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maxharlow / csvmatch

🔎 Finds fuzzy matches between CSV files
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CSVmatch great but install problem in Ubuntu Linux #16

Closed sfd99 closed 6 years ago

sfd99 commented 6 years ago

Hi Max, I think that csvmatch is clever and great!

But when trying to install with: pip install csvmatch
in my PC with Ubuntu Linux 14.04 LTS 32-bit, (it includes:. Python 2.7.6 [GCC 4.8.4] on linux2) I get the errors below.

I'm not familiar w/Python - I'm an R person... and don't understand what these error messages mean.

What can I do to complete the csvmatch install on my PC?.

Love to try it out,,,help, Max! SFd99 San Francisco INSTALL MESSAGES:

~$ pip install csvmatch
Downloading/unpacking csvmatch
  Downloading csvmatch-1.13-py2.py3-none-any.whl
Downloading/unpacking doublemetaphone==0.1 (from csvmatch)
  Downloading DoubleMetaphone-0.1.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/doublemetaphone/setup.py) egg_info for package doublemetaphone

Downloading/unpacking colorama==0.3.9 (from csvmatch)
  Downloading colorama-0.3.9-py2.py3-none-any.whl
Downloading/unpacking chardet==3.0.4 (from csvmatch)
  Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB): 133kB downloaded
Downloading/unpacking jellyfish==0.5.6 (from csvmatch)
  Downloading jellyfish-0.5.6.tar.gz (132kB): 132kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/jellyfish/setup.py) egg_info for package jellyfish

    warning: no previously-included files matching '.git' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): unidecode==0.4.21 in /usr/local/lib/python2.7/dist-packages (from csvmatch)
Downloading/unpacking dedupe==1.8.1 (from csvmatch)
  Downloading dedupe-1.8.1.tar.gz (54kB): 54kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/dedupe/setup.py) egg_info for package dedupe

Downloading/unpacking fastcluster (from dedupe==1.8.1->csvmatch)
  Downloading fastcluster-1.1.24.tar.gz (166kB): 166kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/fastcluster/setup.py) egg_info for package fastcluster
    Version: 1.1.24

Downloading/unpacking dedupe-hcluster (from dedupe==1.8.1->csvmatch)
  Downloading dedupe-hcluster-0.3.2.tar.gz (166kB): 166kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/dedupe-hcluster/setup.py) egg_info for package dedupe-hcluster

Downloading/unpacking affinegap>=1.3 (from dedupe==1.8.1->csvmatch)
  Downloading affinegap-1.10.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/affinegap/setup.py) egg_info for package affinegap

Downloading/unpacking categorical-distance>=1.9 (from dedupe==1.8.1->csvmatch)
  Downloading categorical_distance-1.9-py2-none-any.whl
Downloading/unpacking dedupe-variable-datetime (from dedupe==1.8.1->csvmatch)
  Downloading dedupe_variable_datetime-0.1.5-py2-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): future>=0.14 in /usr/local/lib/python2.7/dist-packages (from dedupe==1.8.1->csvmatch)
Downloading/unpacking rlr>=2.4.3 (from dedupe==1.8.1->csvmatch)
  Downloading rlr-2.4.3-py2.py3-none-any.whl
Downloading/unpacking numpy>=1.12 (from dedupe==1.8.1->csvmatch)
  Downloading numpy-1.14.1.zip (4.9MB): 4.9MB downloaded
  Running setup.py (path:/tmp/pip_build_ray/numpy/setup.py) egg_info for package numpy
    Running from numpy source directory.
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)

    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
    warning: no previously-included files matching '*.swp' found anywhere in distribution
    warning: no previously-included files matching '*.bak' found anywhere in distribution
    warning: no previously-included files matching '*~' found anywhere in distribution
Downloading/unpacking highered>=0.2.0 (from dedupe==1.8.1->csvmatch)
  Downloading highered-0.2.1-py2.py3-none-any.whl
Downloading/unpacking simplecosine>=1.2 (from dedupe==1.8.1->csvmatch)
  Downloading simplecosine-1.2-py2.py3-none-any.whl
Downloading/unpacking haversine>=0.4.1 (from dedupe==1.8.1->csvmatch)
  Downloading haversine-0.4.5.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/haversine/setup.py) egg_info for package haversine

