-0 amd64 1.13-2~ubuntu18.04 [6920 B]
Get:118 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri3-0 amd64 1.13-2~ubuntu18.04 [6568 B]
Get:119 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-present0 amd64 1.13-2~ubuntu18.04 [5552 B]
Get:120 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-sync1 amd64 1.13-2~ubuntu18.04 [8808 B]
Get:121 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-xfixes0 amd64 1.13-2~ubuntu18.04 [9352 B]
Get:122 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence1 amd64 1.3-1 [5028 B]
Get:123 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libegl-mesa0 amd64 18.2.8-0ubuntu0~18.04.2 [87.5 kB]
Get:124 http://archive.ubuntu.com/ubuntu bionic/main amd64 libfile-fcntllock-perl amd64 0.22-3build2 [33.2 kB]
Get:125 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libllvm7 amd64 1:7-3~ubuntu0.18.04.1 [15.9 MB]
Get:126 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsensors4 amd64 1:3.4.0-4 [28.8 kB]
Get:127 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dri amd64 18.2.8-0ubuntu0~18.04.2 [6587 kB]
Get:128 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd0 amd64 1.0.0-2ubuntu2.2 [46.6 kB]
Get:129 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgles1 amd64 1.0.0-2ubuntu2.2 [11.2 kB]
Get:130 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-glx0 amd64 1.13-2~ubuntu18.04 [22.1 kB]
Get:131 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage1 amd64 1:1.1.4-3 [6934 B]
Get:132 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes3 amd64 1:5.0.3-1 [10.8 kB]
Get:133 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx-mesa0 amd64 18.2.8-0ubuntu0~18.04.2 [135 kB]
Get:134 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglx0 amd64 1.0.0-2ubuntu2.2 [28.1 kB]
Get:135 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1 amd64 1.0.0-2ubuntu2.2 [84.8 kB]
Get:136 http://archive.ubuntu.com/ubuntu bionic/main amd64 libglu1-mesa amd64 9.0.0-2.1build1 [168 kB]
Get:137 http://archive.ubuntu.com/ubuntu bionic/main amd64 xorg-sgml-doctools all 1:1.11-1 [12.9 kB]
Get:138 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-dev all 2018.4-4 [251 kB]
Get:139 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-core-dev all 2018.4-4 [2620 B]
Get:140 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxau-dev amd64 1:1.0.8-1 [11.1 kB]
Get:141 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [25.1 kB]
Get:142 http://archive.ubuntu.com/ubuntu bionic/main amd64 xtrans-dev all 1.3.5-1 [70.5 kB]
Get:143 http://archive.ubuntu.com/ubuntu bionic/main amd64 libpthread-stubs0-dev amd64 0.3-4 [4068 B]
Get:144 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb1-dev amd64 1.13-2~ubuntu18.04 [80.0 kB]
Get:145 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-dev amd64 2:1.6.4-3ubuntu0.2 [640 kB]
Get:146 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 mesa-common-dev amd64 18.2.8-0ubuntu0~18.04.2 [559 kB]
Get:147 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd-core-dev amd64 1.0.0-2ubuntu2.2 [12.9 kB]
Get:148 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libegl1 amd64 1.0.0-2ubuntu2.2 [31.9 kB]
Get:149 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgles2 amd64 1.0.0-2ubuntu2.2 [17.4 kB]
Get:150 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libopengl0 amd64 1.0.0-2ubuntu2.2 [31.3 kB]
Get:151 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglvnd-dev amd64 1.0.0-2ubuntu2.2 [3408 B]
Get:152 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-xcb-dev amd64 2:1.6.4-3ubuntu0.2 [9756 B]
Get:153 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri3-dev amd64 1.13-2~ubuntu18.04 [7384 B]
Get:154 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-randr0 amd64 1.13-2~ubuntu18.04 [16.4 kB]
Get:155 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-render0 amd64 1.13-2~ubuntu18.04 [14.7 kB]
Get:156 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-render0-dev amd64 1.13-2~ubuntu18.04 [18.4 kB]
Get:157 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-randr0-dev amd64 1.13-2~ubuntu18.04 [20.4 kB]
Get:158 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-shape0 amd64 1.13-2~ubuntu18.04 [5972 B]
Get:159 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-shape0-dev amd64 1.13-2~ubuntu18.04 [7144 B]
Get:160 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-xfixes0-dev amd64 1.13-2~ubuntu18.04 [11.7 kB]
Get:161 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-sync-dev amd64 1.13-2~ubuntu18.04 [10.6 kB]
Get:162 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-present-dev amd64 1.13-2~ubuntu18.04 [6972 B]
Get:163 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxshmfence-dev amd64 1.3-1 [3692 B]
Get:164 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-dri2-0-dev amd64 1.13-2~ubuntu18.04 [8472 B]
Get:165 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libxcb-glx0-dev amd64 1.13-2~ubuntu18.04 [27.9 kB]
Get:166 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-fixes-dev all 1:2018.4-4 [2620 B]
Get:167 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxfixes-dev amd64 1:5.0.3-1 [11.0 kB]
Get:168 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-damage-dev all 1:2018.4-4 [2620 B]
Get:169 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxdamage-dev amd64 1:1.1.4-3 [5028 B]
Get:170 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-xext-dev all 2018.4-4 [2620 B]
Get:171 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxext-dev amd64 2:1.3.3-1 [82.1 kB]
Get:172 http://archive.ubuntu.com/ubuntu bionic/main amd64 x11proto-xf86vidmode-dev all 2018.4-4 [2632 B]
Get:173 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxxf86vm-dev amd64 1:1.1.4-1 [13.3 kB]
Get:174 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgl1-mesa-dev amd64 18.2.8-0ubuntu0~18.04.2 [4428 B]
Get:175 http://archive.ubuntu.com/ubuntu bionic/main amd64 libglu1-mesa-dev amd64 9.0.0-2.1build1 [206 kB]
Get:176 http://archive.ubuntu.com/ubuntu bionic/main amd64 libice-dev amd64 2:1.0.9-2 [46.8 kB]
Get:177 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [48.7 kB]
Get:178 http://archive.ubuntu.com/ubuntu bionic/main amd64 libsm-dev amd64 2:1.2.2-1 [16.2 kB]
Get:179 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libx11-doc all 2:1.6.4-3ubuntu0.2 [2065 kB]
Get:180 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB]
Get:181 http://archive.ubuntu.com/ubuntu bionic/main amd64 libxrender-dev amd64 1:0.9.10-1 [24.9 kB]
Get:182 http://archive.ubuntu.com/ubuntu bionic/main amd64 manpages-dev all 4.15-1 [2217 kB]
Get:183 http://archive.ubuntu.com/ubuntu bionic/universe amd64 mesa-utils amd64 8.4.0-1 [34.3 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package liblocale-gettext-perl.
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Unpacking libbsd0:amd64 (0.8.7-1) ...
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Unpacking libxdmcp6:amd64 (1:1.1.2-3) ...
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Unpacking libxcb1:amd64 (1.13-2~ubuntu18.04) ...
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Unpacking libx11-data (2:1.6.4-3ubuntu0.2) ...
Selecting previously unselected package libx11-6:amd64.
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Unpacking libx11-6:amd64 (2:1.6.4-3ubuntu0.2) ...
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Unpacking libxext6:amd64 (2:1.3.3-1) ...
Selecting previously unselected package x11-common.
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dpkg-query: no packages found matching nux-tools
Unpacking x11-common (1:7.7+19ubuntu7.1) ...
Selecting previously unselected package libice6:amd64.
Preparing to unpack .../08-libice6_2%3a1.0.9-2_amd64.deb ...
Unpacking libice6:amd64 (2:1.0.9-2) ...
Selecting previously unselected package libsm6:amd64.
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Unpacking libsm6:amd64 (2:1.2.2-1) ...
