Installing biom-format

[Elisa]

Hi everyone,

I tried to install the biom-format (http://biom-format.org/) but I got this error:

biol100070:~ rodrigues$ pip install biom-format
Downloading/unpacking biom-format
  Downloading biom-format-1.3.1.tar.gz (279kB): 279kB downloaded
  Running setup.py (path:/private/var/folders/jl/jlwF1wHyFFWU1b2h+SUSYE+++TM/-Tmp-/pip_build_rodrigues/biom-format/setup.py) egg_info for package biom-format
Downloading/unpacking numpy>=1.3.0 (from biom-format)
  Downloading numpy-1.8.1.tar.gz (3.8MB): 3.8MB downloaded
  Running setup.py (path:/private/var/folders/jl/jlwF1wHyFFWU1b2h+SUSYE+++TM/-Tmp-/pip_build_rodrigues/numpy/setup.py) egg_info for package numpy
    Running from numpy source directory.
    warning: no files found matching 'tools/py3tool.py'
    warning: no files found matching '*' under directory 'doc/f2py'
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
Downloading/unpacking pyqi==0.3.1 (from biom-format)
  Downloading pyqi-0.3.1.tar.gz (236kB): 236kB downloaded
  Running setup.py (path:/private/var/folders/jl/jlwF1wHyFFWU1b2h+SUSYE+++TM/-Tmp-/pip_build_rodrigues/pyqi/setup.py) egg_info for package pyqi
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/private/var/folders/jl/jlwF1wHyFFWU1b2h+SUSYE+++TM/-Tmp-/pip_build_rodrigues/pyqi/setup.py", line 52, in <module>
        ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))
    AttributeError: 'tuple' object has no attribute 'major'
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/private/var/folders/jl/jlwF1wHyFFWU1b2h+SUSYE+++TM/-Tmp-/pip_build_rodrigues/pyqi/setup.py", line 52, in <module>

    ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))

AttributeError: 'tuple' object has no attribute 'major'

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /private/var/folders/jl/jlwF1wHyFFWU1b2h+SUSYE+++TM/-Tmp-/pip_build_rodrigues/pyqi
Storing debug log for failure in /Users/rodrigues/Library/Logs/pip.log
biol100070:~ rodrigues$ which biom
biol100070:~ rodrigues$

Could anyone help me with this??

Thank you,

Elisa.

[Jai Ram Rideout]

Hi Elisa,

Please see this thread:

https://groups.google.com/d/topic/qiime-forum/Yw90DwYIGOg/discussion

-Jai

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[Elisa Matos]

Hi Jai,

Thank you for your quick answer. 

The version of my Python is 2.7. I guess the problem is in numpy.

I got this error again:

biol100070:Desktop rodrigues$ python -c "from biom import __version__; print __version__"

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/biom_format-1.3.1_dev-py2.7.egg/biom/__init__.py", line 26, in <module>

    from biom.util import load_biom_config

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/biom_format-1.3.1_dev-py2.7.egg/biom/util.py", line 18, in <module>

    from numpy import mean, median, min, max

ImportError: No module named numpy

What do you think?

Thank you,

Elisa.

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Elisa Matos
Bióloga - Universidade Federal de Lavras
Mestranda Microbiologia Agrícola - Universidade de São Paulo (USP)/ESALQ
019 34172160

[Jai Ram Rideout]

Hi Elisa,

numpy is a required dependency for the biom-format package. You can install it with:

pip install numpy

-Jai

[Elisa]

Hi Jai,

I already did what you said.

