Building the library fails : ''pandas/index.c: No such file or directory"

[sebpiq]

I just forked and cloned the master branch (last commit from 6th December), and building fails with the following error :

> python setup.py build_ext --inplace
running build_ext
building 'pandas.index' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/home/spiq/pandas/env/local/lib/python2.7/site-packages/numpy/core/include -Ipandas/src/klib -Ipandas/src -I/usr/include/python2.7 -c pandas/index.c -o build/temp.linux-i686-2.7/pandas/index.o
gcc: error: pandas/index.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 4

Any idea ?

[sebpiq]

Commit hash is 67ef67f

[jseabold]

What Cython version are you using?

[sebpiq]

I'm not using Cython

[jseabold]

You have to use Cython to build pandas development version from github.

[jseabold]

http://pandas.pydata.org/pandas-docs/stable/install.html#installing-from-source

[sebpiq]

Ok ... that would be nice to have somehow this info in here : http://pandas.pydata.org/developers.html
But thanks :)

[jseabold]

IMO, it's pretty clear where it is under the installation instructions. Those are just instructions to build the library inplace so you can run the test suite not installation instructions.

[wesm]

The setup.py is supposed to have a better error message-- I did a lot of refactoring of the extensions recently so must have broken that part of the build file somehow.

[sebpiq]

Now I installed all the stuff, followed the instructions, but tests fail.

[changhiskhan]

Which tests are failing?

On Dec 6, 2012, at 11:11 AM, sebpiq [email protected] wrote:

Now I installed all the stuff, followed the instructions, but tests fail.

—
Reply to this email directly or view it on GitHub.

[sebpiq]

Arr ... no no. My bad again. I should think before asking :) Sorry. However, many tests are skipped.

[aflaxman]

it seems that the informative error message has disappeared again, I just landed here googling my build error of:

gcc: pandas/index.c: No such file or directory

and installing cython fixed things

[ghost]

can you try out #2860?

[metakermit]

It still doesn't show any error message about missing cython. Also left me buzzing around the web for some time, searching for the answer. Mentioning it explicitely in these two documents would help:

http://pandas.pydata.org/developers.html#testing
https://github.com/pydata/pandas#installation-from-sources

Also, maybe there's some way to add a dependency on cpython when issuing pip install -e or python setup.py develop.

[ghost]

@Kermit666 , does "it" mean you've tried #2860 and it doesn't fix the problem for you?

[josephdunn]

Could it be a virtualenv screwing things up? I noticed that if I try to install pandas from source, but I have cython installed system-wide, and I'm running from a virtualenv, I get the behavior @Kermit666 mentions. The fix is to create your virtualenv with the --system-site-packages argument.

[ghost]

Tried running in a fresh virtualenv with system-wide cython. With #2860 I get the proper
warning message.

[metakermit]

@y-p I haven't tried that branch, just the master (thought that it was merged by now as a month passed and I didn't notice the "open" note (still adjusting to GitHub)). Anyway, glad to hear it's fixed by now. Hopefully it will get merged soon.

@josephdunn - I didn't have cython installed anywhere. The only problem was that I didn't know it was a dependency since it wasn't mentioned in the guides linked in my last comment.

[jreback]

I believe you link to this page, and its clearly mentioned in order to build dev libraries
http://pandas.pydata.org/pandas-docs/dev/install.html#optional-dependencies

but suppose could be mentioned on developer pages

[ghost]

Merged into master. should be fixed.

[metakermit]

OK, great.

Concerning the docs, I linked to different pages:

http://pandas.pydata.org/developers.html#testing
https://github.com/pydata/pandas#installation-from-sources

They are the first thing I would open when I want to hack on someone's code

• project website - community - developer's page,
• github - README.md.

[metakermit]

This is how I would hint it in the README file:

#3067

[ghost]

@Kermit666, could you verify that the fix in master works for you? there was a report saying
it didn't actually fix the problem.

[metakermit]

Yes, the fix works for me too now:

Exception: Cython-generated file 'pandas/index.c' not found.
                         Cython is required to compile pandas from a development branch.
                         Please install Cython or download a release package of pandas.

On Sun, Mar 17, 2013 at 12:25 AM, y-p [email protected] wrote:

@Kermit666 https://github.com/kermit666, could you verify that the fix
in master works for you? there was a report saying
it didn't actually fix the problem.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/2439#issuecomment-15014115
.

[xchaoinfo]

@metakermit
I try to install pandas using pip in a new virtualenv environment, and encounter with same problem.
I solve the problem by pip install cython in virtualenv.