Selecting previously unselected package libxxf86vm1:amd64.
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Unpacking libxxf86vm1:amd64 (1:1.1.4-1) ...
Selecting previously unselected package perl-modules-5.26.
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Unpacking perl-modules-5.26 (5.26.1-6ubuntu0.3) ...
Selecting previously unselected package libgdbm5:amd64.
Preparing to unpack .../12-libgdbm5_1.14.1-6_amd64.deb ...
Unpacking libgdbm5:amd64 (1.14.1-6) ...
Selecting previously unselected package libgdbm-compat4:amd64.
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Unpacking libgdbm-compat4:amd64 (1.14.1-6) ...
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Unpacking libperl5.26:amd64 (5.26.1-6ubuntu0.3) ...
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Unpacking perl (5.26.1-6ubuntu0.3) ...
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Unpacking gcc-8-base:amd64 (8.3.0-6ubuntu1~18.04) over (8.2.0-1ubuntu2~18.04) ...
Setting up gcc-8-base:amd64 (8.3.0-6ubuntu1~18.04) ...
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Unpacking libstdc++6:amd64 (8.3.0-6ubuntu1~18.04) over (8.2.0-1ubuntu2~18.04) ...
Setting up libstdc++6:amd64 (8.3.0-6ubuntu1~18.04) ...
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Unpacking libgcc1:amd64 (1:8.3.0-6ubuntu1~18.04) over (1:8.2.0-1ubuntu2~18.04) ...
Setting up libgcc1:amd64 (1:8.3.0-6ubuntu1~18.04) ...
Selecting previously unselected package libssl1.1:amd64.
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Unpacking libssl1.1:amd64 (1.1.0g-2ubuntu4.3) ...
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Unpacking openssl (1.1.0g-2ubuntu4.3) ...
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Unpacking ca-certificates (20180409) ...
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Unpacking libelf1:amd64 (0.170-0.4) ...
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Unpacking libexpat1:amd64 (2.2.5-3) ...
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Unpacking readline-common (7.0-3) ...
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Unpacking libreadline7:amd64 (7.0-3) ...
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Unpacking libsqlite3-0:amd64 (3.22.0-1) ...
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Unpacking netbase (5.4) ...
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Unpacking xz-utils (5.2.2-1.3) ...
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Unpacking libdrm-common (2.4.95-1~18.04.1) ...
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Unpacking libdrm2:amd64 (2.4.95-1~18.04.1) ...
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Unpacking libedit2:amd64 (3.1-20170329-1) ...
Selecting previously unselected package libpsl5:amd64.
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Unpacking wget (1.19.4-1ubuntu2.2) ...
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Unpacking libbinutils:amd64 (2.30-21ubuntu1~18.04.1) ...
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Unpacking binutils (2.30-21ubuntu1~18.04.1) ...
Selecting previously unselected package libc-dev-bin.
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Unpacking libc-dev-bin (2.27-3ubuntu1) ...
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Unpacking linux-libc-dev:amd64 (4.15.0-48.51) ...
Selecting previously unselected package libc6-dev:amd64.
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Unpacking libc6-dev:amd64 (2.27-3ubuntu1) ...
Selecting previously unselected package gcc-7-base:amd64.
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Unpacking gcc-7-base:amd64 (7.4.0-1ubuntu1~18.04) ...
Selecting previously unselected package libisl19:amd64.
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Unpacking libisl19:amd64 (0.19-1) ...
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Unpacking libmpfr6:amd64 (4.0.1-1) ...
Selecting previously unselected package libmpc3:amd64.
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Unpacking libmpc3:amd64 (1.1.0-1) ...
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Unpacking cpp-7 (7.4.0-1ubuntu1~18.04) ...
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Unpacking cpp (4:7.4.0-1ubuntu2.2) ...
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Unpacking libxcb-shape0:amd64 (1.13-2~ubuntu18.04) ...
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Unpacking libxcb-shape0-dev:amd64 (1.13-2~ubuntu18.04) ...
Selecting previously unselected package libxcb-xfixes0-dev:amd64.
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Unpacking libxcb-xfixes0-dev:amd64 (1.13-2~ubuntu18.04) ...
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Unpacking libxcb-sync-dev:amd64 (1.13-2~ubuntu18.04) ...
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Unpacking libxcb-present-dev:amd64 (1.13-2~ubuntu18.04) ...
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Unpacking libxshmfence-dev:amd64 (1.3-1) ...
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Unpacking x11proto-fixes-dev (1:2018.4-4) ...
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Unpacking libxfixes-dev:amd64 (1:5.0.3-1) ...
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Unpacking x11proto-xext-dev (2018.4-4) ...
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Unpacking libxext-dev:amd64 (2:1.3.3-1) ...
Selecting previously unselected package x11proto-xf86vidmode-dev.
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Unpacking x11proto-xf86vidmode-dev (2018.4-4) ...
Selecting previously unselected package libxxf86vm-dev:amd64.
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Unpacking libxxf86vm-dev:amd64 (1:1.1.4-1) ...
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Unpacking libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
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Unpacking manpages-dev (4.15-1) ...
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Unpacking mesa-utils (8.4.0-1) ...
Setting up libquadmath0:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up libnpth0:amd64 (1.5-3) ...
Setting up libedit2:amd64 (3.1-20170329-1) ...
Setting up libgomp1:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up libatomic1:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up libglvnd0:amd64 (1.0.0-2ubuntu2.2) ...
Setting up readline-common (7.0-3) ...
Setting up libopengl0:amd64 (1.0.0-2ubuntu2.2) ...
Setting up manpages (4.15-1) ...
Setting up libgles1:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libexpat1:amd64 (2.2.5-3) ...
Setting up libcc1-0:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up make (4.1-9.1ubuntu1) ...
Setting up libldap-common (2.4.45+dfsg-1ubuntu1.2) ...
Setting up libpthread-stubs0-dev:amd64 (0.3-4) ...
Setting up libllvm7:amd64 (1:7-3~ubuntu0.18.04.1) ...
Setting up libreadline7:amd64 (7.0-3) ...
Setting up libpsl5:amd64 (0.19.1-5build1) ...
Setting up libelf1:amd64 (0.170-0.4) ...
Setting up libtsan0:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up libxshmfence1:amd64 (1.3-1) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up libwayland-client0:amd64 (1.16.0-1ubuntu1.1~18.04.1) ...
Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up linux-libc-dev:amd64 (4.15.0-48.51) ...
Setting up libmpfr6:amd64 (4.0.1-1) ...
Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libksba8:amd64 (1.3.5-2) ...
Setting up libglapi-mesa:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up perl-modules-5.26 (5.26.1-6ubuntu0.3) ...
Setting up libgdbm5:amd64 (1.14.1-6) ...
Setting up libbsd0:amd64 (0.8.7-1) ...
Setting up x11proto-dev (2018.4-4) ...
Setting up gnupg-l10n (2.2.4-1ubuntu1.2) ...
Setting up libdrm-common (2.4.95-1~18.04.1) ...
Setting up liblsan0:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up gcc-7-base:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up binutils-common:amd64 (2.30-21ubuntu1~18.04.1) ...
Setting up x11proto-damage-dev (1:2018.4-4) ...
