Announcing EMAN2.3 release

Steve Ludtke

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Apr 26, 2019, 10:08:20 AM4/26/19

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Hi all,
a brief announcement of a new major release: EMAN2.3 (http://eman2.org), with major new features. As always, the distribution also includes SPARX (http://sparx-em.org) and the release of SPHIRE 1.2 (http://sphire.mpg.de). Releases are coordinated among the packages.

New features in EMAN2.3 include:
* A complete CryoET pipeline from tilt series through subnanometer resolution hybrid subtomogram averaging
* fiducial-less fully automated tilt series alignment (also works with fiducials)
* rapid tiled Fourier reconstruction
* full tilt/geometry aware CTF correction
* multi class 3-D particle picker with new ties to deep-learning annotation
* SGD automatic initial model generation
* traditional 3-D subtomogram averaging
* per-particle per-tilt hybrid subtomogram/single particle reconstruction to subnanometer resolution

* A new switchable filter in e2boxer making it dramatically easier to distinguish particles in images
* New improvements to bispectral classification for 2-D unsupervised classification and 3-D refinement
* Focused classification in 3-D refinement available from the workflow interface
* Improvements to e2extractsubparticles as an alternative to focused classification
* Upgrade from Qt4 to Qt5 as part of the process of transitioning to Python3 over the next year
* Many minor bugfixes

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

Gajiwala, Ketan

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Apr 29, 2019, 1:06:10 PM4/29/19

to em...@googlegroups.com, Yee, Jack

Dear Steve,

Can you please help us with the installation of EMAN2.3? We run OS version Centos 7.3. Out IT support, Jack Yee, got the following error message:

set: Variable name must begin with a letter.

ERROR: executing post_install.sh failed

More details are in the forwarded message below.

Many thanks,

Ketan Gajiwala

From: Yee, Jack
Sent: Monday, April 29, 2019 10:00 AM
To: Gajiwala, Ketan <Ketan.G...@pfizer.com>
Subject: RE: [EXTERNAL] [EMAN2] Announcing EMAN2.3 release

Hi Ketan,
I tried to install 2.3 and the error message below. Can you write the developer? OS version Centos 7.3.

Thanks

-Jack

bash-4.2$ sh eman2.3.linux64.sh

Welcome to EMAN2 2.3

EMAN2 will now be installed into this location:

/home/ljsw/EMAN2

- Press ENTER to confirm the location

- Press CTRL-C to abort the installation

- Or specify a different location below

[/home/ljsw/EMAN2] >>> /tools/apps/Crystallography/EMAN2/EMAN2.23

PREFIX=/tools/apps/Crystallography/EMAN2/EMAN2.23

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 ...

set: Variable name must begin with a letter.

ERROR: executing post_install.sh failed

bash-4.2$

-----Original Message-----
From: Gajiwala, Ketan
Sent: Friday, April 26, 2019 7:41 AM
To: Yee, Jack <Jack...@pfizer.com>
Subject: FW: [EXTERNAL] [EMAN2] Announcing EMAN2.3 release

Hi Jack - Can you please upgrade EMAN2? And let me know when you are done? Thank you! - Ketan

-----Original Message-----

From: em...@googlegroups.com <em...@googlegroups.com> On Behalf Of Steve Ludtke

Sent: Friday, April 26, 2019 7:08 AM

To: em...@googlegroups.com

Subject: [EXTERNAL] [EMAN2] Announcing EMAN2.3 release

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fj...@yale.edu

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Apr 29, 2019, 4:21:06 PM4/29/19

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Fantastic! But here's a dumb question about MacOSX installation (which is very convenient). Everthing works, including that e2display.py <file_to_display> puts up a simple display window; but e2display.py without arguments does nothing but give a malloc error, and in neither case do I see the nice browser GUI.

yale172021215183:~ fred$ e2display.py

python(1872,0x70000a848000) malloc: *** error for object 0x7fce4ba10db8: pointer being freed was not allocated

python(1872,0x70000a848000) malloc: *** set a breakpoint in malloc_error_break to debug

Abort trap: 6

-Fred

Steve Ludtke

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Apr 29, 2019, 6:39:03 PM4/29/19

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Hi Fred. There was another series of messages on the group about this. For reasons we don't understand, if you install on a Mac, you need to completely close the terminal window you installed from before trying to run EMAN2 programs (from a new terminal). This has nothing to do with PATH or other environment variable changes, and makes no logical sense, but it seems reproducible so far.

