[GSAS-II] problem installing gsas2 on linux server
Long Yang
dragonyang92 at gmail.com
Mon May 4 12:39:39 CDT 2020
Hi,
I met a problem when conda install gsas2 on an Ubuntu (18.04.3 LTS) server machine. When `conda install gsas2pkg -c briantoby`, 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.
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.
I also tried to download the `gsas2full-Latest-Linux-x86_64.sh` following instruction at https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller <https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller>, but after installation, in the `gsas2full` folder, I didn’t find a `GSASII` folder as step 4 said.
BTW, this linux machine is inside national lab firewall, not sure if this causes a problem.
Thanks!
Long Yang
full error log:
(gsas) anaconda at addie:~/GSASII$ conda install gsas2pkg -c briantoby
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/anaconda/miniconda3/envs/gsas
added / updated specs:
- gsas2pkg
The following NEW packages will be INSTALLED:
apr pkgs/main/linux-64::apr-1.6.3-he40df45_0
asn1crypto pkgs/main/linux-64::asn1crypto-1.3.0-py37_0
blas pkgs/main/linux-64::blas-1.0-mkl
cffi pkgs/main/linux-64::cffi-1.14.0-py37h2e261b9_0
chardet pkgs/main/linux-64::chardet-3.0.4-py37_1003
conda pkgs/main/linux-64::conda-4.8.3-py37_0
conda-package-han~ pkgs/main/linux-64::conda-package-handling-1.6.0-py37h7b6447c_0
cryptography pkgs/main/linux-64::cryptography-2.8-py37h1ba5d50_0
cycler pkgs/main/linux-64::cycler-0.10.0-py37_0
cyrus-sasl pkgs/main/linux-64::cyrus-sasl-2.1.26-h82bf5a1_4
dbus pkgs/main/linux-64::dbus-1.13.12-h746ee38_0
gsas2pkg briantoby/linux-64::gsas2pkg-1.0.6-0
h5py pkgs/main/linux-64::h5py-2.10.0-py37h7918eee_0
hdf5 pkgs/main/linux-64::hdf5-1.10.4-hb1b8bf9_0
idna pkgs/main/noarch::idna-2.9-py_1
imageio pkgs/main/noarch::imageio-2.8.0-py_0
intel-openmp pkgs/main/linux-64::intel-openmp-2020.0-166
kiwisolver pkgs/main/linux-64::kiwisolver-1.2.0-py37hfd86e86_0
krb5 pkgs/main/linux-64::krb5-1.16.4-h173b8e3_0
libdb pkgs/main/linux-64::libdb-6.1.26-he6710b0_0
libgfortran-ng pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
libntlm pkgs/main/linux-64::libntlm-1.5-h7b6447c_0
libtiff pkgs/main/linux-64::libtiff-4.1.0-h2733197_0
libutf8proc pkgs/main/linux-64::libutf8proc-2.1.1-h14c3975_0
lz4-c pkgs/main/linux-64::lz4-c-1.8.1.2-h14c3975_0
matplotlib pkgs/main/linux-64::matplotlib-3.1.3-py37_0
matplotlib-base pkgs/main/linux-64::matplotlib-base-3.1.3-py37hef1b27d_0
mkl pkgs/main/linux-64::mkl-2020.0-166
mkl-service pkgs/main/linux-64::mkl-service-2.3.0-py37he904b0f_0
mkl_fft pkgs/main/linux-64::mkl_fft-1.0.15-py37ha843d7b_0
mkl_random pkgs/main/linux-64::mkl_random-1.1.0-py37hd6b4f25_0
numpy pkgs/main/linux-64::numpy-1.18.1-py37h4f9e942_0
numpy-base pkgs/main/linux-64::numpy-base-1.18.1-py37hde5b4d6_1
olefile pkgs/main/linux-64::olefile-0.46-py37_0
pillow pkgs/main/linux-64::pillow-7.1.2-py37hb39fc2d_0
pycosat pkgs/main/linux-64::pycosat-0.6.3-py37h7b6447c_0
pycparser pkgs/main/noarch::pycparser-2.20-py_0
pyopengl pkgs/main/linux-64::pyopengl-3.1.1a1-py37_0
pyopenssl pkgs/main/linux-64::pyopenssl-19.1.0-py37_0
pyparsing pkgs/main/noarch::pyparsing-2.4.7-py_0
pyqt pkgs/main/linux-64::pyqt-5.9.2-py37h05f1152_2
pysocks pkgs/main/linux-64::pysocks-1.7.1-py37_0
python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0
qt pkgs/main/linux-64::qt-5.9.7-h5867ecd_1
requests pkgs/main/linux-64::requests-2.23.0-py37_0
ruamel_yaml pkgs/main/linux-64::ruamel_yaml-0.15.87-py37h7b6447c_0
scipy pkgs/main/linux-64::scipy-1.4.1-py37h0b6359f_0
serf pkgs/main/linux-64::serf-1.3.9-h1c830df_0
sip pkgs/main/linux-64::sip-4.19.8-py37hf484d3e_0
svn pkgs/main/linux-64::svn-1.10.2-h52f66ed_0
tornado pkgs/main/linux-64::tornado-6.0.4-py37h7b6447c_1
tqdm pkgs/main/noarch::tqdm-4.45.0-py_0
urllib3 pkgs/main/linux-64::urllib3-1.25.8-py37_0
yaml pkgs/main/linux-64::yaml-0.1.7-had09818_2
zstd pkgs/main/linux-64::zstd-1.3.7-h0b5b093_0
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(700): An error occurred while installing package'briantoby::gsas2pkg-1.0.6-0'.
Rolling back transaction: done
LinkError: post-link script failed for package briantoby::gsas2pkg-1.0.6-0
location of failed script: /opt/anaconda/miniconda3/envs/gsas/bin/.gsas2pkg-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: Preparing to install GSAS-II from APS subversion server
/opt/anaconda/miniconda3/envs/gsas/bin/python
Running bootstrap from /opt/anaconda/miniconda3/envs/gsas/GSASII at 2020-05-04 13:26:16.993798
Id: $Id: bootstrap.py 3515 2018-07-30 02:14:14Z toby $
**********************************************************************
Preloading matplotlib to build fonts...
Checking python packages...
Sorry, this version of Python cannot be used
for GSAS-II. It is missing the following package(s):
wx
Please install these package(s) and try running this again.
Showing first error:
stderr: mkdir: cannot create directory ‘/opt/anaconda/miniconda3/envs/gsas/GSASII’: File exists
Traceback (most recent call last):
File "/opt/anaconda/miniconda3/envs/gsas/GSASII/bootstrap.py", line 187, in <module>
exec('import '+pkg)
File "<string>", line 1, in <module>
File "/opt/anaconda/miniconda3/envs/gsas/lib/python3.7/site-packages/wx/__init__.py", line 12, in <module>
__version__ = wx.__version__.VERSION_STRING
AttributeError: module 'wx' has no attribute '__version__'
return code: 1
()
(gsas) anaconda at addie:~/GSASII$
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