Setting up libmpx2:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up libx11-xcb1:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up x11proto-xext-dev (2018.4-4) ...
Setting up patch (2.7.6-2ubuntu1) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Setting up publicsuffix (20180223.1310-1) ...
Setting up libssl1.1:amd64 (1.1.0g-2ubuntu4.3) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
Setting up xz-utils (5.2.2-1.3) ...
update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/lzma.1.gz because associated file /usr/share/man/man1/xz.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/unlzma.1.gz because associated file /usr/share/man/man1/unxz.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzcat.1.gz because associated file /usr/share/man/man1/xzcat.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzmore.1.gz because associated file /usr/share/man/man1/xzmore.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzless.1.gz because associated file /usr/share/man/man1/xzless.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzdiff.1.gz because associated file /usr/share/man/man1/xzdiff.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzcmp.1.gz because associated file /usr/share/man/man1/xzcmp.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzgrep.1.gz because associated file /usr/share/man/man1/xzgrep.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzegrep.1.gz because associated file /usr/share/man/man1/xzegrep.1.gz (of link group lzma) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/lzfgrep.1.gz because associated file /usr/share/man/man1/xzfgrep.1.gz (of link group lzma) doesn't exist
Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libfakeroot:amd64 (1.22-2ubuntu1) ...
Setting up openssl (1.1.0g-2ubuntu4.3) ...
Setting up wget (1.19.4-1ubuntu2.2) ...
Setting up libsqlite3-0:amd64 (3.22.0-1) ...
Setting up liblocale-gettext-perl (1.07-3build2) ...
Setting up libx11-doc (2:1.6.4-3ubuntu0.2) ...
Setting up libpciaccess0:amd64 (0.14-1) ...
Setting up libsensors4:amd64 (1:3.4.0-4) ...
Setting up libgles2:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libmpc3:amd64 (1.1.0-1) ...
Setting up libc-dev-bin (2.27-3ubuntu1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3) ...
Setting up libgdbm-compat4:amd64 (1.14.1-6) ...
Setting up libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ...
Setting up x11-common (1:7.7+19ubuntu7.1) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up ca-certificates (20180409) ...
debconf: unable to initialize frontend: Dialog
debconf: (TERM is not set, so the dialog frontend is not usable.)
debconf: falling back to frontend: Readline
Updating certificates in /etc/ssl/certs...
133 added, 0 removed; done.
Setting up manpages-dev (4.15-1) ...
Setting up libc6-dev:amd64 (2.27-3ubuntu1) ...
Setting up libglvnd-core-dev:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libassuan0:amd64 (2.5.1-2) ...
Setting up libitm1:amd64 (8.3.0-6ubuntu1~18.04) ...
Setting up libx11-data (2:1.6.4-3ubuntu0.2) ...
Setting up libxau6:amd64 (1:1.0.8-1) ...
Setting up libwayland-server0:amd64 (1.16.0-1ubuntu1.1~18.04.1) ...
Setting up netbase (5.4) ...
Setting up libisl19:amd64 (0.19-1) ...
Setting up x11proto-core-dev (2018.4-4) ...
Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libasan4:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up libxshmfence-dev:amd64 (1.3-1) ...
Setting up libbinutils:amd64 (2.30-21ubuntu1~18.04.1) ...
Setting up libcilkrts5:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libubsan0:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up gpgconf (2.2.4-1ubuntu1.2) ...
Setting up x11proto-fixes-dev (1:2018.4-4) ...
Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up x11proto-xf86vidmode-dev (2018.4-4) ...
Setting up libxau-dev:amd64 (1:1.0.8-1) ...
Setting up fakeroot (1.22-2ubuntu1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/fakeroot.1.gz because associated file /usr/share/man/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/faked.1.gz because associated file /usr/share/man/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/es/man1/fakeroot.1.gz because associated file /usr/share/man/es/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/es/man1/faked.1.gz because associated file /usr/share/man/es/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/fr/man1/fakeroot.1.gz because associated file /usr/share/man/fr/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/fr/man1/faked.1.gz because associated file /usr/share/man/fr/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/sv/man1/fakeroot.1.gz because associated file /usr/share/man/sv/man1/fakeroot-sysv.1.gz (of link group fakeroot) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/sv/man1/faked.1.gz because associated file /usr/share/man/sv/man1/faked-sysv.1.gz (of link group fakeroot) doesn't exist
Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libgcc-7-dev:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up cpp-7 (7.4.0-1ubuntu1~18.04) ...
Setting up libdrm2:amd64 (2.4.95-1~18.04.1) ...
Setting up libstdc++-7-dev:amd64 (7.4.0-1ubuntu1~18.04) ...
Setting up libdrm-intel1:amd64 (2.4.95-1~18.04.1) ...
Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ...
Setting up libperl5.26:amd64 (5.26.1-6ubuntu0.3) ...
Setting up gpgsm (2.2.4-1ubuntu1.2) ...
Setting up gnupg-utils (2.2.4-1ubuntu1.2) ...
Setting up libice6:amd64 (2:1.0.9-2) ...
Setting up pinentry-curses (1.1.0-1) ...
Setting up libdrm-radeon1:amd64 (2.4.95-1~18.04.1) ...
Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libdrm-nouveau2:amd64 (2.4.95-1~18.04.1) ...
Setting up libxcb1:amd64 (1.13-2~ubuntu18.04) ...
Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up gpg (2.2.4-1ubuntu1.2) ...
Setting up binutils-x86-64-linux-gnu (2.30-21ubuntu1~18.04.1) ...
Setting up cpp (4:7.4.0-1ubuntu2.2) ...
Setting up libxcb-present0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-dri2-0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libsm6:amd64 (2:1.2.2-1) ...
Setting up libxcb-dri3-0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-glx0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-randr0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-xfixes0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-render0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libdrm-amdgpu1:amd64 (2.4.95-1~18.04.1) ...
Setting up libdrm-dev:amd64 (2.4.95-1~18.04.1) ...
Setting up libgbm1:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libx11-6:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up libgl1-mesa-dri:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up gpg-agent (2.2.4-1ubuntu1.2) ...
Setting up gpg-wks-server (2.2.4-1ubuntu1.2) ...
Setting up libxcb-sync1:amd64 (1.13-2~ubuntu18.04) ...
Setting up perl (5.26.1-6ubuntu0.3) ...
Setting up libfile-fcntllock-perl (0.22-3build2) ...
Setting up libice-dev:amd64 (2:1.0.9-2) ...
Setting up libalgorithm-diff-perl (1.19.03-1) ...
Setting up libxcb-shape0:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxrender1:amd64 (1:0.9.10-1) ...
Setting up libxcb1-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-glx0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libegl-mesa0:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up binutils (2.30-21ubuntu1~18.04.1) ...
Setting up libx11-dev:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-1) ...
Setting up libxcb-sync-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libx11-xcb-dev:amd64 (2:1.6.4-3ubuntu0.2) ...
Setting up libsm-dev:amd64 (2:1.2.2-1) ...
Setting up libxdamage1:amd64 (1:1.1.4-3) ...
Setting up mesa-common-dev:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libxext6:amd64 (2:1.3.3-1) ...
Setting up libxfixes3:amd64 (1:5.0.3-1) ...
Setting up gcc-7 (7.4.0-1ubuntu1~18.04) ...
Setting up g++-7 (7.4.0-1ubuntu1~18.04) ...
Setting up libdpkg-perl (1.19.0.5ubuntu2.1) ...