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

Steve Ludtke

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Apr 30, 2019, 12:03:54 AM4/30/19

to em...@googlegroups.com, Yee, Jack

Perhaps try bash instead of sh? It works for us on CentOS 7.6, so a bit confused. If bash doesn't work, could you try downloading it again? Seems very odd...

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

fj...@yale.edu

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Apr 30, 2019, 4:05:29 PM4/30/19

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Alas, a new terminal window, restarting Terminal, using XQuartz11, rebooting the machine, still yield the same problem for me...

Fred

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shadow walker

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Apr 30, 2019, 5:12:26 PM4/30/19

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Hi Fred,

Can you post here or send me the following items, privately, if you wish?

1. There should be 3 files in a folder named install_logs in your binary installation: info_log.txt, list_log.txt, install_log.txt

2. Output of commands:

a. conda info -a

b. conda list -e

c. conda list --explicit

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nancy meyer

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Apr 30, 2019, 5:14:00 PM4/30/19

to EMAN2

Just FYI, having same issue at the moment (malloc error when testing e2display.py) installing 2.3 on MacBook running Mojave 10.14.3. Fred, if you find the solution, would you mind posting? Thx.

- Nancy

Mario Borgnia

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Apr 30, 2019, 5:51:35 PM4/30/19

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Hi all,

Same problem here:

e2display.py

python(81770,0x70000a36f000) malloc: *** error for object 0x7fd5614e5f88: pointer being freed was not allocated

*** set a breakpoint in malloc_error_break to debug

Abort trap: 6

Attached are some log files

Thanks!

Mario

conda_list_e.txt

conda_list_explicit.txt

conda_info_a.txt

python_report.txt

Steve Ludtke

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Apr 30, 2019, 6:56:23 PM4/30/19

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Hmm. Very frustrating. I just did another test on a different mac running 10.14.4 on a fresh user account, and my trick of closing the session doesn't seem to work (I get the crash too). Maybe it's random, and I just got lucky. Thanks everyone for the reports. We will dig into this aggressively. We have people installing for a workshop next week, so this is a major issue issue for us.

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

<conda_list_e.txt><conda_list_explicit.txt><conda_info_a.txt><python_report.txt>

Steve Ludtke

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Apr 30, 2019, 7:14:27 PM4/30/19

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Ok, some progress. I think I understand what led to my previous confusion. If you launch it from an empty folder it doesn't crash. If there are files, it does crash. I'm digging into it...

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

On Apr 30, 2019, at 4:51 PM, Mario Borgnia <mbor...@gmail.com> wrote:

<conda_list_e.txt><conda_list_explicit.txt><conda_info_a.txt><python_report.txt>

Steve Ludtke

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Apr 30, 2019, 8:32:54 PM4/30/19

to em...@googlegroups.com, Tunay Durmaz

Ok, with some effort, I have it down to the function level:

music:x admin$ python

Python 2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 12:28:59) 

[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> from EMAN2 import *

>>> EMUtil.get_image_count("./sl4043.img")

python(4293,0x10b5435c0) malloc: *** error for object 0x7f8c6419d938: pointer being freed was not allocated

python(4293,0x10b5435c0) malloc: *** set a breakpoint in malloc_error_break to debug

Abort trap: 6

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

Steve Ludtke

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Apr 30, 2019, 8:46:48 PM4/30/19

to em...@googlegroups.com, Tunay Durmaz

Ok, got it, and it's reproducible. It appears to be a problem with the boost exception generation code:

