<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Brian,<div class=""><br class=""></div><div class="">Thanks for your suggestion. After a long journey, I kind of found a temporary solution to install. The problem is from, as you pointed out, the `wx` package on linux. I wrote my solution below and share with the community in case anyone have similar problem when conda install gsas2.</div><div class=""><br class=""></div><div class="">1. conda install wxpython #it will install 4.0.4 version on my case</div><div class="">2. go to ~/anaconda.../lib/python3.7/site-packages/wx/__init__.py</div><div class="">comment out all the lines within the file, and manually add `__version__=“4.0.4”`</div><div class="">3. conda install gsas2pkg -c briantoby #now, the bootstrap.py error finally passes. and in my case, GSASII is installed successfully now.</div><div class="">4. go to ~/anaconda.../lib/python3.7/site-packages/wx/__init__.py</div><div class="">uncomment the lines did in step 2, but leave `__version__=“4.0.4”` there, and still comment out `import wx.__version__` line, otherwise, similar error will happen again every time calling the GSASII bootstrap.py.</div><div class=""><br class=""></div><div class="">In this way, I can use GSASIIscriptable without problem, I am not using GUI on the linux server, so I didn’t check whether this solution will cause any problem on GSASII GUI.</div><div class=""><br class=""></div><div class="">Thanks!</div><div class="">Long</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 4, 2020, at 3:21 PM, Toby, Brian H. <<a href="mailto:toby@anl.gov" class="">toby@anl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Long,
<div class=""><br class="">
</div>
<div class=""> The error message you show:</div>
<div class=""><br class="">
</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class="">
<div class="">Traceback (most recent call last):</div>
<div class=""> File "/opt/anaconda/miniconda3/envs/gsas/GSASII/bootstrap.py", line 187, in <module></div>
<div class=""> exec('import '+pkg)</div>
<div class=""> File "<string>", line 1, in <module></div>
<div class=""> File "/opt/anaconda/miniconda3/envs/gsas/lib/python3.7/site-packages/wx/__init__.py", line 12, in <module></div>
<div class=""> __version__ = wx.__version__.VERSION_STRING</div>
<div class="">AttributeError: module 'wx' has no attribute '__version__'</div>
</blockquote>
<div class="">
<div class=""><br class="">
</div>
<div class="">seems to show that wx is installed, but is not functioning properly. I think that using
<font face="Courier" size="2" class=""><span style="font-style: normal;" class="">import wx</span></font> from inside python will demonstrate this. Installation into Linux is turning into a big challenge. I think this is because there are so many dists with
different vintages of libraries. </div>
<div class=""><br class="">
</div>
<div class="">I am only going to be of limited help with this, but I am concerned that you have mentioned you both used conda and pip to install wx. That could be a problem and you might need to clear house and reinstall python. You might do some research to see if
there is some extra ubuntu package (glib or something like that?) that is needed to make this work. Alternately, you might want to install ubuntu python and the packages we need via the Ubuntu. I think I have done that in Ubuntu a few years ago, so I think
this works too. </div>
<div class=""><br class="">
</div>
<div class="">You do not need to use GSAS-II as a diagnostic, start by seeing if you can get to the point where "<font face="Courier" size="2" class=""><span style="font-style: normal;" class="">import wx</span></font>” works in python. Once you have that, you can test
with GSAS-II using </div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><path>python /opt/anaconda/miniconda3/envs/gsas/GSASII/GSASII.py</div>
<div class=""><br class="">
</div>
<div class="">once that works, take a look at the <font face="Courier" size="2" class=""><span style="font-style: normal;" class="">/opt/anaconda/miniconda3/envs/gsas/GSASII/makeLinux.py</span></font></div>
<div class="">script to see if you want what that does (it could use some input from dedicated Linux users FWIW.)</div>