Setting up libxrender-dev:amd64 (1:0.9.10-1) ...
Setting up gcc (4:7.4.0-1ubuntu2.2) ...
Setting up libxcb-dri2-0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxcb-render0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libegl1:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libalgorithm-merge-perl (0.08-3) ...
Setting up libxcb-dri3-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up dpkg-dev (1.19.0.5ubuntu2.1) ...
Setting up libalgorithm-diff-xs-perl (0.04-5) ...
Setting up libldap-2.4-2:amd64 (2.4.45+dfsg-1ubuntu1.2) ...
Setting up libxext-dev:amd64 (2:1.3.3-1) ...
Setting up libxcb-shape0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up g++ (4:7.4.0-1ubuntu2.2) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/c++.1.gz because associated file /usr/share/man/man1/g++.1.gz (of link group c++) doesn't exist
Setting up libxxf86vm1:amd64 (1:1.1.4-1) ...
Setting up libxxf86vm-dev:amd64 (1:1.1.4-1) ...
Setting up libxfixes-dev:amd64 (1:5.0.3-1) ...
Setting up dirmngr (2.2.4-1ubuntu1.2) ...
Setting up libglx-mesa0:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libxcb-randr0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up build-essential (12.4ubuntu1) ...
Setting up libxcb-xfixes0-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libxdamage-dev:amd64 (1:1.1.4-3) ...
Setting up gpg-wks-client (2.2.4-1ubuntu1.2) ...
Setting up libxcb-present-dev:amd64 (1.13-2~ubuntu18.04) ...
Setting up libglx0:amd64 (1.0.0-2ubuntu2.2) ...
Setting up gnupg (2.2.4-1ubuntu1.2) ...
Setting up libgl1:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libglu1-mesa:amd64 (9.0.0-2.1build1) ...
Setting up mesa-utils (8.4.0-1) ...
Setting up libglvnd-dev:amd64 (1.0.0-2ubuntu2.2) ...
Setting up libgl1-mesa-dev:amd64 (18.2.8-0ubuntu0~18.04.2) ...
Setting up libglu1-mesa-dev:amd64 (9.0.0-2.1build1) ...
Processing triggers for libc-bin (2.27-3ubuntu1) ...
Processing triggers for ca-certificates (20180409) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Removing intermediate container b96d2a72e160
 ---> 34c96cbdfc45
Step 3/4 : RUN cd /tmp &&     wget https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh &&     bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2
 ---> Running in 31eb568c7942
PREFIX=/opt/EMAN2
installing: python-2.7.16-h9bab390_0 ...
Python 2.7.16 :: Anaconda, Inc.
installing: asn1crypto-0.24.0-py27_0 ...
installing: backports-1.0-py27_1 ...
installing: backports.functools_lru_cache-1.5-py27_1 ...
installing: beautifulsoup4-4.7.1-py27_1 ...
installing: bzip2-1.0.6-h14c3975_5 ...
installing: ca-certificates-2019.1.23-0 ...
installing: certifi-2019.3.9-py27_0 ...
installing: cffi-1.12.3-py27h2e261b9_0 ...
installing: chardet-3.0.4-py27_1 ...
installing: conda-4.6.14-py27_0 ...
installing: conda-build-3.17.8-py27_0 ...
installing: contextlib2-0.5.5-py27hbf4c468_0 ...
installing: cryptography-2.6.1-py27h1ba5d50_0 ...
installing: enum34-1.1.6-py27_1 ...
installing: filelock-3.0.10-py27_0 ...
installing: futures-3.2.0-py27_0 ...
installing: glob2-0.6-py27_1 ...
installing: gsl-2.4-h14c3975_4 ...
installing: icu-58.2-h9c2bf20_1 ...
installing: idna-2.8-py27_0 ...
installing: ipaddress-1.0.22-py27_0 ...
installing: jinja2-2.10.1-py27_0 ...
installing: libarchive-3.3.3-h5d8350f_5 ...
installing: libedit-3.1.20181209-hc058e9b_0 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libgfortran-ng-7.3.0-hdf63c60_0 ...
installing: liblief-0.9.0-h7725739_2 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libxml2-2.9.9-he19cac6_0 ...
installing: lz4-c-1.8.1.2-h14c3975_0 ...
installing: lzo-2.10-h49e0be7_2 ...
installing: markupsafe-1.1.1-py27h7b6447c_0 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1b-h7b6447c_1 ...
installing: patchelf-0.9-he6710b0_3 ...
installing: pip-19.0.3-py27_0 ...
installing: pkginfo-1.5.0.1-py27_0 ...
installing: psutil-5.6.1-py27h7b6447c_0 ...
installing: py-lief-0.9.0-py27h7725739_2 ...
installing: pycosat-0.6.3-py27h14c3975_0 ...
installing: pycparser-2.19-py27_0 ...
installing: pyopenssl-19.0.0-py27_0 ...
installing: pysocks-1.6.8-py27_0 ...
installing: python-libarchive-c-2.8-py27_6 ...
installing: pytz-2019.1-py_0 ...
installing: pyyaml-5.1-py27h7b6447c_0 ...
installing: readline-7.0-h7b6447c_5 ...
installing: requests-2.21.0-py27_0 ...
installing: ruamel_yaml-0.15.46-py27h14c3975_0 ...
installing: scandir-1.10.0-py27h7b6447c_0 ...
installing: setuptools-41.0.0-py27_0 ...
installing: six-1.12.0-py27_0 ...
installing: soupsieve-1.8-py27_0 ...
installing: sqlite-3.28.0-h7b6447c_0 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: tqdm-4.31.1-py27_1 ...
installing: urllib3-1.24.1-py27_0 ...
installing: wheel-0.33.1-py27_0 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: zstd-1.3.7-h0b5b093_0 ...
installing: eman2-2.3-h6bb024c_0 ...
+ source /opt/EMAN2/bin/activate
++ _CONDA_ROOT=/opt/EMAN2
++ . /opt/EMAN2/etc/profile.d/conda.sh
+++ export CONDA_EXE=/opt/EMAN2/bin/conda
+++ CONDA_EXE=/opt/EMAN2/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
+++ CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
+++ '[' -z '' ']'
+++ export CONDA_SHLVL=0
+++ CONDA_SHLVL=0
+++ '[' -n x ']'
+++ '[' -n '' ']'
+++++ dirname /opt/EMAN2/bin/conda
++++ dirname /opt/EMAN2/bin
+++ PATH=/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export PATH
+++ '[' -z '' ']'
+++ PS1=
++ conda activate
++ '[' 1 -lt 1 ']'
++ local cmd=activate
++ shift
++ case "$cmd" in
++ __conda_activate activate
++ '[' -n '' ']'
++ local cmd=activate
++ shift
++ local ask_conda
++ OLDPATH=/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ __add_sys_prefix_to_path
++ '[' -n '' ']'
+++ dirname /opt/EMAN2/bin/conda
++ SYSP=/opt/EMAN2/bin
+++ dirname /opt/EMAN2/bin
++ SYSP=/opt/EMAN2
++ '[' -n '' ']'
++ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export PATH
+++ PS1=
+++ /opt/EMAN2/bin/conda shell.posix activate
++ ask_conda='PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/EMAN2'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/opt/EMAN2/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/EMAN2/bin/python'\'''
++ PATH=/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ eval 'PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_PREFIX='\''/opt/EMAN2'\''
export CONDA_SHLVL='\''1'\''
export CONDA_DEFAULT_ENV='\''base'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
export CONDA_EXE='\''/opt/EMAN2/bin/conda'\''
export _CE_M='\'''\''
export _CE_CONDA='\'''\''
export CONDA_PYTHON_EXE='\''/opt/EMAN2/bin/python'\'''
+++ PS1='(base) '
+++ export PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export CONDA_PREFIX=/opt/EMAN2
+++ CONDA_PREFIX=/opt/EMAN2
+++ export CONDA_SHLVL=1
+++ CONDA_SHLVL=1
+++ export CONDA_DEFAULT_ENV=base
+++ CONDA_DEFAULT_ENV=base
+++ export 'CONDA_PROMPT_MODIFIER=(base) '
+++ CONDA_PROMPT_MODIFIER='(base) '
+++ export CONDA_EXE=/opt/EMAN2/bin/conda
+++ CONDA_EXE=/opt/EMAN2/bin/conda
+++ export _CE_M=
+++ _CE_M=
+++ export _CE_CONDA=
+++ _CE_CONDA=
+++ export CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
+++ CONDA_PYTHON_EXE=/opt/EMAN2/bin/python
++ __conda_hashr
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
+ mkdir /opt/EMAN2/install_logs
+ conda info -a
+ conda list
+ conda install eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
+ '[' 9 -lt 1 ']'
+ local cmd=install
+ tee /opt/EMAN2/install_logs/install_log.txt
+ shift
+ case "$cmd" in
+ OLDPATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/EMAN2/bin/conda
+ SYSP=/opt/EMAN2/bin
++ dirname /opt/EMAN2/bin
+ SYSP=/opt/EMAN2
+ '[' -n '' ']'
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ /opt/EMAN2/bin/conda install eman-deps=14.1 -c cryoem -c defaults -c conda-forge -y
Collecting package metadata: ...working... done
Solving environment: ...working... 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - file://home/eman2/anaconda2/conda-bld/linux-64::eman2==2.3=h6bb024c_0
done

