Package Details: neuron 7.4-1

Git Clone URL: https://aur.archlinux.org/neuron.git (read-only)
Package Base: neuron
Description: Empirically-based simulations of neurons and networks of neurons
Upstream URL: http://www.neuron.yale.edu
Licenses: GPL
Submitter: None
Maintainer: rouzbeh
Last Packager: rouzbeh
Votes: 7
Popularity: 0.059760
First Submitted: 2010-09-12 23:29
Last Updated: 2015-11-30 20:45

Latest Comments

DGalt commented on 2016-06-10 04:23

getting "Error: A failure occurred in build()". Initially thought it was due to it not being able to find Interviews, so ran makepkg after editing PKGBUILD to include --without-iv, but still fails (although with slightly different message).

Initial attempt: http://pastebin.com/dGEYNDqw
Second attempt: http://pastebin.com/JJ9DdHH6

What's weird is Interviews is installed in /usr (I see the InterViews folder in /usr/include). I just went ahead and installed neuron on my arch install on my laptop and it went fine - not sure why it's not working on my other machine. My other machine is more up-to-date, though - 4.6.2-1 vs 4.4.5-1

Edit: after updating my laptop to 4.6.2-1 and trying to re-install neuron I get the same series of errors that are shown in the "Second attempt" pastebin

rouzbeh commented on 2016-01-05 11:57

That's a tough one. I don't see how it can be due to packaging. I'm looking into it :)

brk0_0 commented on 2016-01-04 22:10

When I open nrngui and click Tools -> Model View, the program crashes. The problem is: the file /usr/lib/python/neuron/hoc.cpython-35m-x86_64-linux-gnu.so should be called simply nuc.so.

Is this an upstream bug?

rouzbeh commented on 2015-11-30 17:58

I am going to push an upadte for neuron 7.4 shortly.

rouzbeh commented on 2015-11-30 17:50

Try commenting out the line

patch -p1 < $srcdir/patch.diff

in the PKGBUILD file.

mark commented on 2015-11-30 17:33

I'm having troubles installing the package with python2 (python3 works just fine). I've replaced "python" with "python2". The error I'm getting is

[code]
nrnpython.cpp:169:32: error: invalid conversion from 'char* (*)(FILE*, FILE*, const char*) {aka char* (*)(_IO_FILE*, _IO_FILE*, const char*)}' to 'char* (*)(FILE*, FILE*, char*) {aka char* (*)(_IO_FILE*, _IO_FILE*, char*)}' [-fpermissive]
PyOS_ReadlineFunctionPointer = nrnpython_getline;
Makefile:562: recipe for target 'nrnpython.lo' failed

I have no idea what I am doing really and I'm quite clueless where to start looking for the problem. I have numpy, scipy (for python2) and mpich2. Any hints much appreciated.

achilleas.k commented on 2014-09-09 14:02

Great. Thanks again rouzbeh.

achilleas.k commented on 2014-09-09 14:01

Most excellent. Thanks again rouzbeth.

rouzbeh commented on 2014-09-09 10:26

Alright folks, some changes:

1. Turns out removing .la files results in nrnivmodl not working anymore. For now we have to keep them.
2. There is now a patch to make neuron compile with Python 3. The new version of the PKGBUILD applies the patch and compiles neuron for the latest version of Python. If you want to have it work with Python 2.x simply replace all instance of "python" with "python2" in the PKGBUILD.

achilleas.k commented on 2014-08-19 03:55

Great! Thanks for getting it to install with python.

rouzbeh commented on 2014-07-24 14:00

New version to correct the md5. While at it, I also had another attempt at getting the python library to install. There is an error compiling for python 3, so for now we have to use python 2. But at least it works.

achilleas.k commented on 2014-07-10 14:56

The md5sum appears to be wrong.

Also, I'd like to be able to install with python support as well as install the python module, so I can "import neuron" in a python session and work from there. I know that in order to do this, one must ./configure with "--with-nrnpython=/path/to/python/binary". If I add it to the PKGBUILD, I get an error during the package() phase "/usr/bin/ld: cannot find -lnrnpython". I assume this has to do with the fakeroot environment but I'm not very familiar with how fakeroots are set up for things like this, so I can't get it to build the package.

Installing the python module is straightforward after that, of course, since it just requires running the setup.py (i.e., the two lines that are commented out). So, is it possible to get this package to install with py support, or should I just build and make from source to get this?

rouzbeh commented on 2014-04-04 14:10

Updated to add options=('libtool'). Thanks achilleas.k

achilleas.k commented on 2014-04-04 01:11

I need to add options=('libtool') otherwise I get errors when compiling with nrnivmodl.

achilleas.k commented on 2014-04-03 19:33

Why is the nrnpython installation disabled in the PKGBUILD?

#cd "src/nrnpython/"
#python2 setup.py install --root="$pkgdir/"

rouzbeh commented on 2013-11-23 10:46

Thanks xgdgsc!

xgdgsc commented on 2013-11-23 07:01

The md5sum of the package has changed.

rouzbeh commented on 2013-05-01 09:49

Thanks belevtsoff1

Anonymous comment on 2013-04-30 10:50

Looks like they have fixed the problem and the patch is not needed anymore. The md5sum of the package has changed and the patch fails to apply now. I have successfully compiled and installed the package by changing md5 and commenting out the patch line in the PKGBUID

Cheers

rouzbeh commented on 2013-01-16 13:41

Thanks alkemir. I haev implemented all your suggested changes. Although I am a bit baffled by the type problem. I will try to figure out what has changed.

Anonymous comment on 2013-01-14 07:22

Final comment:

To install the python bindings, you ened to go into src/nrnpython and run sudo python2 steup.py install.

Best regards

Anonymous comment on 2013-01-14 07:06

Hi again!

There is a typo in the configure option --with-paranrn, there is a n missing:
--with-pararn.

It will not configure correctly with this option unless you have MPI packages installed. I dont know how this should be handled.

Anonymous comment on 2013-01-14 06:24

Currently neuron fails to compile complaining about int32_t and u_int32_t not being defined in /src/gnu/RNG.h .

I added the definitions and it compiled. Can you please look into the issue? I am not familiar enough with software to understand the real nature of the problem and thefore the right way to fix it.


#ifndef int32_t
#if defined(HAVE_SYS_TYPES_H)
#include <sys/types.h>
#endif
#if defined(HAVE_INTTYPES_H)
#include <inttypes.h>
#endif
#endif
#endif

//Here is what I added:
typedef int int32_t;
typedef unsigned int u_int32_t;
typedef int32_t _G_int32_t;
typedef u_int32_t _G_uint32_t;

rouzbeh commented on 2012-05-11 14:29

Adopted and updated. They have updated interviews without changing the version number.

mschu commented on 2011-09-11 09:22

Thanks for your message. Unfortunately, your fix doesn't work for me and I don't have the time to fix it properly.

I'm orphaning the package for now, you're welcome to adopt it.

macin commented on 2011-09-09 18:09

Hi! I get this message, when I attempt to use nrnivmodl:
link: cannot find the library `/usr/lib/libnrniv.la' or unhandled argument `/usr/lib/libnrniv.la'

Actually, without option '!libtool' in the pkgbuild of neuron and interviews, it seems everything works well.