From the binary install:

arq3% python

Python 2.7.14 |Anaconda, Inc.| (default, Mar 27 2018, 12:28:59)

[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> from EMAN2 import *

>>> EMUtil.get_image_count("/Volumes/data/stevel/trp_25_04.hdf")

1

>>> EMUtil.get_image_count("/Volumes/data/stevel/sieve.py")

python(53613,0x1115835c0) malloc: *** error for object 0x7ffa3705f288: pointer being freed was not allocated

python(53613,0x1115835c0) malloc: *** set a breakpoint in malloc_error_break to debug

zsh: abort python

From the source install:

Python 2.7.14 |Anaconda, Inc.| (default, Dec 7 2017, 11:07:58)

[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin

Type "help", "copyright", "credits" or "license" for more information.

>>> from EMAN2 import *

>>> EMUtil.get_image_count("/Volumes/data/stevel/trp_25_04.hdf")

1

>>> EMUtil.get_image_count("/Volumes/data/stevel/sieve.py")

Traceback (most recent call last):

File "<stdin>", line 1, in <module>

File "/Volumes/data/stevel/EMAN2/anaconda2/lib/python2.7/site-packages/EMAN2db.py", line 545, in db_get_image_count

raise Exception(fsp)

Exception: /Volumes/data/stevel/sieve.py

That is, what should be a normal operating Exception is instead producing a segfault.