## Package Plan ##

  environment location: /opt/EMAN2

  added / updated specs:
    - eman-deps=14.1


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    absl-py-0.7.1              |           py27_0         154 KB
    backports.shutil_get_terminal_size-1.0.0|           py27_2           8 KB
    backports.weakref-1.0.post1|           py27_0           8 KB
    backports_abc-0.5          |   py27h7b3c97b_0          12 KB
    blas-1.0                   |              mkl           6 KB
    bleach-1.5.0               |           py27_0          21 KB
    boost-1.63.0               |           py27_5         325 KB  conda-forge
    boost-cpp-1.63.0           |                2        17.6 MB  conda-forge
    bsddb-1.0                  |           py27_1         202 KB
    configparser-3.7.4         |           py27_0          41 KB
    cryptography-2.3.1         |   py27hc365091_0         576 KB
    cudatoolkit-8.0            |                3       322.4 MB
    cudnn-7.0.5                |        cuda8.0_0       249.3 MB
    cupti-8.0.61               |                0         1.4 MB
    cycler-0.10.0              |           py27_0          13 KB
    db-5.3.28                  |                1         2.4 MB
    dbus-1.13.6                |       h746ee38_0         587 KB
    decorator-4.4.0            |           py27_1          18 KB
    eman-deps-14.1             |                1           3 KB  cryoem
    expat-2.2.6                |       he6710b0_0         187 KB
    fftw-mpi-3.3.6             |                2         3.9 MB  cryoem
    fontconfig-2.13.0          |       h9420a91_0         291 KB
    freetype-2.9.1             |       h8a8886c_1         822 KB
    ftgl-2.1.3                 |                1         687 KB  cryoem
    funcsigs-1.0.2             |   py27h83f16ab_0          20 KB
    functools32-3.2.3.2        |           py27_1          23 KB
    future-0.17.1              |           py27_0         710 KB
    glib-2.56.2                |       hd408876_0         5.0 MB
    gst-plugins-base-1.14.0    |       hbbd80ab_1         6.3 MB
    gstreamer-1.14.0           |       hb453b48_1         3.8 MB
    hdf5-1.8.18                |       h6792536_1         4.2 MB
    html5lib-0.9999999         |           py27_0         183 KB
    intel-openmp-2019.3        |              199         886 KB
    ipython-5.8.0              |           py27_0         1.0 MB
    ipython_genutils-0.2.0     |           py27_0          38 KB
    jpeg-9b                    |       h024ee3a_2         248 KB
    kiwisolver-1.1.0           |   py27he6710b0_0          91 KB
    libarchive-3.3.3           |       h7d0bbab_0         1.5 MB
    libgcc-7.2.0               |       h69d50b8_2         304 KB
    libpng-1.6.34              |       hb9fc6fc_0         334 KB
    libprotobuf-3.7.1          |       hd408876_0         4.7 MB
    libtiff-4.0.9              |       he85c1e1_2         567 KB
    libuuid-1.0.3              |       h1bed415_2          16 KB
    libxcb-1.13                |       h1bed415_1         502 KB
    markdown-3.1               |           py27_0         111 KB
    matplotlib-2.2.3           |   py27hb69df0a_0         6.5 MB
    mkl-2018.0.3               |                1       198.7 MB
    mkl_fft-1.0.6              |   py27h7dd41cf_0         148 KB
    mkl_random-1.0.1           |   py27h4414c95_1         361 KB
    mock-2.0.0                 |           py27_0         100 KB
    nose-1.3.7                 |           py27_2         213 KB
    numpy-1.13.3               |   py27hdbf6ddf_4         3.9 MB
    openmpi-2.0.2              |                0         2.6 MB  cryoem
    openssl-1.0.2r             |       h7b6447c_0         3.2 MB
    pathlib2-2.3.3             |           py27_0          31 KB
    pbr-5.1.3                  |             py_0          74 KB
    pcre-8.43                  |       he6710b0_0         260 KB
    pexpect-4.7.0              |           py27_0          80 KB
    pickleshare-0.7.5          |           py27_0          12 KB
    prompt_toolkit-1.0.15      |   py27h1b593e1_0         333 KB
    protobuf-3.7.1             |   py27he6710b0_0         657 KB
    ptyprocess-0.6.0           |           py27_0          22 KB
    pydusa-1.15                |         np113_11         120 KB  cryoem
    pygments-2.3.1             |           py27_0         1.4 MB
    pyopengl-3.1.0             |           py27_0         982 KB  conda-forge
    pyparsing-2.4.0            |             py_0          58 KB
    pyqt-5.9.2                 |   py27h05f1152_2         5.4 MB
    python-2.7.14              |      h1571d57_31        11.8 MB
    python-dateutil-2.8.0      |           py27_0         279 KB
    qt-5.9.6                   |       h8703b6f_2        87.1 MB
    scikit-learn-0.19.2        |   py27h4989274_0         5.3 MB
    scipy-1.1.0                |   py27hd20e5f9_0        17.9 MB
    simplegeneric-0.8.1        |           py27_2           9 KB
    singledispatch-3.4.0.3     |   py27h9bcb476_0          15 KB
    sip-4.19.8                 |   py27hf484d3e_0         291 KB
    subprocess32-3.5.3         |   py27h7b6447c_0          44 KB
    tensorflow-gpu-1.5.0       |                0           3 KB
    tensorflow-gpu-base-1.5.0  |   py27had95abb_0       131.0 MB
    tensorflow-tensorboard-1.5.1|   py27hf484d3e_1         2.9 MB
    tornado-5.1.1              |   py27h7b6447c_0         643 KB
    traitlets-4.3.2            |   py27hd6ce930_0         126 KB
    wcwidth-0.1.7              |   py27h9e3e1ab_0          25 KB
    werkzeug-0.15.2            |             py_0         263 KB
    ------------------------------------------------------------
                                           Total:        1.09 GB

