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daler / metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
https://daler.github.io/metaseq
MIT License
87 stars 36 forks source link

install issues #1

Closed brwnj closed 12 years ago

brwnj commented 12 years ago

i was attempting to check this out and think it would be really useful, but i'm having issues installing.

$ git clone git://github.com/daler/metaseq.git
Cloning into 'metaseq'...
remote: Counting objects: 471, done.
remote: Compressing objects: 100% (207/207), done.
remote: Total 471 (delta 257), reused 468 (delta 254)
Receiving objects: 100% (471/471), 2.81 MiB | 1.34 MiB/s, done.
Resolving deltas: 100% (257/257), done.

$ cd metaseq/
total 48
-rw-r--r--   1 brownj  staff   2.1K Nov  5 09:40 README.rst
drwxr-xr-x   4 brownj  staff   136B Nov  5 09:40 doc/
-rw-r--r--   1 brownj  staff    10K Nov  5 09:40 ez_setup.py
drwxr-xr-x  19 brownj  staff   646B Nov  5 09:40 metaseq/
-rw-r--r--   1 brownj  staff    73B Nov  5 09:40 requirements.txt
-rw-r--r--   1 brownj  staff   1.7K Nov  5 09:40 setup.py
brownj at bbp in ~/devel/metaseq on master

$ python setup.py install
running install
running bdist_egg
running egg_info
creating metaseq.egg-info
writing requirements to metaseq.egg-info/requires.txt
writing metaseq.egg-info/PKG-INFO
writing top-level names to metaseq.egg-info/top_level.txt
writing dependency_links to metaseq.egg-info/dependency_links.txt
writing manifest file 'metaseq.egg-info/SOURCES.txt'
reading manifest file 'metaseq.egg-info/SOURCES.txt'
writing manifest file 'metaseq.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.7-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-2.7
creating build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/__init__.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/array_helpers.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/colormap_adjust.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/filetype_adapters.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/genomic_signal.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/helpers.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/minibrowser.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/plotutils.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/rebin_naive.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/results_table.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/stats.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/tables.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
copying metaseq/version.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq
creating build/lib.macosx-10.7-x86_64-2.7/metaseq/test
copying metaseq/test/__init__.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test
copying metaseq/test/test.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test
creating build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/__init__.py -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/construct_example_deseq.R -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/ex.deseq -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/gdc.bam -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/gdc.bam.bai -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/gdc.bed -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/gdc.bigbed -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
copying metaseq/test/data/x.bam -> build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data
running build_ext
cythoning metaseq/rebin.pyx to metaseq/rebin.c
building 'metaseq.rebin' extension
creating build/temp.macosx-10.7-x86_64-2.7
creating build/temp.macosx-10.7-x86_64-2.7/metaseq
/usr/bin/clang -fno-strict-aliasing -Os -w -pipe -march=native -Qunused-arguments -mmacosx-version-min=10.7 -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/lib/python2.7/site-packages/numpy/core/include -I/usr/local/Cellar/python/2.7.3/include/python2.7 -c metaseq/rebin.c -o build/temp.macosx-10.7-x86_64-2.7/metaseq/rebin.o
/usr/bin/clang -bundle -undefined dynamic_lookup -L/usr/local/Cellar/readline/6.2.2/lib -L/usr/local/lib build/temp.macosx-10.7-x86_64-2.7/metaseq/rebin.o -o build/lib.macosx-10.7-x86_64-2.7/metaseq/rebin.so
creating build/bdist.macosx-10.7-x86_64
creating build/bdist.macosx-10.7-x86_64/egg
creating build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/__init__.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/array_helpers.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/colormap_adjust.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/filetype_adapters.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/genomic_signal.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/helpers.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/minibrowser.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/plotutils.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/rebin.so -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/rebin_naive.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/results_table.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/stats.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/tables.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
creating build/bdist.macosx-10.7-x86_64/egg/metaseq/test
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/__init__.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test
creating build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/__init__.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/construct_example_deseq.R -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/ex.deseq -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/gdc.bam -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/gdc.bam.bai -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/gdc.bed -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/gdc.bigbed -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/data/x.bam -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/test/test.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq/test
copying build/lib.macosx-10.7-x86_64-2.7/metaseq/version.py -> build/bdist.macosx-10.7-x86_64/egg/metaseq
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/array_helpers.py to array_helpers.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/colormap_adjust.py to colormap_adjust.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/filetype_adapters.py to filetype_adapters.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/genomic_signal.py to genomic_signal.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/helpers.py to helpers.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/minibrowser.py to minibrowser.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/plotutils.py to plotutils.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/rebin_naive.py to rebin_naive.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/results_table.py to results_table.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/stats.py to stats.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/tables.py to tables.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/test/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/test/data/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/test/test.py to test.pyc
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/version.py to version.pyc
creating stub loader for metaseq/rebin.so
byte-compiling build/bdist.macosx-10.7-x86_64/egg/metaseq/rebin.py to rebin.pyc
creating build/bdist.macosx-10.7-x86_64/egg/EGG-INFO
installing scripts to build/bdist.macosx-10.7-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying and adjusting metaseq/scripts/download_metaseq_example_data.py -> build/scripts-2.7
changing mode of build/scripts-2.7/download_metaseq_example_data.py from 644 to 755
creating build/bdist.macosx-10.7-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/download_metaseq_example_data.py -> build/bdist.macosx-10.7-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.macosx-10.7-x86_64/egg/EGG-INFO/scripts/download_metaseq_example_data.py to 755
copying metaseq.egg-info/PKG-INFO -> build/bdist.macosx-10.7-x86_64/egg/EGG-INFO
copying metaseq.egg-info/SOURCES.txt -> build/bdist.macosx-10.7-x86_64/egg/EGG-INFO
copying metaseq.egg-info/dependency_links.txt -> build/bdist.macosx-10.7-x86_64/egg/EGG-INFO
copying metaseq.egg-info/requires.txt -> build/bdist.macosx-10.7-x86_64/egg/EGG-INFO
copying metaseq.egg-info/top_level.txt -> build/bdist.macosx-10.7-x86_64/egg/EGG-INFO
writing build/bdist.macosx-10.7-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
metaseq.helpers: module references __file__
creating dist
creating 'dist/metaseq-0.1dev-py2.7-macosx-10.7-x86_64.egg' and adding 'build/bdist.macosx-10.7-x86_64/egg' to it
removing 'build/bdist.macosx-10.7-x86_64/egg' (and everything under it)
Processing metaseq-0.1dev-py2.7-macosx-10.7-x86_64.egg
creating /usr/local/lib/python2.7/site-packages/metaseq-0.1dev-py2.7-macosx-10.7-x86_64.egg
Extracting metaseq-0.1dev-py2.7-macosx-10.7-x86_64.egg to /usr/local/lib/python2.7/site-packages
Adding metaseq 0.1dev to easy-install.pth file
Installing download_metaseq_example_data.py script to /usr/local/share/python

