{compute,correct}GCBias errors

[radaniba]

Hello

I am using the latest version of deepTools and I am running through this error while running the {compute, correct}GCBias pair :

Traceback (most recent call last):
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/bin/computeGCBias", line 10, in <module>
    from scipy.stats import poisson
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/stats/__init__.py", line 321, in <module>
    from .stats import *
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/stats/stats.py", line 180, in <module>
    import scipy.special as special
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/special/__init__.py", line 603, in <module>
    from .basic import *
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/special/basic.py", line 18, in <module>
    from . import orthogonal
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/special/orthogonal.py", line 101, in <module>
    from scipy import linalg
  File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/linalg/__init__.py", line 188, in <module>
    from ._decomp_update import *
  File "scipy/linalg/_decomp_update.pyx", line 1, in init scipy.linalg._decomp_update (scipy/linalg/_decomp_update.c:35875)
ImportError: /genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/linalg/cython_lapack.so: undefined symbol: zlacn2_

Any idea on what can cause this ?

ps : am using scipy 0.16.0

[radaniba]

Ok I downgraded to Scipy 0.12 and it worked

Any dependencies specs somewhere in the doc ?

[fidelram]

Hi,

This is an error from scipy. See this answer: http://stackoverflow.com/questions/32011231/undefined-symbol-in-scipys-lapack-library

-fidel

On Thu, Aug 20, 2015 at 11:04 PM, Radhouane Aniba notifications@github.com wrote:

Hello

I am using the latest version of deepTools and I am running through this error while running the {compute, correct}GCBias pair :

Traceback (most recent call last): File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/bin/computeGCBias", line 10, in from scipy.stats import poisson File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/stats/init.py", line 321, in from .stats import File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/stats/stats.py", line 180, in import scipy.special as special File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/special/init.py", line 603, in from .basic import File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/special/basic.py", line 18, in from . import orthogonal File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/special/orthogonal.py", line 101, in from scipy import linalg File "/genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/linalg/init.py", line 188, in from ._decomp_update import * File "scipy/linalg/_decomp_update.pyx", line 1, in init scipy.linalg._decomp_update (scipy/linalg/_decomp_update.c:35875) ImportError: /genesis/extscratch/shahlab/pipelines/virtual_environments/chip-seq/lib/python2.7/site-packages/scipy/linalg/cythonlapack.so: undefined symbol: zlacn2

Any idea on what can cause this ?

— Reply to this email directly or view it on GitHub https://github.com/fidelram/deepTools/issues/96.

Fidel Ramirez

[fidelram]

Hi,

The error was from scipy, not from deepTools. Something was wrong with your installation.

I have tested deepTools with the latest scipy version 0.15. In the setup.py says that deepTools requires scipy >= 0.10

Fidel Ramírez

On 21 Aug 2015, at 00:27, Radhouane Aniba notifications@github.com wrote:

Ok I downgraded to Scipy 0.12 and it worked

Any dependencies specs somewhere in the doc ?

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

[radaniba]

Hi @fidelram ! Thanks yes I saw this and fixed my isue by downgrading scipy and it worked just fine. Thank you