The following NEW packages will be INSTALLED:

  absl-py            pkgs/main/linux-64::absl-py-0.7.1-py27_0
  backports.shutil_~ pkgs/main/linux-64::backports.shutil_get_terminal_size-1.0.0-py27_2
  backports.weakref  pkgs/main/linux-64::backports.weakref-1.0.post1-py27_0
  backports_abc      pkgs/main/linux-64::backports_abc-0.5-py27h7b3c97b_0
  blas               pkgs/main/linux-64::blas-1.0-mkl
  bleach             pkgs/free/linux-64::bleach-1.5.0-py27_0
  boost              conda-forge/linux-64::boost-1.63.0-py27_5
  boost-cpp          conda-forge/linux-64::boost-cpp-1.63.0-2
  bsddb              pkgs/free/linux-64::bsddb-1.0-py27_1
  configparser       pkgs/main/linux-64::configparser-3.7.4-py27_0
  cudatoolkit        pkgs/free/linux-64::cudatoolkit-8.0-3
  cudnn              pkgs/main/linux-64::cudnn-7.0.5-cuda8.0_0
  cupti              pkgs/main/linux-64::cupti-8.0.61-0
  cycler             pkgs/main/linux-64::cycler-0.10.0-py27_0
  db                 pkgs/free/linux-64::db-5.3.28-1
  dbus               pkgs/main/linux-64::dbus-1.13.6-h746ee38_0
  decorator          pkgs/main/linux-64::decorator-4.4.0-py27_1
  eman-deps          cryoem/linux-64::eman-deps-14.1-1
  expat              pkgs/main/linux-64::expat-2.2.6-he6710b0_0
  fftw-mpi           cryoem/linux-64::fftw-mpi-3.3.6-2
  fontconfig         pkgs/main/linux-64::fontconfig-2.13.0-h9420a91_0
  freetype           pkgs/main/linux-64::freetype-2.9.1-h8a8886c_1
  ftgl               cryoem/linux-64::ftgl-2.1.3-1
  funcsigs           pkgs/main/linux-64::funcsigs-1.0.2-py27h83f16ab_0
  functools32        pkgs/main/linux-64::functools32-3.2.3.2-py27_1
  future             pkgs/main/linux-64::future-0.17.1-py27_0
  glib               pkgs/main/linux-64::glib-2.56.2-hd408876_0
  gst-plugins-base   pkgs/main/linux-64::gst-plugins-base-1.14.0-hbbd80ab_1
  gstreamer          pkgs/main/linux-64::gstreamer-1.14.0-hb453b48_1
  hdf5               pkgs/main/linux-64::hdf5-1.8.18-h6792536_1
  html5lib           pkgs/free/linux-64::html5lib-0.9999999-py27_0
  intel-openmp       pkgs/main/linux-64::intel-openmp-2019.3-199
  ipython            pkgs/main/linux-64::ipython-5.8.0-py27_0
  ipython_genutils   pkgs/main/linux-64::ipython_genutils-0.2.0-py27_0
  jpeg               pkgs/main/linux-64::jpeg-9b-h024ee3a_2
  kiwisolver         pkgs/main/linux-64::kiwisolver-1.1.0-py27he6710b0_0
  libgcc             pkgs/main/linux-64::libgcc-7.2.0-h69d50b8_2
  libpng             pkgs/main/linux-64::libpng-1.6.34-hb9fc6fc_0
  libprotobuf        pkgs/main/linux-64::libprotobuf-3.7.1-hd408876_0
  libtiff            pkgs/main/linux-64::libtiff-4.0.9-he85c1e1_2
  libuuid            pkgs/main/linux-64::libuuid-1.0.3-h1bed415_2
  libxcb             pkgs/main/linux-64::libxcb-1.13-h1bed415_1
  markdown           pkgs/main/linux-64::markdown-3.1-py27_0
  matplotlib         pkgs/main/linux-64::matplotlib-2.2.3-py27hb69df0a_0
  mkl                pkgs/main/linux-64::mkl-2018.0.3-1
  mkl_fft            pkgs/main/linux-64::mkl_fft-1.0.6-py27h7dd41cf_0
  mkl_random         pkgs/main/linux-64::mkl_random-1.0.1-py27h4414c95_1
  mock               pkgs/main/linux-64::mock-2.0.0-py27_0
  nose               pkgs/main/linux-64::nose-1.3.7-py27_2
  numpy              pkgs/main/linux-64::numpy-1.13.3-py27hdbf6ddf_4
  openmpi            cryoem/linux-64::openmpi-2.0.2-0
  pathlib2           pkgs/main/linux-64::pathlib2-2.3.3-py27_0
  pbr                pkgs/main/noarch::pbr-5.1.3-py_0
  pcre               pkgs/main/linux-64::pcre-8.43-he6710b0_0
  pexpect            pkgs/main/linux-64::pexpect-4.7.0-py27_0
  pickleshare        pkgs/main/linux-64::pickleshare-0.7.5-py27_0
  prompt_toolkit     pkgs/main/linux-64::prompt_toolkit-1.0.15-py27h1b593e1_0
  protobuf           pkgs/main/linux-64::protobuf-3.7.1-py27he6710b0_0
  ptyprocess         pkgs/main/linux-64::ptyprocess-0.6.0-py27_0
  pydusa             cryoem/linux-64::pydusa-1.15-np113_11
  pygments           pkgs/main/linux-64::pygments-2.3.1-py27_0
  pyopengl           conda-forge/linux-64::pyopengl-3.1.0-py27_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.0-py_0
  pyqt               pkgs/main/linux-64::pyqt-5.9.2-py27h05f1152_2
  python-dateutil    pkgs/main/linux-64::python-dateutil-2.8.0-py27_0
  qt                 pkgs/main/linux-64::qt-5.9.6-h8703b6f_2
  scikit-learn       pkgs/main/linux-64::scikit-learn-0.19.2-py27h4989274_0
  scipy              pkgs/main/linux-64::scipy-1.1.0-py27hd20e5f9_0
  simplegeneric      pkgs/main/linux-64::simplegeneric-0.8.1-py27_2
  singledispatch     pkgs/main/linux-64::singledispatch-3.4.0.3-py27h9bcb476_0
  sip                pkgs/main/linux-64::sip-4.19.8-py27hf484d3e_0
  subprocess32       pkgs/main/linux-64::subprocess32-3.5.3-py27h7b6447c_0
  tensorflow-gpu     pkgs/main/linux-64::tensorflow-gpu-1.5.0-0
  tensorflow-gpu-ba~ pkgs/main/linux-64::tensorflow-gpu-base-1.5.0-py27had95abb_0
  tensorflow-tensor~ pkgs/main/linux-64::tensorflow-tensorboard-1.5.1-py27hf484d3e_1
  tornado            pkgs/main/linux-64::tornado-5.1.1-py27h7b6447c_0
  traitlets          pkgs/main/linux-64::traitlets-4.3.2-py27hd6ce930_0
  wcwidth            pkgs/main/linux-64::wcwidth-0.1.7-py27h9e3e1ab_0
  werkzeug           pkgs/main/noarch::werkzeug-0.15.2-py_0

The following packages will be DOWNGRADED:

  cryptography                         2.6.1-py27h1ba5d50_0 --> 2.3.1-py27hc365091_0
  libarchive                               3.3.3-h5d8350f_5 --> 3.3.3-h7d0bbab_0
  openssl                                 1.1.1b-h7b6447c_1 --> 1.0.2r-h7b6447c_0
  python                                  2.7.16-h9bab390_0 --> 2.7.14-h1571d57_31



