How to install lmfit without root？

[Li Zhang]

Hello everyone,

I try to install lmfit-0.9.3 on a CentOS6.4 server, I met some problems which I can't solve it. However I don't have root authority, the administrator think that it should be installed in my own directory.

Way 1: I downloaded lmfit-py-0.9.3 from https://github.com/lmfit/lmfit-py/releases/tag/0.9.3:

$ tar -zxvf lmfit-py-0.9.3.tar.gz,

$./configure --prefix=/home/....

###ERROR    bash: ./configure: No such file or directory

Way 2: downloaded from http://cars9.uchicago.edu/software/python/lmfit/installation.html#downloads

$ tar -zxvf lmfit-0.9.3.tar.gz,

$ cd lmfit-0.9.3

$ python setup.py build

$ python setup.py install

####error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in the
installation directory:

    [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/test-easy-install-2899.write-test'

The installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

    /usr/local/lib/python2.7/dist-packages/

Perhaps your account does not have write access to this directory?  If the
installation directory is a system-owned directory, you may need to sign in
as the administrator or "root" account.  If you do not have administrative
access to this machine, you may wish to choose a different installation
directory, preferably one that is listed in your PYTHONPATH environment
variable.

For information on other options, you may wish to consult the
documentation at:

  https://pythonhosted.org/setuptools/easy_install.html

Please make the appropriate changes for your system and try again.

####

I tried to change the setup.py file, however I didn't find the directory term.

Way 3: 

$pip install lmfit --don't work

$easy_install -U lmfit --don't work

Could you tell me the answer if you know?

With Best Regards

Li Zhang

[Matt Newville]

Hi Li,

On Tue, May 31, 2016 at 10:21 PM, Li Zhang <lizhang...@gmail.com> wrote:

Hello everyone,

I try to install lmfit-0.9.3 on a CentOS6.4 server, I met some problems which I can't solve it. However I don't have root authority, the administrator think that it should be installed in my own directory.

Way 1: I downloaded lmfit-py-0.9.3 from https://github.com/lmfit/lmfit-py/releases/tag/0.9.3:

$ tar -zxvf lmfit-py-0.9.3.tar.gz,

$./configure --prefix=/home/....

###ERROR    bash: ./configure: No such file or directory

That's not how (most) Python packages install.
 

Way 2: downloaded from http://cars9.uchicago.edu/software/python/lmfit/installation.html#downloads

$ tar -zxvf lmfit-0.9.3.tar.gz,

$ cd lmfit-0.9.3

$ python setup.py build

$ python setup.py install

####error: can't create or remove files in install directory

Since you're using Python2.7, I believe that doing
  python setup.py install --user

should work to install to $HOME/.local/lib/python2.7/site-packages/lmfit-0.9.3.     Try

    python setup.py install --help

for more info on installation options.

--Matt

[Li Zhang]

Hi Matt,

Thank you very much for the usefull suggestion. I have installed it as your suggestion, but there are two SyntaxError for parameter.py and asteval.py.

when lmfit is imported, the error :

---> 21 from lmfit import minimize,Parameters,Parameter,report_fit

ImportError: No module named lmfit

What's the problem?

The installation information is as following:

######

$python setup.py build

$python setup.py install --user

running install

running bdist_egg

running egg_info

writing requirements to lmfit.egg-info/requires.txt

writing lmfit.egg-info/PKG-INFO

writing top-level names to lmfit.egg-info/top_level.txt

writing dependency_links to lmfit.egg-info/dependency_links.txt

reading manifest file 'lmfit.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

warning: no files found matching 'README.txt'

warning: no previously-included files found matching '*.pyc'

warning: no previously-included files found matching 'core.*'

warning: no previously-included files found matching '*~'

warning: no previously-included files found matching '*.pdf'

warning: no files found matching '*.dat' under directory 'tests'

warning: no previously-included files matching '*' found under directory 'doc/_build'

warning: no previously-included files matching '*.pdf' found under directory 'doc'

writing manifest file 'lmfit.egg-info/SOURCES.txt'

installing library code to build/bdist.linux-x86_64/egg

running install_lib

running build_py

creating build/bdist.linux-x86_64/egg

creating build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/_differentialevolution.py -> build/bdist.linux-x86_64/egg/lmfit

creating build/bdist.linux-x86_64/egg/lmfit/uncertainties

copying build/lib/lmfit/uncertainties/__init__.py -> build/bdist.linux-x86_64/egg/lmfit/uncertainties