Here is a diff between <works and >broken

4,9d3

< _ipyw_jlab_nb_ext_conf 0.1.0 py27h172cb35_0

< alabaster 0.7.10 py27h9dd7d6e_0

< anaconda 5.1.0 py27_2

< anaconda-client 1.6.9 py27_0

< anaconda-navigator 1.7.0 py27_0

< anaconda-project 0.8.2 py27h2dc806c_0

11d4

< appscript 1.0.1 py27h451298e_1

13,19c6,8

< astroid 1.6.1 py27_0

< astropy 2.0.3 py27h1de35cc_0

< attrs 17.4.0 py27_0

< babel 2.5.3 py27_0

< backports 1.0 py27hb4f9756_1

< backports.functools_lru_cache 1.4 py27h2aca819_1

< backports.shutil_get_terminal_size 1.0.0 py27hc9115de_2

---

> backports 1.0 py27_1

> backports.functools_lru_cache 1.5 py27_1

> backports.shutil_get_terminal_size 1.0.0 py27_2

22,24c11

< beautifulsoup4 4.6.0 py27h9416283_1

< bitarray 0.8.1 py27h1de35cc_1

< bkcharts 0.2 py27haafc882_0

---

> beautifulsoup4 4.7.1 py27_1

26d12

< blaze 0.11.3 py27hb49378a_0

28d13

< bokeh 0.12.13 py27h5233db4_0

31,32d15

< boto 2.48.0 py27hacdd0fd_1

< bottleneck 1.2.1 py27h71f98a3_0

34c17

< bzip2 1.0.6 hd86a083_4

---

> bzip2 1.0.6 h1de35cc_5

36d18

< cdecimal 2.3 py27h1de35cc_3

38,49c20,24

< cffi 1.11.4 py27h342bebf_0

< chardet 3.0.4 py27h2842e91_1

< click 6.7 py27h2b86a94_0

< cloudpickle 0.5.2 py27_1

< clyent 1.2.2 py27hc0ae608_0

< cmake 3.9.4 h30c3106_0

< colorama 0.3.9 py27hbbe92b6_0

< conda 4.4.10 py27_0

< conda-build 3.4.1 py27_0

< conda-env 2.6.0 h36134e3_0

< conda-verify 2.0.0 py27hbebe81d_0

< configparser 3.5.0 py27hc7edf1b_0

---

> cffi 1.12.3 py27hb5b8e2f_0

> chardet 3.0.4 py27_1

> conda 4.6.14 py27_0

> conda-build 3.17.8 py27_0

> configparser 3.7.4 py27_0

51,52c26

< cryptography 2.1.4 py27hdbc5e8f_0

< curl 7.58.0 ha441bb4_0

---

> cryptography 2.3.1 py27hdbc3d79_0

54,58d27

< cython 0.27.3 py27h6429b90_0

< cytoolz 0.9.0 py27h1de35cc_0

< dask 0.16.1 py27_0

< dask-core 0.16.1 py27_0

< datashape 0.5.4 py27hd6a1745_0

60,63c29,30

< dbus 1.12.2 h5243cc1_1

< decorator 4.2.1 py27_0

< distributed 1.20.2 py27_0

< docutils 0.14 py27h0befae3_0

---

> dbus 1.13.6 h90a0687_0

> decorator 4.4.0 py27_1

65,69c32,34

< entrypoints 0.2.3 py27hd680fb1_2

< enum34 1.1.6 py27hf475452_1

< et_xmlfile 1.0.1 py27hc42f929_0

< expat 2.2.5 hb8e80ba_0

< fastcache 1.0.2 py27h1de35cc_2

---

> eman2 2.3 h04f5b5a_0 file://users/eman/anaconda/conda-bld

> enum34 1.1.6 py27_1

> expat 2.2.6 h0a44026_0

71,74c36,37

< filelock 2.0.13 py27h2c227fa_0

< flask 0.12.2 py27h3ac5568_0

< flask-cors 3.0.3 py27h13db576_0

< freetype 2.8 h12048fb_1

---

> filelock 3.0.10 py27_0

> freetype 2.9.1 hb4e5f40_0

77c40

< functools32 3.2.3.2 py27h8ceab06_1

---

> functools32 3.2.3.2 py27_1

79,80c42

< futures 3.2.0 py27h1b80678_0

< get_terminal_size 1.0.0 h7520d66_0

---

> futures 3.2.0 py27_0

82,88c44,45

< gevent 1.2.2 py27hc02608c_0

< glib 2.53.6 h33f6a65_2

< glob2 0.6 py27h55c9705_0