Downloading and Extracting Packages
mock-2.0.0           | 100 KB    | ########## | 100% 
fftw-mpi-3.3.6       | 3.9 MB    | ########## | 100% 
scipy-1.1.0          | 17.9 MB   | ########## | 100% 
tensorflow-gpu-base- | 131.0 MB  | ########## | 100% 
decorator-4.4.0      | 18 KB     | ########## | 100% 
pickleshare-0.7.5    | 12 KB     | ########## | 100% 
pexpect-4.7.0        | 80 KB     | ########## | 100% 
ipython-5.8.0        | 1.0 MB    | ########## | 100% 
pyparsing-2.4.0      | 58 KB     | ########## | 100% 
mkl_random-1.0.1     | 361 KB    | ########## | 100% 
dbus-1.13.6          | 587 KB    | ########## | 100% 
libuuid-1.0.3        | 16 KB     | ########## | 100% 
sip-4.19.8           | 291 KB    | ########## | 100% 
db-5.3.28            | 2.4 MB    | ########## | 100% 
libpng-1.6.34        | 334 KB    | ########## | 100% 
singledispatch-3.4.0 | 15 KB     | ########## | 100% 
ftgl-2.1.3           | 687 KB    | ########## | 100% 
pcre-8.43            | 260 KB    | ########## | 100% 
backports_abc-0.5    | 12 KB     | ########## | 100% 
funcsigs-1.0.2       | 20 KB     | ########## | 100% 
libarchive-3.3.3     | 1.5 MB    | ########## | 100% 
libtiff-4.0.9        | 567 KB    | ########## | 100% 
scikit-learn-0.19.2  | 5.3 MB    | ########## | 100% 
subprocess32-3.5.3   | 44 KB     | ########## | 100% 
jpeg-9b              | 248 KB    | ########## | 100% 
bsddb-1.0            | 202 KB    | ########## | 100% 
cudatoolkit-8.0      | 322.4 MB  | ########## | 100% 
pygments-2.3.1       | 1.4 MB    | ########## | 100% 
gst-plugins-base-1.1 | 6.3 MB    | ########## | 100% 
eman-deps-14.1       | 3 KB      | ########## | 100% 
fontconfig-2.13.0    | 291 KB    | ########## | 100% 
functools32-3.2.3.2  | 23 KB     | ########## | 100% 
bleach-1.5.0         | 21 KB     | ########## | 100% 
backports.shutil_get | 8 KB      | ########## | 100% 
cupti-8.0.61         | 1.4 MB    | ########## | 100% 
numpy-1.13.3         | 3.9 MB    | ########## | 100% 
libxcb-1.13          | 502 KB    | ########## | 100% 
pydusa-1.15          | 120 KB    | ########## | 100% 
absl-py-0.7.1        | 154 KB    | ########## | 100% 
ipython_genutils-0.2 | 38 KB     | ########## | 100% 
mkl_fft-1.0.6        | 148 KB    | ########## | 100% 
tornado-5.1.1        | 643 KB    | ########## | 100% 
freetype-2.9.1       | 822 KB    | ########## | 100% 
backports.weakref-1. | 8 KB      | ########## | 100% 
ptyprocess-0.6.0     | 22 KB     | ########## | 100% 
intel-openmp-2019.3  | 886 KB    | ########## | 100% 
libprotobuf-3.7.1    | 4.7 MB    | ########## | 100% 
python-2.7.14        | 11.8 MB   | ########## | 100% 
glib-2.56.2          | 5.0 MB    | ########## | 100% 
gstreamer-1.14.0     | 3.8 MB    | ########## | 100% 
boost-cpp-1.63.0     | 17.6 MB   | ########## | 100% 
cryptography-2.3.1   | 576 KB    | ########## | 100% 
cycler-0.10.0        | 13 KB     | ########## | 100% 
wcwidth-0.1.7        | 25 KB     | ########## | 100% 
expat-2.2.6          | 187 KB    | ########## | 100% 
python-dateutil-2.8. | 279 KB    | ########## | 100% 
boost-1.63.0         | 325 KB    | ########## | 100% 
openssl-1.0.2r       | 3.2 MB    | ########## | 100% 
matplotlib-2.2.3     | 6.5 MB    | ########## | 100% 
simplegeneric-0.8.1  | 9 KB      | ########## | 100% 
tensorflow-gpu-1.5.0 | 3 KB      | ########## | 100% 
libgcc-7.2.0         | 304 KB    | ########## | 100% 
hdf5-1.8.18          | 4.2 MB    | ########## | 100% 
werkzeug-0.15.2      | 263 KB    | ########## | 100% 
protobuf-3.7.1       | 657 KB    | ########## | 100% 
pbr-5.1.3            | 74 KB     | ########## | 100% 
cudnn-7.0.5          | 249.3 MB  | ########## | 100% 
mkl-2018.0.3         | 198.7 MB  | ########## | 100% 
pyqt-5.9.2           | 5.4 MB    | ########## | 100% 
prompt_toolkit-1.0.1 | 333 KB    | ########## | 100% 
configparser-3.7.4   | 41 KB     | ########## | 100% 
pathlib2-2.3.3       | 31 KB     | ########## | 100% 
qt-5.9.6             | 87.1 MB   | ########## | 100% 
nose-1.3.7           | 213 KB    | ########## | 100% 
kiwisolver-1.1.0     | 91 KB     | ########## | 100% 
markdown-3.1         | 111 KB    | ########## | 100% 
blas-1.0             | 6 KB      | ########## | 100% 
openmpi-2.0.2        | 2.6 MB    | ########## | 100% 
pyopengl-3.1.0       | 982 KB    | ########## | 100% 
traitlets-4.3.2      | 126 KB    | ########## | 100% 
html5lib-0.9999999   | 183 KB    | ########## | 100% 
tensorflow-tensorboa | 2.9 MB    | ########## | 100% 
future-0.17.1        | 710 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... 
done
+ local t1=0
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ '[' 0 = 0 ']'
+ __conda_reactivate
+ local ask_conda
+ OLDPATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/EMAN2/bin/conda
+ SYSP=/opt/EMAN2/bin
++ dirname /opt/EMAN2/bin
+ SYSP=/opt/EMAN2
+ '[' -n '' ']'
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
++ PS1='(base) '
++ /opt/EMAN2/bin/conda shell.posix reactivate
+ ask_conda='PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
. "/opt/EMAN2/etc/conda/activate.d/eman-deps_activate.sh"'
+ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ eval 'PS1='\''(base) '\''
export PATH='\''/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(base) '\''
. "/opt/EMAN2/etc/conda/activate.d/eman-deps_activate.sh"'
++ PS1='(base) '
++ export PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/opt/EMAN2/bin:/opt/EMAN2/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
++ export 'CONDA_PROMPT_MODIFIER=(base) '
++ CONDA_PROMPT_MODIFIER='(base) '
++ . /opt/EMAN2/etc/conda/activate.d/eman-deps_activate.sh
+++ echo
+++ echo 'INFO: eman-deps activation script is making the following environmental changes:'
+++ set -x
+++ LDFLAGS=
+++ LDFLAGS=
+++ CXXFLAGS=
+++ set +x

INFO: eman-deps activation script is making the following environmental changes:

+ cat

INSTALLATION IS NOW COMPLETE

Please, go to http://blake.bcm.edu/emanwiki/EMAN2/Install/BinaryInstallAnaconda
for detailed installation instructions, testing and troubleshooting information.
If this installation is on a Linux cluster,
you will require additional steps before installation is complete!

cat: /opt/EMAN2/.messages.txt: No such file or directory
installation finished.
INFO: Running package tests in a subshell

INFO: eman-deps activation script is making the following environmental changes:
++++ LDFLAGS=
++++ LDFLAGS=
++++ CXXFLAGS=
++++ set +x

