Bray-Curtis computation gives VisibleDeprecationWarning

[gregcaporaso]

This shouldn't be affecting results, just noting here so we can track it. Tagging for 1.9.1 in case it's an easy fix.

$ beta_diversity.py -i otu_table.biom -m bray_curtis -o o
/Users/caporaso/.virtualenvs/qiime/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2499: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  VisibleDeprecationWarning)

$ beta_diversity.py -i otu_table.biom -m unweighted_unifrac -t rep_set.tre -o o
# no deprecation warning from UniFrac

$ print_qiime_config.py

System information
==================
         Platform:  darwin
   Python version:  2.7.5 (default, Mar  9 2014, 22:15:05)  [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)]
Python executable:  /Users/caporaso/.virtualenvs/qiime/bin/python

QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:
 https://github.com/biocore/qiime-default-reference/releases/tag/0.1.2

Dependency versions
===================
          QIIME library version:    1.9.0-dev, master@52866ea
           QIIME script version:    1.9.0-dev
qiime-default-reference version:    0.1.2
                  NumPy version:    1.9.1
                  SciPy version:    0.15.1
                 pandas version:    0.15.2
             matplotlib version:    1.4.2
            biom-format version:    2.1.3
                   h5py version:    2.4.0 (HDF5 version: 1.8.13)
                   qcli version:    0.1.1
                   pyqi version:    0.3.2
             scikit-bio version:    0.2.2
                 PyNAST version:    1.2.2
                Emperor version:    0.9.5
                burrito version:    0.9.0
       burrito-fillings version:    Installed.
              sortmerna version:    /bin/sh: /Users/caporaso/.virtualenvs/qiime/bin/sortmerna: Malformed Mach-o file
              sumaclust version:    Not installed.
                  swarm version:    Installed, but can't identify version.
                          gdata:    Installed.

[jairideout]

This isn't an easy fix because PyCogent will need to be updated. Alternatively, we could catch and silence these warnings, though that seems dangerous.

[gregcaporaso]

Agree. Is this coming directly from PyCogent's Bray-Curtis implementation? If so, maybe we could just call SciPy's Bray-Curtis instead?

[jairideout]

Yes, this is coming from PyCogent's beta diversity implementations. Most of the beta diversity implementations have this issue, so it isn't just limited to Bray-Curtis.

[gregcaporaso]

Ok, probably not worth dealing with now then.

On Wed, Apr 22, 2015 at 9:18 AM, Jai Ram Rideout notifications@github.com wrote:

Yes, this is coming from PyCogent's beta diversity implementations. Most of the beta diversity implementations have this issue, so it isn't just limited to Bray-Curtis.

Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/1983#issuecomment-95253683.