< gmp 6.1.2 hb37e062_1

< gmpy2 2.0.8 py27h4bc979a_2

< greenlet 0.4.12 py27h081ed54_0

< grin 1.2.1 py27_4

---

> glib 2.56.2 hd9629dc_0

> glob2 0.6 py27_1

90d46

< h5py 2.7.1 py27h75626f5_0

92d47

< heapdict 1.0.0 py27_2

95,101c50,53

< idna 2.6 py27hedea723_1

< imageio 2.2.0 py27h37746d9_0

< imagesize 0.7.1 py27h4f7bcc8_0

< intel-openmp 2018.0.0 h8158457_8

< ipaddress 1.0.19 py27_0

< ipykernel 4.8.0 py27_0

< ipython 5.4.1 py27_2

---

> idna 2.8 py27_0

> intel-openmp 2019.3 199

> ipaddress 1.0.22 py27_0

> ipython 5.8.0 py27_0

103,109c55

< ipywidgets 7.1.1 py27_0

< isort 4.2.15 py27h5bf637f_0

< itsdangerous 0.24 py27h3948ded_1

< jbig 2.1 h4d881f8_0

< jdcal 1.3 py27hfeaf94f_0

< jedi 0.11.1 py27_0

< jinja2 2.10 py27h70b8dc5_0

---

> jinja2 2.10.1 py27_0

111,117d56

< jsonschema 2.6.0 py27hd9b497e_0

< jupyter 1.0.0 py27_4

< jupyter_client 5.2.2 py27_0

< jupyter_console 5.2.0 py27h9702a86_1

< jupyter_core 4.4.0 py27h5ea6ba4_0

< jupyterlab 0.31.5 py27_0

< jupyterlab_launcher 0.10.2 py27_0

119,123c58,61

< lazy-object-proxy 1.3.1 py27h712ce3f_0

< libcurl 7.58.0 hf30b1f0_0

< libcxx 4.0.1 h579ed51_0

< libcxxabi 4.0.1 hebd6815_0

< libedit 3.1 hb4e282d_0

---

> libarchive 3.3.3 h786848e_5

> libcxx 4.0.1 hcfea43d_1

> libcxxabi 4.0.1 hcfea43d_1

> libedit 3.1.20181209 hb402a30_0

126a65

> liblief 0.9.0 h2a1bed3_2

129,137c68,70

< libsodium 1.0.15 hd9e47c5_0

< libssh2 1.8.0 h322a93b_4

< libtiff 4.0.9 h0dac147_0

< libuv 1.26.0 h1de35cc_0

< libxml2 2.9.7 hab757c2_0

< libxslt 1.1.32 hb819dd2_0

< llvmlite 0.21.0 py27hac8ee23_0

< locket 0.2.0 py27ha10513d_1

< lxml 4.1.1 py27hef8c89e_1

---

> libtiff 4.0.9 hcb84e12_2

> libxml2 2.9.9 hab757c2_0

> lz4-c 1.8.1.2 h1de35cc_0

139,145c72,75

< markdown 3.0.1 py27_0

< markupsafe 1.0 py27hd3c86fa_1

< matplotlib 2.2.2 py27ha7267d0_0

< mccabe 0.6.1 py27h1f69e8d_0

< mistune 0.8.3 py27_0

< mkl 2018.0.1 hfbd8650_4

< mkl-service 1.1.2 py27hcba3029_4

---

> markdown 3.1 py27_0

> markupsafe 1.1.1 py27h1de35cc_0

> matplotlib 2.2.3 py27h54f8f79_0

> mkl 2018.0.3 1

147,161c77,78

< mpc 1.0.3 h7a72875_5

< mpfr 3.1.5 h711e7fd_2

< mpmath 1.0.0 py27h6b0eff6_2

< msgpack-python 0.5.1 py27h04f5b5a_0

< multipledispatch 0.4.9 py27h10993aa_0

< navigator-updater 0.1.0 py27ha63e0b4_0

< nbconvert 5.3.1 py27h6455e4c_0

< nbformat 4.4.0 py27hddc86d0_0

< ncurses 6.0 hd04f020_2

< networkx 2.1 py27_0

< nltk 3.2.5 py27h2e86947_0

< nose 1.3.7 py27h2ee3cb8_2

< notebook 5.4.0 py27_0

< numba 0.36.2 np114py27he3a832a_0

< numexpr 2.6.4 py27hf375000_0

---

> ncurses 6.1 h0a44026_1

> nose 1.3.7 py27_2

163,165d79

< numpydoc 0.7.0 py27h022f19e_0

< odo 0.5.1 py27h992a9f7_0

< olefile 0.45.1 py27_0

167d80

< openpyxl 2.4.10 py27_0

169,177c82

< packaging 16.8 py27h24b219a_0

< pandas 0.22.0 py27h0a44026_0