I got this error:

biol100070:~ rodrigues$ pip install numpy

Requirement already satisfied (use --upgrade to upgrade): numpy in /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python

Cleaning up...

biol100070:~ rodrigues$ sudo pip install biom-format

Password:

Downloading/unpacking biom-format

  Downloading biom-format-1.3.1.tar.gz (279kB): 279kB downloaded

  Running setup.py (path:/private/tmp/pip_build_root/biom-format/setup.py) egg_info for package biom-format

Downloading/unpacking numpy>=1.3.0 (from biom-format)

  Downloading numpy-1.8.1.tar.gz (3.8MB): 3.8MB downloaded

  Running setup.py (path:/private/tmp/pip_build_root/numpy/setup.py) egg_info for package numpy

    Running from numpy source directory.

    warning: no files found matching 'tools/py3tool.py'

    warning: no files found matching '*' under directory 'doc/f2py'

    warning: no previously-included files matching '*.pyc' found anywhere in distribution

    warning: no previously-included files matching '*.pyo' found anywhere in distribution

    warning: no previously-included files matching '*.pyd' found anywhere in distribution

Downloading/unpacking pyqi==0.3.1 (from biom-format)

  Downloading pyqi-0.3.1.tar.gz (236kB): 236kB downloaded

  Running setup.py (path:/private/tmp/pip_build_root/pyqi/setup.py) egg_info for package pyqi

    Traceback (most recent call last):

      File "<string>", line 17, in <module>

      File "/private/tmp/pip_build_root/pyqi/setup.py", line 52, in <module>

        ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))

    AttributeError: 'tuple' object has no attribute 'major'

    Complete output from command python setup.py egg_info:

    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/private/tmp/pip_build_root/pyqi/setup.py", line 52, in <module>

    ver = '.'.join(map(str, [sys.version_info.major, sys.version_info.minor]))

AttributeError: 'tuple' object has no attribute 'major'

----------------------------------------

Cleaning up...

Command python setup.py egg_info failed with error code 1 in /private/tmp/pip_build_root/pyqi

Storing debug log for failure in /Users/rodrigues/Library/Logs/pip.log

biol100070:~ rodrigues$ 

I have no idea what I can do more..

Thanks,

Elisa

[Jai Ram Rideout]

Hi Elisa,

Please send me the output of:

pip --version

sudo pip --version

Thanks,

Jai

[Elisa Matos]

Hi Jai,

See the outputs below:

biol100070:~ rodrigues$ pip --version

pip 1.5.4 from /Library/Python/2.6/site-packages/pip-1.5.4-py2.6.egg (python 2.6)

biol100070:~ rodrigues$ sudo pip --version

Password:

pip 1.5.4 from /Library/Python/2.6/site-packages/pip-1.5.4-py2.6.egg (python 2.6)

Thank you,

Elisa.

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[Jai Ram Rideout]

Hi Elisa,

Sorry for the slow reply. From the output you sent, it looks like you have Python 2.6 installed, which is why you're getting an error when installing biom-format. You'll need to upgrade to Python 2.7 in order to install this package.

-Jai

[Elisa Matos]

Hi Jai,

I'm sorry! I sent a wrong output because I had been done this test before.

The right output is:

MacQIIME biol100070:~ $ pip --version

pip 1.5.4 from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg (python 2.7)

MacQIIME biol100070:~ $ sudo pip --version

Password:

pip 1.5.4 from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg (python 2.7)

I tried again to install biom-format using pip and I got this error:


Cleaning up...

Command /Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-ljWpah-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/scipy

Storing debug log for failure in /Users/rodrigues/.pip/pip.log

I am using a computer that I installed biom-format properly. I am getting this error in an other computer that I really need to use and I have no idea how to fix this. 


Thank you,


Elisa.


 

 

---

Date: Mon, 28 Apr 2014 10:48:26 -0400
Subject: Re: [qiime-forum 1.8.0] Installing biom-format
From: jai.r...@gmail.com
To: qiime...@googlegroups.com

[Jai Ram Rideout]

Hi Elisa,

It looks like you're using MacQIIME, so you shouldn't need to install biom-format yourself (it comes installed with MacQIIME). Is there a reason that you're not able to use the biom-format version that's installed via MacQIIME?

-Jai