jeremymanning
commented
6 years ago Thanks for your report-- we'll check this out and fix!
Closed galenwilkerson closed 5 years ago
jeremymanning
commented
6 years ago Thanks for your report-- we'll check this out and fix!
andrewheusser
commented
6 years ago hmmm, this is an odd bug since one of our automated tests is miniconda/python3.6... @lmcinnes, have you come across any issues like this?
andrewheusser
commented
6 years ago @galenwilkerson - could you try: apt-get install python3-dev and let us know if that fixes it?
galenwilkerson
commented
6 years ago Hi, will this break my python 3.6 conda environment? Thanks
andrewheusser
commented
6 years ago I dont think so, but to be sure you could set up a test env e.g. conda create -n myenv python=3.6
galenwilkerson
commented
6 years ago OK, i've created a test environment:
conda create -n testenv python=3.6$ source activate testenvpip install hypertools... installed correctly until this:
Collecting tables (from deepdish->hypertools)
Using cached https://files.pythonhosted.org/packages/98/bb/0192955689d2e5972e2714300433eff57e5bef4147248cb15c7b6f04ae9e/tables-3.4.3.tar.gz
Complete output from command python setup.py egg_info:
/tmp/H5closezhuqzz80.c:1:1: warning: return type defaults to ‘int’ [-Wimplicit-int]
main (int argc, char **argv) {
^
/tmp/H5closezhuqzz80.c: In function ‘main’:
/tmp/H5closezhuqzz80.c:2:5: warning: implicit declaration of function ‘H5close’ [-Wimplicit-function-declaration]
H5close();
^
/usr/bin/ld: cannot find -lhdf5
collect2: error: ld returned 1 exit status
* Using Python 3.6.5 |Anaconda, Inc.| (default, Mar 29 2018, 18:21:58)
* USE_PKGCONFIG: False
* Found conda env: ``/home/galen/miniconda3/envs/testenv``
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-2y5swrs2/tables/
environment info:
$ conda info
Current conda install:
platform : linux-64
conda version : 4.3.30
conda is private : False
conda-env version : 4.3.30
conda-build version : not installed
python version : 3.6.0.final.0
requests version : 2.12.4
root environment : /home/galen/miniconda3 (writable)
default environment : /home/galen/miniconda3/envs/testenv
envs directories : /home/galen/miniconda3/envs
/home/galen/.conda/envs
package cache : /home/galen/miniconda3/pkgs
/home/galen/.conda/pkgs
channel URLs : https://repo.continuum.io/pkgs/main/linux-64
https://repo.continuum.io/pkgs/main/noarch
https://repo.continuum.io/pkgs/free/linux-64
https://repo.continuum.io/pkgs/free/noarch
https://repo.continuum.io/pkgs/r/linux-64
https://repo.continuum.io/pkgs/r/noarch
https://repo.continuum.io/pkgs/pro/linux-64
https://repo.continuum.io/pkgs/pro/noarch
config file : None
netrc file : None
offline mode : False
user-agent : conda/4.3.30 requests/2.12.4 CPython/3.6.0 Linux/4.4.0-119-generic debian/stretch/sid glibc/2.23
UID:GID : 1000:1000conda list
# packages in environment at /home/galen/miniconda3/envs/testenv:
#
ca-certificates 2018.03.07 0
certifi 2018.4.16 py36_0
libedit 3.1 heed3624_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 7.2.0 hdf63c60_3
libstdcxx-ng 7.2.0 hdf63c60_3
ncurses 6.0 h9df7e31_2
openssl 1.0.2o h20670df_0
pip 9.0.3 py36_0
pip 10.0.1 <pip>
python 3.6.5 hc3d631a_0
readline 7.0 ha6073c6_4
setuptools 39.0.1 py36_0
sqlite 3.23.1 he433501_0
tk 8.6.7 hc745277_3
wheel 0.31.0 py36_0
xz 5.2.3 h55aa19d_2
zlib 1.2.11 ha838bed_2 OK, just installed HDF5 successfully with
conda install HDF5
Running
pip install hypertools
...