<div class=""><br class="">
</div>
<div class="">Brian</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 4, 2020, at 12:39 PM, Long Yang via GSAS-II <<a href="mailto:gsas-ii@aps.anl.gov" class="">gsas-ii@aps.anl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi,
<div class=""><br class="">
</div>
<div class="">I met a problem when conda install gsas2 on an Ubuntu (18.04.3 LTS) server machine. When `<span style="orphans: 2; widows: 2; background-color: rgb(247, 247, 247);" class="">conda install gsas2pkg -c briantoby`</span>, it seems like always stuck
at running the bootstrap saying not finding `wx` package. I pasted the error log in the bottom. python version is 3.7.3, and I have no such problem conda install gsas2 on my mac machine before.</div>
<div class=""><br class="">
</div>
<div class="">I tried to conda install and pip install the wxpython first, and I am making sure that I have wxpython 4.0.4 inside my conda environment, then install gsas2, but still same error. </div>
<div class=""><br class="">
</div>
<div class="">I also tried to download the `gsas2full-Latest-Linux-x86_64.sh` following instruction at <a href="https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller" class="">https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller</a>,
but after installation, in the `gsas2full` folder, I didn’t find a `GSASII` folder as step 4 said.</div>
<div class=""><br class="">
</div>
<div class="">BTW, this linux machine is inside national lab firewall, not sure if this causes a problem.</div>
<div class=""><br class="">
</div>
<div class="">Thanks!</div>
<div class="">Long Yang</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">full error log:</div>
<div class="">(gsas) anaconda@addie:~/GSASII$ conda install gsas2pkg -c briantoby<br class="">
Collecting package metadata (current_repodata.json): done<br class="">
Solving environment: done<br class="">
<br class="">
## Package Plan ##<br class="">
<br class="">
environment location: /opt/anaconda/miniconda3/envs/gsas<br class="">
<br class="">
added / updated specs:<br class="">
- gsas2pkg<br class="">
<br class="">
<br class="">
The following NEW packages will be INSTALLED:<br class="">
<br class="">
apr pkgs/main/linux-64::apr-1.6.3-he40df45_0<br class="">
asn1crypto pkgs/main/linux-64::asn1crypto-1.3.0-py37_0<br class="">
blas pkgs/main/linux-64::blas-1.0-mkl<br class="">
cffi pkgs/main/linux-64::cffi-1.14.0-py37h2e261b9_0<br class="">
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003<br class="">
conda pkgs/main/linux-64::conda-4.8.3-py37_0<br class="">
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0<br class="">
cryptography pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0<br class="">
cycler pkgs/main/linux-64::cycler-0.10.0-py37_0<br class="">
cyrus-sasl pkgs/main/linux-64::cyrus-sasl-2.1.26-h82bf5a1_4<br class="">
dbus pkgs/main/linux-64::dbus-1.13.12-h746ee38_0<br class="">
gsas2pkg briantoby/linux-64::gsas2pkg-1.0.6-0<br class="">
h5py pkgs/main/linux-64::h5py-2.10.0-py37h7918eee_0<br class="">
hdf5 pkgs/main/linux-64::hdf5-1.10.4-hb1b8bf9_0<br class="">
idna pkgs/main/noarch::idna-2.9-py_1<br class="">
imageio pkgs/main/noarch::imageio-2.8.0-py_0<br class="">
intel-openmp pkgs/main/linux-64::intel-openmp-2020.0-166<br class="">
kiwisolver pkgs/main/linux-64::kiwisolver-1.2.0-py37hfd86e86_0<br class="">
krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0<br class="">
libdb pkgs/main/linux-64::libdb-6.1.26-he6710b0_0<br class="">
libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0<br class="">
libntlm pkgs/main/linux-64::libntlm-1.5-h7b6447c_0<br class="">
libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0<br class="">
libutf8proc pkgs/main/linux-64::libutf8proc-2.1.1-h14c3975_0<br class="">
lz4-c pkgs/main/linux-64::lz4-c-1.8.1.2-h14c3975_0<br class="">
matplotlib pkgs/main/linux-64::matplotlib-3.1.3-py37_0<br class="">
matplotlib-base pkgs/main/linux-64::matplotlib-base-3.1.3-py37hef1b27d_0<br class="">
mkl pkgs/main/linux-64::mkl-2020.0-166<br class="">
mkl-service pkgs/main/linux-64::mkl-service-2.3.0-py37he904b0f_0<br class="">
mkl_fft pkgs/main/linux-64::mkl_fft-1.0.15-py37ha843d7b_0<br class="">
mkl_random pkgs/main/linux-64::mkl_random-1.1.0-py37hd6b4f25_0<br class="">