copying build/lib/lmfit/uncertainties/umath.py -> build/bdist.linux-x86_64/egg/lmfit/uncertainties

creating build/bdist.linux-x86_64/egg/lmfit/ui

copying build/lib/lmfit/ui/ipy_fitter.py -> build/bdist.linux-x86_64/egg/lmfit/ui

copying build/lib/lmfit/ui/__init__.py -> build/bdist.linux-x86_64/egg/lmfit/ui

copying build/lib/lmfit/ui/basefitter.py -> build/bdist.linux-x86_64/egg/lmfit/ui

copying build/lib/lmfit/printfuncs.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/astutils.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/minimizer.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/model.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/lineshapes.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/_version.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/parameter.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/asteval.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/ordereddict.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/models.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/confidence.py -> build/bdist.linux-x86_64/egg/lmfit

copying build/lib/lmfit/__init__.py -> build/bdist.linux-x86_64/egg/lmfit

byte-compiling build/bdist.linux-x86_64/egg/lmfit/_differentialevolution.py to _differentialevolution.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/uncertainties/__init__.py to __init__.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/uncertainties/umath.py to umath.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/ui/ipy_fitter.py to ipy_fitter.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/ui/__init__.py to __init__.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/ui/basefitter.py to basefitter.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/printfuncs.py to printfuncs.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/astutils.py to astutils.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/minimizer.py to minimizer.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/model.py to model.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/lineshapes.py to lineshapes.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/_version.py to _version.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/parameter.py to parameter.pyc

SyntaxError: ('invalid syntax', ('build/bdist.linux-x86_64/egg/lmfit/parameter.py', 101, 29, '                          for key in sym_unique}\n'))

byte-compiling build/bdist.linux-x86_64/egg/lmfit/asteval.py to asteval.pyc

SyntaxError: ('invalid syntax', ('build/bdist.linux-x86_64/egg/lmfit/asteval.py', 89, 49, '        py_symtable = {sym: __builtins__[sym] for sym in FROM_PY\n'))

byte-compiling build/bdist.linux-x86_64/egg/lmfit/ordereddict.py to ordereddict.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/models.py to models.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/confidence.py to confidence.pyc

byte-compiling build/bdist.linux-x86_64/egg/lmfit/__init__.py to __init__.pyc

creating build/bdist.linux-x86_64/egg/EGG-INFO

copying lmfit.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO

copying lmfit.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying lmfit.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying lmfit.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

copying lmfit.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO

zip_safe flag not set; analyzing archive contents...

creating 'dist/lmfit-0.9.3-py2.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it

removing 'build/bdist.linux-x86_64/egg' (and everything under it)

Processing lmfit-0.9.3-py2.6.egg

removing '/home/zhangli/.local/lib/python2.6/site-packages/lmfit-0.9.3-py2.6.egg' (and everything under it)

creating /home/zhangli/.local/lib/python2.6/site-packages/lmfit-0.9.3-py2.6.egg

Extracting lmfit-0.9.3-py2.6.egg to /home/zhangli/.local/lib/python2.6/site-packages

SyntaxError: ('invalid syntax', ('/home/zhangli/.local/lib/python2.6/site-packages/lmfit-0.9.3-py2.6.egg/lmfit/parameter.py', 101, 29, '                          for key in sym_unique}\n'))

SyntaxError: ('invalid syntax', ('/home/zhangli/.local/lib/python2.6/site-packages/lmfit-0.9.3-py2.6.egg/lmfit/asteval.py', 89, 49, '        py_symtable = {sym: __builtins__[sym] for sym in FROM_PY\n'))

lmfit 0.9.3 is already the active version in easy-install.pth

Installed /home/zhangli/.local/lib/python2.6/site-packages/lmfit-0.9.3-py2.6.egg

Processing dependencies for lmfit==0.9.3

Searching for scipy==0.7.2

Best match: scipy 0.7.2

Adding scipy 0.7.2 to easy-install.pth file

Using /usr/lib64/python2.6/site-packages

Searching for numpy==1.4.1

Best match: numpy 1.4.1

Adding numpy 1.4.1 to easy-install.pth file

Using /usr/lib64/python2.6/site-packages

Finished processing dependencies for lmfit==0.9.3

Li :)

在 2016年6月1日星期三 UTC+8下午7:09:52，Matt Newville写道：

[Matt Newville]

Hi Li,

Oh, but this time you're using Python 2.6, which lmfit 0.9.3 doesn't support.  Your previous output showed Python 2.7, which is supported.

--Matt