Installed /usr/local/lib/python2.7/site-packages/metaseq-0.1dev-py2.7-macosx-10.7-x86_64.egg
Processing dependencies for metaseq==0.1dev
Searching for matplotlib
Reading http://pypi.python.org/simple/matplotlib/
Reading http://matplotlib.sourceforge.net
Reading http://sourceforge.net/project/showfiles.php?group_id=80706&package_id=82474
error: None

Everything seemed to install except for metaseq.integration, except now I receive:

In [1]: import metaseq
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-3365faa9d779> in <module>()
----> 1 import metaseq

/Users/brownj/devel/metaseq/metaseq/__init__.py in <module>()
      4 from helpers import data_dir, example_filename, nice_colormap, \
      5         gfffeature_to_interval
----> 6 from genomic_signal import genomic_signal
      7 import plotutils
      8 import integration

/Users/brownj/devel/metaseq/metaseq/genomic_signal.py in <module>()
     32 from bx.bbi.bigwig_file import BigWigFile
     33 
---> 34 from array_helpers import _array, _array_parallel, _local_coverage, \
     35     _local_coverage_bigwig, _local_count
     36 import filetype_adapters

/Users/brownj/devel/metaseq/metaseq/array_helpers.py in <module>()
      6 import genomic_signal
      7 import sys
----> 8 from rebin import rebin, float_rebin
      9 from helpers import chunker
     10 import filetype_adapters

ImportError: No module named rebin

I can't remember at which step statsmodels was required, but it should probably be added to your required packages list.

daler commented 12 years ago

Hmm, thanks for reporting this.

The errors you pasted seem to be cause by failing to import the rebin module rather than anything having to do with integration. It doesn't look like there was any problems Cython-izing the rebin code in your install log, so it's not clear what's preventing rebin from being imported.

On my machine I use setup.py develop. Can you try that (instead of install) to see if that helps?

(and thanks for the heads-up, I'll add statsmodels to requirements.txt)

brwnj commented 12 years ago

python setup.py develop fixed everything. thanks.

daler commented 12 years ago

OK, good. I'll have to poke around some more to figure out why this is happening.