Downloading/unpacking BTrees>=4.1.4 (from dedupe==1.8.1->csvmatch)
  Downloading BTrees-4.4.1.tar.gz (166kB): 166kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/BTrees/setup.py) egg_info for package BTrees
    warning: no previously-included files matching '*.dll' found anywhere in distribution
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.so' found anywhere in distribution
    warning: no previously-included files matching 'coverage.xml' found anywhere in distribution
    no previously-included directories found matching 'docs/_build'
    no previously-included directories found matching 'persistent/__pycache__'
    In file included from persistent/cPersistence.h:18:0,
                     from persistent/cPersistence.c:19:
    persistent/_compat.h:18:20: fatal error: Python.h: No such file or directory
     #include "Python.h"
                        ^
    compilation terminated.
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/tmp/pip_build_ray/BTrees/setup.py", line 158, in <module>
        """
      File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
        _setup_distribution = dist = klass(attrs)
      File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 239, in __init__
        self.fetch_build_eggs(attrs.pop('setup_requires'))
      File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 264, in fetch_build_eggs
        replace_conflicting=True
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 620, in resolve
        dist = best[req.key] = env.best_match(req, ws, installer)
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 858, in best_match
        return self.obtain(req, installer) # try and download/install
      File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 870, in obtain
        return installer(requirement)
      File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 314, in fetch_build_egg
        return cmd.easy_install(req)
      File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 616, in easy_install
        return self.install_item(spec, dist.location, tmpdir, deps)
      File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 646, in install_item
        dists = self.install_eggs(spec, download, tmpdir)
      File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 834, in install_eggs
        return self.build_and_install(setup_script, setup_base)
      File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1040, in build_and_install
        self.run_setup(setup_script, setup_base, args)
      File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1028, in run_setup
        raise DistutilsError("Setup script exited with %s" % (v.args[0],))
    distutils.errors.DistutilsError: Setup script exited with error: command 'i686-linux-gnu-gcc' failed with exit status 1
    Complete output from command python setup.py egg_info:
    warning: no previously-included files matching '*.dll' found anywhere in distribution

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

warning: no previously-included files matching '*.pyo' found anywhere in distribution

warning: no previously-included files matching '*.so' found anywhere in distribution

warning: no previously-included files matching 'coverage.xml' found anywhere in distribution

no previously-included directories found matching 'docs/_build'

no previously-included directories found matching 'persistent/__pycache__'

In file included from persistent/cPersistence.h:18:0,

                 from persistent/cPersistence.c:19:

persistent/_compat.h:18:20: fatal error: Python.h: No such file or directory

 #include "Python.h"

                    ^

compilation terminated.

Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/tmp/pip_build_ray/BTrees/setup.py", line 158, in <module>

    """

  File "/usr/lib/python2.7/distutils/core.py", line 111, in setup

    _setup_distribution = dist = klass(attrs)

  File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 239, in __init__

    self.fetch_build_eggs(attrs.pop('setup_requires'))

  File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 264, in fetch_build_eggs

    replace_conflicting=True

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 620, in resolve

    dist = best[req.key] = env.best_match(req, ws, installer)

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 858, in best_match

    return self.obtain(req, installer) # try and download/install

  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 870, in obtain

    return installer(requirement)

  File "/usr/lib/python2.7/dist-packages/setuptools/dist.py", line 314, in fetch_build_egg

    return cmd.easy_install(req)

  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 616, in easy_install

    return self.install_item(spec, dist.location, tmpdir, deps)

  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 646, in install_item

    dists = self.install_eggs(spec, download, tmpdir)

  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 834, in install_eggs

    return self.build_and_install(setup_script, setup_base)

  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1040, in build_and_install

    self.run_setup(setup_script, setup_base, args)

  File "/usr/lib/python2.7/dist-packages/setuptools/command/easy_install.py", line 1028, in run_setup

    raise DistutilsError("Setup script exited with %s" % (v.args[0],))

distutils.errors.DistutilsError: Setup script exited with error: command 'i686-linux-gnu-gcc' failed with exit status 1

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_ray/BTrees
Storing debug log for failure in /home/ray/.pip/pip.log
maxharlow commented 6 years ago

I think this might be because Python needs some extra stuff installed to compile the libraries being used by CSV Match. Could you try running:

sudo apt-get install python-dev

Then try installing csvmatch again. Let me know if it works.

sfd99 commented 6 years ago

Hi Max! Thanks for replying. PC with Ubuntu Linux 14.04 LTS 32-bit, (it includes: Python 2.7.6 [GCC 4.8.4]).

As suggested, I did: sudo apt-get install python-dev That seemed to work fine.