Traceback (most recent call last):
  File "/opt/EMAN2/bin/conda-index", line 7, in <module>
    from conda_build.cli.main_index import main
  File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/cli/main_index.py", line 10, in <module>
    from conda_build.index import DEFAULT_SUBDIRS, MAX_THREADS_DEFAULT
  File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/index.py", line 25, in <module>
    import pytz
ImportError: No module named pytz
Traceback (most recent call last):
  File "/opt/EMAN2/bin/conda-build", line 7, in <module>
    from conda_build.cli.main_build import main
  File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/cli/main_build.py", line 19, in <module>
    import conda_build.build as build
  File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/build.py", line 63, in <module>
    from conda_build import environ, source, tarcheck, utils
  File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/environ.py", line 29, in <module>
    from conda_build.index import get_build_index
  File "/opt/EMAN2/lib/python2.7/site-packages/conda_build/index.py", line 25, in <module>
    import pytz
ImportError: No module named pytz
To re-run the tests for the above failed package, please enter:
. /opt/EMAN2/bin/activate
conda-build --override-channels --channel local --test <full-path-to-failed.tar.bz2>
ERROR: 1 test failed
The command '/bin/sh -c cd /tmp &&     wget https://cryoem.bcm.edu/cryoem/static/software/release-2.3/eman2.3.linux64.sh &&     bash ./eman2.3.linux64.sh -b -t -p /opt/EMAN2' returned a non-zero code: 1

Bug in emplot3d.py

Data file to plot:

Steps to reproduce:

Run e2display.py
Select file to plot
Click Plot 3D
Drag mouse while left-clicking
On Mac Option + LeftClick

Traceback (most recent call last):
  File "/miniconda/lib/python2.7/site-packages/eman2_gui/emplot3d.py", line 891, in mouseMoveEvent
    self.add_shape("lcross",EMShape(("scrlabel",0,0,0,self.scrlim[2]-220,self.scrlim[3]-10,"%1.5g (%s), %1.5g"%(lc[0],recip,lc[1]),120.0,-1))) 
NameError: global name 'lc' is not defined

eman2.3: FFTW3 not found during cmake compile

Hi specialists,

I'm trying to install eman2.31 on my ubuntu 16.04 system but met some problems.
I use cmake3.9 and can't find FFTW3. However, I have install fftw3.3.8 and make them in bashrc.
Here is the log file, please help me.

(base) linzhaohan@linzhaohan-MS-7B89:~/Downloads/eman2/build$ cmake ..
-- CMAKE_PREFIX_PATH="/home/linzhaohan/anaconda2;/home/linzhaohan/anaconda2/.."
PYTHON_EXECUTABLE: /home/linzhaohan/anaconda2/bin/python
PYTHON_LIBRARIES: /home/linzhaohan/anaconda2/lib/libpython2.7.so
PYTHON_INCLUDE_DIRS: /home/linzhaohan/anaconda2/include/python2.7
PYTHON_INCLUDE_PATH: /home/linzhaohan/anaconda2/include/python2.7
PYTHON_INCLUDE_DIR: /home/linzhaohan/anaconda2/include/python2.7
Python site-packages: /home/linzhaohan/anaconda2/lib/python2.7/site-packages
-- NUMPY_INCLUDE_DIR="/home/linzhaohan/anaconda2/lib/python2.7/site-packages/numpy/core/include"
-- Boost version: 1.58.0
-- Found the following Boost libraries:
-- python
Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python.so
Boost_INCLUDE_DIR: /usr/local/include
-- HDF5_LIBRARY="/home/linzhaohan/anaconda2/lib/libhdf5.so"
CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3F not found. please install FFTW3F first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:1 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)

CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3D not found. please install FFTW3D first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:2 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)

CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3F_THREADS not found. please install FFTW3F_THREADS first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:4 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)

CMake Error at cmake/functions.cmake:51 (MESSAGE):
ERROR: FFTW3D_THREADS not found. please install FFTW3D_THREADS first!
Call Stack (most recent call first):
cmake/FindFFTW3.cmake:5 (CHECK_REQUIRED_LIB)
libEM/CMakeLists.txt:95 (find_package)

CMake Error at /usr/local/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find FFTW3 (missing: FFTW3F_INCLUDE_PATH FFTW3F_LIBRARY
FFTW3D_INCLUDE_PATH FFTW3D_LIBRARY FFTW3F_THREADS_INCLUDE_PATH
FFTW3F_THREADS_LIBRARY FFTW3D_THREADS_INCLUDE_PATH FFTW3D_THREADS_LIBRARY)
Call Stack (most recent call first):
/usr/local/share/cmake-3.9/Modules/FindPackageHandleStandardArgs.cmake:377 (_FPHSA_FAILURE_MESSAGE)
cmake/FindFFTW3.cmake:11 (find_package_handle_standard_args)
libEM/CMakeLists.txt:95 (find_package)

-- Configuring incomplete, errors occurred!
See also "/home/linzhaohan/Downloads/eman2/build/CMakeFiles/CMakeOutput.log".
See also "/home/linzhaohan/Downloads/eman2/build/CMakeFiles/CMakeError.log".

Thanks a lot!

Best,
Zhaohan Lin

Old style QtCore.QObject.connect() added

Commit 817961d contains old-style QtCore.QObject.connect().

ask some update problems about EMAN2

Hi, I'm a graduate student for biophysics.
I'm studying Single Particle Analysis recently, and I find EMAN2.
It's a wonderful software and helps me a lot. Thanks for your work!

Though I know it's a matter to solve dependencies problem of old codes. I still want to ask that do you have a plan or schedule to update EMAN2 from python2 to python3?

Anyway, best wishes! :)

Questionable detection of 8-bit-packed mode from MRC headers

Having recently engaged in the exercise of building the EMAN2 2.3 release from source, I had the opportunity to analyze compiler warnings to look for any that indicated genuine problems. There was a lot of noise, but a little signal, all of which appears still to apply to the current head. I'll be splitting that into four separate issues, of which this is the first.

libEM/mrcio.cpp:206-207 is this:

		is_8_bit_packed = (mrch.mode == MRC_UHEX       ||
							   (mrch.imod_flags & 16) == 1  ||  double_nx);

But the condition (mrch.imod_flags & 16) == 1 never evaluates to true, because anything & 16 always evaluates to either 0 or 16. From code analysis alone, I suspect that (mrch.imod_flags & 16) != 0 would be consistent with the intention, but I am not sufficiently familiar with the details of the MRC format to confirm that.

Fix broken programs

This is the main issue to track fixing individual programs.

It was created by ZenHub, https://app.zenhub.com/workspace/o/cryoem/eman2/boards?repos=48064767, as an Epic issue, but doesn't show the sub-issues, maybe, because ZenHub is not used organization-wide.

OpenMPI test fails on TravisCI

Disabled openmpi test in PR #218, but, probably, needs to be fixed before the release. Tracking in this issue.

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	parser.add_argument("--dark", default = None, type=str, help="Use this dark reference.",guitype='filebox', browser="EMMovieDataTable(withmodal=True,multiselect=True)", row=2, col=0,rowspan=1, colspan=2, mode="align",mode="movie")
	parser.add_argument("--gain", default = None, type=str, help="Use this gain reference.",guitype='filebox', browser="EMMovieDataTable(withmodal=True,multiselect=True)", row=3, col=0,rowspan=1, colspan=2, mode="align",mode="movie")

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eman2's Issues

Data file to plot:

Steps to reproduce:

BEGIN ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h

END ### CHECK_REQUIRED_LIB HDF5 hdf5 hdf5.h

Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.

Data file to plot:

Steps to reproduce:

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Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.