numpy pkgs/main/linux-64::numpy-1.18.1-py37h4f9e942_0<br class="">
numpy-base pkgs/main/linux-64::numpy-base-1.18.1-py37hde5b4d6_1<br class="">
olefile pkgs/main/linux-64::olefile-0.46-py37_0<br class="">
pillow pkgs/main/linux-64::pillow-7.1.2-py37hb39fc2d_0<br class="">
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0<br class="">
pycparser pkgs/main/noarch::pycparser-2.20-py_0<br class="">
pyopengl pkgs/main/linux-64::pyopengl-3.1.1a1-py37_0<br class="">
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0<br class="">
pyparsing pkgs/main/noarch::pyparsing-2.4.7-py_0<br class="">
pyqt pkgs/main/linux-64::pyqt-5.9.2-py37h05f1152_2<br class="">
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0<br class="">
python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0<br class="">
qt pkgs/main/linux-64::qt-5.9.7-h5867ecd_1<br class="">
requests pkgs/main/linux-64::requests-2.23.0-py37_0<br class="">
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0<br class="">
scipy pkgs/main/linux-64::scipy-1.4.1-py37h0b6359f_0<br class="">
serf pkgs/main/linux-64::serf-1.3.9-h1c830df_0<br class="">
sip pkgs/main/linux-64::sip-4.19.8-py37hf484d3e_0<br class="">
svn pkgs/main/linux-64::svn-1.10.2-h52f66ed_0<br class="">
tornado pkgs/main/linux-64::tornado-6.0.4-py37h7b6447c_1<br class="">
tqdm pkgs/main/noarch::tqdm-4.45.0-py_0<br class="">
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0<br class="">
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2<br class="">
zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0<br class="">
<br class="">
<br class="">
Proceed ([y]/n)? y<br class="">
<br class="">
Preparing transaction: done<br class="">
Verifying transaction: done<br class="">
Executing transaction: done<br class="">
<br class="">
</div>
<div class="">ERROR <a href="http://conda.core.link/" class="">conda.core.link</a>:_execute(700): An error occurred while installing package'briantoby::gsas2pkg-1.0.6-0'.<br class="">
Rolling back transaction: done<br class="">
<br class="">
LinkError: post-link script failed for package briantoby::gsas2pkg-1.0.6-0<br class="">
location of failed script: /opt/anaconda/miniconda3/envs/gsas/bin/.gsas2pkg-post-link.sh<br class="">
==> script messages <==<br class="">
<None><br class="">
==> script output <==<br class="">
stdout: Preparing to install GSAS-II from APS subversion server<br class="">
/opt/anaconda/miniconda3/envs/gsas/bin/python<br class="">
Running bootstrap from /opt/anaconda/miniconda3/envs/gsas/GSASII at 2020-05-04 13:26:16.993798<br class="">
Id: $Id: bootstrap.py 3515 2018-07-30 02:14:14Z toby $<br class="">
**********************************************************************<br class="">
Preloading matplotlib to build fonts...<br class="">
Checking python packages...<br class="">
Sorry, this version of Python cannot be used<br class="">
for GSAS-II. It is missing the following package(s):<br class="">
wx<br class="">
<br class="">
Please install these package(s) and try running this again.<br class="">
Showing first error:<br class="">
<br class="">
stderr: mkdir: cannot create directory ‘/opt/anaconda/miniconda3/envs/gsas/GSASII’: File exists<br class="">
Traceback (most recent call last):<br class="">
File "/opt/anaconda/miniconda3/envs/gsas/GSASII/bootstrap.py", line 187, in <module><br class="">
exec('import '+pkg)<br class="">
File "<string>", line 1, in <module><br class="">
File "/opt/anaconda/miniconda3/envs/gsas/lib/python3.7/site-packages/wx/__init__.py", line 12, in <module><br class="">
__version__ = wx.__version__.VERSION_STRING<br class="">
AttributeError: module 'wx' has no attribute '__version__'<br class="">
<br class="">
return code: 1<br class="">
<br class="">
()<br class="">
<br class="">
(gsas) anaconda@addie:~/GSASII$<br class="">
<br class="">
</div>
</div>
_______________________________________________<br class="">
GSAS-II mailing list<br class="">
<a href="mailto:GSAS-II@aps.anl.gov" class="">GSAS-II@aps.anl.gov</a><br class="">
<a href="https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii" class="">https://mailman.aps.anl.gov/mailman/listinfo/gsas-ii</a></div>
</blockquote>
</div>
<br class="">
</div>
</div>
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