Then, repeated the pip install step: pip install csvmatch

Got this response: $ sudo apt-get install python-dev

[sudo] password: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  libpython-dev libpython2.7-dev python2.7-dev
The following NEW packages will be installed:
  libpython-dev libpython2.7-dev python-dev python2.7-dev
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.1 MB of archives.
After this operation, 31.1 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
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============== Below, TRY PIP install csvmatch again =============== ~$ pip install csvmatch

Downloading/unpacking csvmatch
  Downloading csvmatch-1.13-py2.py3-none-any.whl
Downloading/unpacking doublemetaphone==0.1 (from csvmatch)
  Downloading DoubleMetaphone-0.1.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/doublemetaphone/setup.py) egg_info for package doublemetaphone

Downloading/unpacking colorama==0.3.9 (from csvmatch)
  Downloading colorama-0.3.9-py2.py3-none-any.whl
Downloading/unpacking chardet==3.0.4 (from csvmatch)
  Downloading chardet-3.0.4-py2.py3-none-any.whl (133kB): 133kB downloaded
Downloading/unpacking jellyfish==0.5.6 (from csvmatch)
  Downloading jellyfish-0.5.6.tar.gz (132kB): 132kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/jellyfish/setup.py) egg_info for package jellyfish

    warning: no previously-included files matching '.git' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): unidecode==0.4.21 in /usr/local/lib/python2.7/dist-packages (from csvmatch)
Downloading/unpacking dedupe==1.8.1 (from csvmatch)
  Downloading dedupe-1.8.1.tar.gz (54kB): 54kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/dedupe/setup.py) egg_info for package dedupe

Downloading/unpacking fastcluster (from dedupe==1.8.1->csvmatch)
  Downloading fastcluster-1.1.24.tar.gz (166kB): 166kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/fastcluster/setup.py) egg_info for package fastcluster
    Version: 1.1.24

Downloading/unpacking dedupe-hcluster (from dedupe==1.8.1->csvmatch)
  Downloading dedupe-hcluster-0.3.2.tar.gz (166kB): 166kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/dedupe-hcluster/setup.py) egg_info for package dedupe-hcluster

Downloading/unpacking affinegap>=1.3 (from dedupe==1.8.1->csvmatch)
  Downloading affinegap-1.10.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/affinegap/setup.py) egg_info for package affinegap

Downloading/unpacking categorical-distance>=1.9 (from dedupe==1.8.1->csvmatch)
  Downloading categorical_distance-1.9-py2-none-any.whl
Downloading/unpacking dedupe-variable-datetime (from dedupe==1.8.1->csvmatch)
  Downloading dedupe_variable_datetime-0.1.5-py2-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): future>=0.14 in /usr/local/lib/python2.7/dist-packages (from dedupe==1.8.1->csvmatch)
Downloading/unpacking rlr>=2.4.3 (from dedupe==1.8.1->csvmatch)
  Downloading rlr-2.4.3-py2.py3-none-any.whl
Downloading/unpacking numpy>=1.12 (from dedupe==1.8.1->csvmatch)
  Downloading numpy-1.14.2.zip (4.9MB): 4.9MB downloaded
  Running setup.py (path:/tmp/pip_build_ray/numpy/setup.py) egg_info for package numpy
    Running from numpy source directory.
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)

    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
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  Downloading highered-0.2.1-py2.py3-none-any.whl
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  Downloading haversine-0.4.5.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/haversine/setup.py) egg_info for package haversine

Downloading/unpacking BTrees>=4.1.4 (from dedupe==1.8.1->csvmatch)
  Downloading BTrees-4.4.1.tar.gz (166kB): 166kB downloaded
  Running setup.py (path:/tmp/pip_build_ray/BTrees/setup.py) egg_info for package BTrees
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    Installed /tmp/pip_build_ray/BTrees/persistent-4.2.4.2-py2.7-linux-i686.egg

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Requirement already satisfied (use --upgrade to upgrade): simplejson in /usr/lib/python2.7/dist-packages (from dedupe==1.8.1->csvmatch)
Downloading/unpacking zope.index (from dedupe==1.8.1->csvmatch)
  Downloading zope.index-4.3.0.tar.gz (71kB): 71kB downloaded
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  Downloading Levenshtein_search-1.4.4.tar.gz
  Running setup.py (path:/tmp/pip_build_ray/Levenshtein-search/setup.py) egg_info for package Levenshtein-search

Downloading/unpacking datetime-distance (from dedupe-variable-datetime->dedupe==1.8.1->csvmatch)
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  Running setup.py (path:/tmp/pip_build_ray/pylbfgs/setup.py) egg_info for package pylbfgs

Downloading/unpacking pyhacrf-datamade>=0.2.0 (from highered>=0.2.0->dedupe==1.8.1->csvmatch)
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  Running setup.py (path:/tmp/pip_build_ray/pyhacrf-datamade/setup.py) egg_info for package pyhacrf-datamade
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'maintiner_email'
      warnings.warn(msg)