< pandoc 1.19.2.1 ha5e8f32_1

< pandocfilters 1.4.2 py27hed78c4e_1

< parso 0.1.1 py27he57c4c6_0

< partd 0.3.8 py27h7560dbf_0

< path.py 10.5 py27h0d68f8b_0

< pathlib2 2.3.0 py27he09da1e_0

< patsy 0.5.0 py27_0

---

> pathlib2 2.3.3 py27_0

179,187c84,88

< pcre 8.41 hfb6ab37_1

< pep8 1.7.1 py27_0

< pexpect 4.3.1 py27_0

< pickleshare 0.7.4 py27h37e3d41_0

< pillow 5.0.0 py27hfcce615_0

< pip 9.0.1 py27h1567d89_4

< pkginfo 1.4.1 py27ha9221e7_0

< pluggy 0.6.0 py27had36429_0

< ply 3.10 py27h6279b8a_0

---

> pcre 8.43 h0a44026_0

> pexpect 4.7.0 py27_0

> pickleshare 0.7.5 py27_0

> pip 19.0.3 py27_0

> pkginfo 1.5.0.1 py27_0

190,198c91,95

< psutil 5.4.3 py27h1de35cc_0

< ptyprocess 0.5.2 py27h70f6364_0

< py 1.5.2 py27he6783ac_0

< pyaudio 0.2.7 py27h3777516_1

< pycodestyle 2.3.1 py27h5b634e0_0

< pycosat 0.6.3 py27h6c51c7e_0

< pycparser 2.18 py27h0d28d88_1

< pycrypto 2.6.1 py27h1de35cc_7

< pycurl 7.43.0.1 py27hdbc3d79_0

---

> psutil 5.6.1 py27h1de35cc_0

> ptyprocess 0.6.0 py27_0

> py-lief 0.9.0 py27h1413db1_2

> pycosat 0.6.3 py27h1de35cc_0

> pycparser 2.19 py27_0

200,203c97

< pyflakes 1.6.0 py27h4446e76_0

< pygments 2.2.0 py27h1a556bb_0

< pylint 1.8.2 py27_0

< pyodbc 4.0.22 py27h0a44026_0

---

> pygments 2.3.1 py27_0

205,233c99,115

< pyopenssl 17.5.0 py27hfda213f_0

< pyparsing 2.2.0 py27h5bb6aaf_0

< pyqt 5.6.0 py27hf21fe59_6

< pysocks 1.6.7 py27h1cff6a6_1

< pytables 3.4.2 py27ha4551b8_2

< pytest 3.3.2 py27_0

< python 2.7.14 hde5916a_29

< python-dateutil 2.6.1 py27hd56c96b_1

< python.app 2 py27hf2d5e94_7

< pytz 2017.3 py27h803c07a_0

< pywavelets 0.5.2 py27hd99e88a_0

< pyyaml 3.12 py27ha7932d0_1

< pyzmq 16.0.3 py27h91ccc67_0

< qt 5.6.2 h9975529_14

< qtawesome 0.4.4 py27hdeb2f59_0

< qtconsole 4.3.1 py27hdc90b4f_0

< qtpy 1.3.1 py27h39159f8_0

< readline 7.0 hc1231fa_4

< requests 2.18.4 py27h9b2b37c_1

< rhash 1.3.6 hdbc3d79_0

< rope 0.10.7 py27hffa1879_0

< ruamel_yaml 0.15.35 py27h1de35cc_1

< scandir 1.6 py27h97aa1ee_0

< scikit-image 0.13.1 py27h1de35cc_1

< scikit-learn 0.19.1 py27h9788993_0

< scipy 1.0.0 py27h793f721_0

< seaborn 0.8.1 py27h6bd0ddc_0

< send2trash 1.4.2 py27_0

< setuptools 38.4.0 py27_0

---

> pyopenssl 19.0.0 py27_0

> pyparsing 2.4.0 py_0

> pyqt 5.9.2 py27h655552a_2

> pysocks 1.6.8 py27_0

> python 2.7.14 h138c1fe_31

> python-dateutil 2.8.0 py27_0

> python-libarchive-c 2.8 py27_6

> pytz 2019.1 py_0

> pyyaml 5.1 py27h1de35cc_0

> qt 5.9.6 h45cd832_2

> readline 7.0 h1de35cc_5

> requests 2.21.0 py27_0

> ruamel_yaml 0.15.46 py27h1de35cc_0

> scandir 1.10.0 py27h1de35cc_0

> scikit-learn 0.19.2 py27h4f467ca_0

> scipy 1.1.0 py27hf5b7bf4_0

> setuptools 41.0.0 py27_0

236,251c118,122

< sip 4.18.1 py27h6300f65_2

< six 1.11.0 py27h7252ba3_1

< snowballstemmer 1.2.1 py27h68ac032_0

