search

pymc-devs / pymc2

THIS IS THE **OLD** PYMC PROJECT (VERSION 2). PLEASE USE PYMC INSTEAD:
http://pymc-devs.github.com/pymc/
Other
879 stars 229 forks source link

Same EOF errors using pip, easy_install, and source installation #151

Closed reventropy closed 7 years ago

reventropy commented 7 years ago

Line #159 in pymc/gibbsit.f:" parameter (maxseries=20)" get_parameters: got "unexpected EOF while parsing (, line 0)" on '' Line #162 in pymc/gibbsit.f:" parameter (maxqcnt=20)" get_parameters: got "unexpected EOF while parsing (, line 0)" on '' Line #162 in pymc/gibbsit.f:" parameter (maxqcnt=20)" get_parameters: got "unexpected EOF while parsing (, line 0)" on '' Line #196 in pymc/gibbsit.f:" parameter (wasize=maxiterates2)" get_parameters: got "unexpected EOF while parsing (, line 0)" on '' Line #196 in pymc/gibbsit.f:" parameter (wasize=maxiterates2)" get_parameters: got "unexpected EOF while parsing (, line 0)" on '' Line #196 in pymc/gibbsit.f:" parameter (wasize=maxiterates*2)" get_parameters: got "unexpected EOF while parsing (, line 0)" on ''

reventropy commented 7 years ago

Other details:

DISTRIB_ID=LinuxMint DISTRIB_RELEASE=18 DISTRIB_CODENAME=sarah DISTRIB_DESCRIPTION="Linux Mint 18 Sarah" NAME="Ubuntu" VERSION="16.04 LTS (Xenial Xerus)" ID=ubuntu ID_LIKE=debian

Python 2.7.12 I've checked that all dependencies are satisfied.

fonnesbeck commented 7 years ago

Not sure about this. Which Fortran compiler are you using? Does this occur on Python3?

reventropy commented 7 years ago

Thanks for the response. I'm using gfortran 5.4.0. I've successfully installed Pymc 3, but the module I'm interested in using depends on Pymc 2.

reventropy commented 7 years ago

I don't currently have python 3 installed, but it's worth a shot.

fonnesbeck commented 7 years ago

Is it possible for you also to try gcc/gfortran 6.2+?

reventropy commented 7 years ago

I'll try that next. I just tried a pip install on Python 3 and got the same EOF errors in addition to this:

/usr/local/lib/python3.5/dist-packages/numpy/distutils/system_info.py:572: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  self.calc_info()
IOError: [Errno 2] No such file or directory: 'skip:ppnd7'. Skipping file "skip:ppnd7".
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(na)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension(nx)' to 'dimension(nb)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (nmu)' to 'dimension(nmu)'. Ignoring.
updatevars:gradlike: attempt to change 'dimension (na)' to 'dimension(na)'. Ignoring.
rmbadname1: Replacing "index" with "index_bn".
reventropy commented 7 years ago

Upgraded gcc to 6.2. Same issue.. I was able to install it without issue on a machine running CentOS6. Was hoping to install it on my laptop but I'll move on for now..

fonnesbeck commented 7 years ago

OK, sorry about that. I will leave the issue open.

I encourage you to look at PyMC3, unless you have a good reason to stay with PyMC 2.x. There are some much more efficient samplers in the newer package.

vanzod commented 7 years ago

This is the same I reported with issue #150. I will close that one and keep the discussion here.

dataoverflow commented 7 years ago

Same problem here with Ubuntu 16.04.2/Python3.5. Creating a separate virtual env where I first installed older numpy followed by pymc somewhat solves the problem:

pip install numpy==1.10.1
pip install pymc

The latest numpy breaks compatibility?

fonnesbeck commented 7 years ago

It looks like the current master of Numpy fixes this. I was able to replicate this issue in 1.12 (the current conda version), but updating to master via pip allows PyMC to be installed. Please confirm:

pip install -U git+https://github.com/numpy/numpy.git
dataoverflow commented 7 years ago

Thanks Chris, I can confirm that installing numpy from master branch solves the problem.

fonnesbeck commented 7 years ago

Thank you for confirming.