Installation problem on Ubuntu 16.04, Python 2.7

Mike Angstadt

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Dec 1, 2017, 2:52:32 PM12/1/17

to hddm-users

I'm having trouble getting HDDM to install on my Ubuntu 16.04 machine. The error message I'm receiving boils down to a file not being found:

x86_64-linux-gnu-gcc: error: src/wfpt.c: No such file or directory

x86_64-linux-gnu-gcc: fatal error: no input files

This seems very similar to an error I saw on a post on the list from 5 years ago, when it was indicated it was a packaging error, but I haven't seen any other reports of anything similar since then.

The full text of the install attempt is included below. I'm using pip install HDDM in a virtual environment with Python 2.7.12

Any ideas?

Collecting hddm

Using cached HDDM-0.6.1.tar.gz

Requirement already satisfied: NumPy>=1.6.0 in ./mangstad/lib/python2.7/site-packages (from hddm)

Requirement already satisfied: SciPy>=0.6.0 in ./mangstad/lib/python2.7/site-packages (from hddm)

Requirement already satisfied: kabuki>=0.6.0 in ./mangstad/lib/python2.7/site-packages (from hddm)

Requirement already satisfied: PyMC>=2.3.3 in ./mangstad/lib/python2.7/site-packages (from hddm)

Requirement already satisfied: pandas>=0.12.0 in ./mangstad/lib/python2.7/site-packages (from hddm)

Requirement already satisfied: patsy in ./mangstad/lib/python2.7/site-packages (from hddm)

Requirement already satisfied: matplotlib>=1.0.0 in ./mangstad/lib/python2.7/site-packages (from kabuki>=0.6.0->hddm)

Requirement already satisfied: pytz>=2011k in ./mangstad/lib/python2.7/site-packages (from pandas>=0.12.0->hddm)

Requirement already satisfied: python-dateutil in ./mangstad/lib/python2.7/site-packages (from pandas>=0.12.0->hddm)

Requirement already satisfied: six in ./mangstad/lib/python2.7/site-packages (from patsy->hddm)

Requirement already satisfied: cycler>=0.10 in ./mangstad/lib/python2.7/site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->hddm)

Requirement already satisfied: subprocess32 in ./mangstad/lib/python2.7/site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->hddm)

Requirement already satisfied: backports.functools-lru-cache in ./mangstad/lib/python2.7/site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->hddm)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./mangstad/lib/python2.7/site-packages (from matplotlib>=1.0.0->kabuki>=0.6.0->hddm)

Building wheels for collected packages: hddm

Running setup.py bdist_wheel for hddm ... error

Complete output from command /home/slab/environments/mangstad/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_NPAtO/hddm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/tmpp1VYggpip-wheel- --python-tag cp27:

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-2.7

creating build/lib.linux-x86_64-2.7/hddm

copying hddm/generate.py -> build/lib.linux-x86_64-2.7/hddm

copying hddm/diag.py -> build/lib.linux-x86_64-2.7/hddm

copying hddm/__init__.py -> build/lib.linux-x86_64-2.7/hddm

copying hddm/likelihoods.py -> build/lib.linux-x86_64-2.7/hddm

copying hddm/utils.py -> build/lib.linux-x86_64-2.7/hddm

copying hddm/MPLTraits_qt.py -> build/lib.linux-x86_64-2.7/hddm

copying hddm/MPLTraits.py -> build/lib.linux-x86_64-2.7/hddm

creating build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/test_models.py -> build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/__init__.py -> build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/matlab_values.py -> build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/test_generate.py -> build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/test_likelihoods.py -> build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/benchmark.py -> build/lib.linux-x86_64-2.7/hddm/tests

copying hddm/tests/test_optimization.py -> build/lib.linux-x86_64-2.7/hddm/tests

creating build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/__init__.py -> build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/hddm_transformed.py -> build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/base.py -> build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/hddm_truncated.py -> build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/hddm_stimcoding.py -> build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/hddm_regression.py -> build/lib.linux-x86_64-2.7/hddm/models

copying hddm/models/hddm_info.py -> build/lib.linux-x86_64-2.7/hddm/models

creating build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/__init__.py -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/plot_posterior_quantiles.py -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/simple_model.py -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/postpred.py -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/cavanagh_theta_nn.csv -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/simple_subjs_difficulty.csv -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/simple_difficulty.csv -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/simple_subjs_difficulty_single.csv -> build/lib.linux-x86_64-2.7/hddm/examples

copying hddm/examples/simple_difficulty.conf -> build/lib.linux-x86_64-2.7/hddm/examples

running build_ext

building 'wfpt' extension

creating build/temp.linux-x86_64-2.7

creating build/temp.linux-x86_64-2.7/src

x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -I/home/slab/environments/mangstad/local/lib/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c src/wfpt.c -o build/temp.linux-x86_64-2.7/src/wfpt.o

x86_64-linux-gnu-gcc: error: src/wfpt.c: No such file or directory

x86_64-linux-gnu-gcc: fatal error: no input files

compilation terminated.

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

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

Failed building wheel for hddm

Running setup.py clean for hddm

Failed to build hddm

Installing collected packages: hddm

Running setup.py install for hddm ... error

Complete output from command /home/slab/environments/mangstad/bin/python2.7 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-_NPAtO/hddm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-LdK_M0-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/slab/environments/mangstad/include/site/python2.7/hddm:

running install