< sortedcollections 0.5.3 py27h8094be4_0

< sortedcontainers 1.5.9 py27_0

< sphinx 1.6.6 py27_0

< sphinxcontrib 1.0 py27hd2ed746_1

< sphinxcontrib-websupport 1.0.1 py27h857890b_1

< spyder 3.2.6 py27_0

< sqlalchemy 1.2.1 py27h1de35cc_0

< sqlite 3.22.0 h3efe00b_0

< ssl_match_hostname 3.5.0.1 py27h8780752_2

< statsmodels 0.8.0 py27h6d68dbf_0

< subprocess32 3.2.7 py27h24b2887_0

< sympy 1.1.1 py27hce55102_0

< tblib 1.3.2 py27ha684fc4_0

---

> sip 4.19.8 py27h0a44026_0

> six 1.12.0 py27_0

> soupsieve 1.8 py27_0

> sqlite 3.28.0 ha441bb4_0

> subprocess32 3.5.3 py27h1de35cc_0

253,257c124,125

< terminado 0.8.1 py27_1

< testpath 0.3.1 py27h72d81a5_0

< tk 8.6.7 h35a86e2_3

< toolz 0.9.0 py27_0

< tornado 4.5.3 py27_0

---

> tk 8.6.8 ha441bb4_0

> tornado 5.1.1 py27h1de35cc_0

260,263c128

< typing 3.6.2 py27h646fea0_0

< unicodecsv 0.14.1 py27h170f95c_0

< unixodbc 2.3.4 h4cb4dde_1

< urllib3 1.22 py27hc3787e9_0

---

> urllib3 1.24.1 py27_0

265,274c130,132

< webencodings 0.5.1 py27h19a9f58_1

< werkzeug 0.14.1 py27_0

< wheel 0.30.0 py27h677a027_1

< widgetsnbextension 3.1.0 py27_0

< wrapt 1.10.11 py27hd341262_0

< xlrd 1.1.0 py27hbd41ed1_1

< xlsxwriter 1.0.2 py27h7f1064a_0

< xlwings 0.11.5 py27_0

< xlwt 1.2.0 py27hbeec4ae_0

< xz 5.2.3 h0278029_2

---

> werkzeug 0.15.2 py_0

> wheel 0.33.1 py27_0

> xz 5.2.4 h1de35cc_4

276,278c134,135

< zeromq 4.2.2 ha360ad0_2

< zict 0.1.3 py27h5fff8b1_0

< zlib 1.2.11 hf3cbc9b_2

---

> zlib 1.2.11 h1de35cc_3

> zstd 1.3.7 h5bba6e5_0

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

Steve Ludtke

unread,

Apr 30, 2019, 11:01:45 PM4/30/19

to em...@googlegroups.com

Ok, the problem turned out to be a very very slight version issue with one of the dependencies in Anaconda. New installs of the binaries should now work, and broken installs should be fixable with:

conda install eman-deps=14.1=1 -c cryoem -c defaults -c conda-forge

(answer yes to any questions)

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

On Apr 30, 2019, at 4:51 PM, Mario Borgnia <mbor...@gmail.com> wrote:

<conda_list_e.txt><conda_list_explicit.txt><conda_info_a.txt><python_report.txt>

nancy meyer

unread,

May 1, 2019, 1:07:15 PM5/1/19

to EMAN2

Thank you very much. The above solution worked.

- Nancy

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<conda_list_e.txt><conda_list_explicit.txt><conda_info_a.txt><python_report.txt>

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fj...@yale.edu

unread,

May 1, 2019, 9:40:21 PM5/1/19

to EMAN2

Ah! Now I see why closing and opening the terminal window didn't work: I was using my Macbook Pro with two external displays. Running just with the built-in display now at home, e2display.py worked great. Now I've just applied the new patch.

Fred

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