Downloading/unpacking persistent (from BTrees>=4.1.4->dedupe==1.8.1->csvmatch)
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Requirement already satisfied (use --upgrade to upgrade): zope.interface in /usr/lib/python2.7/dist-packages (from BTrees>=4.1.4->dedupe==1.8.1->csvmatch)
Requirement already satisfied (use --upgrade to upgrade): setuptools in /usr/lib/python2.7/dist-packages (from zope.index->dedupe==1.8.1->csvmatch)
Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/lib/python2.7/dist-packages (from zope.index->dedupe==1.8.1->csvmatch)
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Installing collected packages: csvmatch, doublemetaphone, colorama, chardet, jellyfish, dedupe, fastcluster, dedupe-hcluster, affinegap, categorical-distance, dedupe-variable-datetime, rlr, numpy, highered, simplecosine, haversine, BTrees, zope.index, Levenshtein-search, datetime-distance, pylbfgs, pyhacrf-datamade, persistent, python-dateutil
Compiling /tmp/pip_build_ray/csvmatch/csvmatch-titles.txt.py ...
  File "/tmp/pip_build_ray/csvmatch/csvmatch-titles.txt.py", line 1
    Mr.?
       ^
SyntaxError: invalid syntax

Cleaning up...
Exception:
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/pip/basecommand.py", line 122, in main
    status = self.run(options, args)
  File "/usr/lib/python2.7/dist-packages/pip/commands/install.py", line 283, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 1436, in install
    requirement.install(install_options, global_options, *args, **kwargs)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 672, in install
    self.move_wheel_files(self.source_dir, root=root)
  File "/usr/lib/python2.7/dist-packages/pip/req.py", line 902, in move_wheel_files
    pycompile=self.pycompile,
  File "/usr/lib/python2.7/dist-packages/pip/wheel.py", line 206, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/lib/python2.7/dist-packages/pip/wheel.py", line 193, in clobber
    os.makedirs(destsubdir)
  File "/usr/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/dist-packages/csvmatch-1.13.dist-info'

Storing debug log for failure in /home/ray/.pip/pip.log

==== END OF FAILED INSTALL OUTPUT ====

maxharlow commented 6 years ago

Could you try:

pip install --user csvmatch

And if that doesn't work:

sudo pip install csvmatch
sfd99 commented 6 years ago

ok Max - almost there!! :-) did:
pip install --user csvmatch

After 5 minutes of a lot of compilations, END RESULT:

Successfully installed csvmatch doublemetaphone colorama chardet jellyfish dedupe fastcluster dedupe-hcluster affinegap categorical-distance dedupe-variable-datetime rlr numpy highered simplecosine haversine BTrees zope.index Levenshtein-search datetime-distance pylbfgs pyhacrf-datamade persistent python-dateutil Cleaning up...

AND THEN... $ csvmatch data1.csv data2.csv
--fields1 name
--fields2 'Person Name'

OR: ~$ csvmatch

OR EVEN: $ csvmatch data1.csv data2.csv --fields1 name --fields2 'Person Name'

RESULT is always: csvmatch: command not found

I wonder if I should 1st switch (ie: cd <folder)>), before running the csvmatch command in the Linux Terminal?. But which Linux folder
should I "cd" to?. (csvmatch seems to have installed ok...)

Max, thanks f/your patience and determination to help a Linux + R-citizen! :-)

maxharlow commented 6 years ago

Ok, this is progress. What we've done there is just install it for your user account only, so there are no problems with permissions. However, your computer isn't set up to look for programs only installed in that way. Running this should hopefully fix that:

echo "PATH=\$PATH:/usr/local/bin" >> ~/.bashrc
sfd99 commented 6 years ago

Max. did that and got:

~$ echo "PATH=\$PATH:/usr/local/bin" >> ~/.bashrc
~$ csvmatch
csvmatch: command not found

and also did:

~$ csvmatch.py
csvmatch.py: command not found

Just wanted to see if the call would at least "recognize" csvmatch somewhere in the "PATH"...

btw: looked in the Linux folder: /usr/local/bin but there is no csvmatch file there...

Maybe, the csvmatch file is hiding in another folder?. Mystery!

maxharlow commented 6 years ago

I see you've closed the issue -- did you manage to get it working? If not closing and reopening your terminal might do it.

sfd99 commented 6 years ago

Hi Max, No, I didn't close the issue. (I thought you had closed it...).

Anyhow, no - I could not get csvmatch to work in my Linux PC.

Again Max, thank you so much for your patience and endurance with this R-guy. :-)

We really tried... csvmatch is (obviously) an easy & useful prog, but now I'm trying to find a poor-man's (ie: non-Python) substitute... (maybe an R package? or a similar Linux app?).

Very best to you, Max!.

maxharlow commented 6 years ago

Oh, sorry to hear that. Happy to keep trying if you have a current error message or anything? Apologies it has not been more straightforward!