galenwilkerson
commented
6 years ago Hmm, now although it says installed correctly, doesn't seem to truly import hypertools:
$ pip install hypertools
Requirement already satisfied: hypertools in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (0.5.0)
Requirement already satisfied: numpy>=1.10.4 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (1.14.2)
Requirement already satisfied: pandas>=0.18.0 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.22.0)
Requirement already satisfied: six in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (1.11.0)
Requirement already satisfied: umap-learn>=0.1.5 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.2.3)
Requirement already satisfied: future in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.16.0)
Requirement already satisfied: hdbscan>=0.8.11 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.8.12)
Requirement already satisfied: scikit-learn>=0.19.1 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.19.1)
Requirement already satisfied: scipy>=1.0.0 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (1.0.1)
Requirement already satisfied: deepdish in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.3.6)
Requirement already satisfied: PPCA>=0.0.2 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.0.3)
Requirement already satisfied: matplotlib>=1.5.1 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (2.2.2)
Requirement already satisfied: requests in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (2.18.4)
Requirement already satisfied: seaborn>=0.8.1 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from hypertools) (0.8.1)
Requirement already satisfied: pytz>=2011k in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from pandas>=0.18.0->hypertools) (2018.4)
Requirement already satisfied: python-dateutil>=2 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from pandas>=0.18.0->hypertools) (2.7.2)
Requirement already satisfied: numba>=0.34 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from umap-learn>=0.1.5->hypertools) (0.37.0)
Requirement already satisfied: tables in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from deepdish->hypertools) (3.4.3)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from matplotlib>=1.5.1->hypertools) (2.2.0)
Requirement already satisfied: cycler>=0.10 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from matplotlib>=1.5.1->hypertools) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from matplotlib>=1.5.1->hypertools) (1.0.1)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from requests->hypertools) (3.0.4)
Requirement already satisfied: idna<2.7,>=2.5 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from requests->hypertools) (2.6)
Requirement already satisfied: certifi>=2017.4.17 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from requests->hypertools) (2018.4.16)
Requirement already satisfied: urllib3<1.23,>=1.21.1 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from requests->hypertools) (1.22)
Requirement already satisfied: llvmlite>=0.22.0.dev0 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from numba>=0.34->umap-learn>=0.1.5->hypertools) (0.22.0)
Requirement already satisfied: numexpr>=2.5.2 in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from tables->deepdish->hypertools) (2.6.4)
Requirement already satisfied: setuptools in /home/galen/miniconda3/envs/testenv/lib/python3.6/site-packages (from kiwisolver>=1.0.1->matplotlib>=1.5.1->hypertools) (39.0.1)
(testenv) galen@fibonacci:~/Dropbox$
(testenv) galen@fibonacci:~/Dropbox$ ipython
Python 3.5.2 (default, Nov 23 2017, 16:37:01)
Type 'copyright', 'credits' or 'license' for more information
IPython 6.1.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: import hypertools
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-48afb9e37bd3> in <module>()
----> 1 import hypertools
ImportError: No module named 'hypertools'$ conda list
# packages in environment at /home/galen/miniconda3/envs/testenv:
#
ca-certificates 2018.03.07 0
certifi 2018.4.16 py36_0
chardet 3.0.4 <pip>
cycler 0.10.0 <pip>
deepdish 0.3.6 <pip>
future 0.16.0 <pip>
hdbscan 0.8.12 <pip>
hdf5 1.10.1 h9caa474_1
hypertools 0.5.0 <pip>
idna 2.6 <pip>
kiwisolver 1.0.1 <pip>
libedit 3.1 heed3624_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 7.2.0 hdf63c60_3
libgfortran-ng 7.2.0 hdf63c60_3
libstdcxx-ng 7.2.0 hdf63c60_3
llvmlite 0.22.0 <pip>
matplotlib 2.2.2 <pip>
ncurses 6.0 h9df7e31_2
numba 0.37.0 <pip>
numexpr 2.6.4 <pip>
numpy 1.14.2 <pip>
openssl 1.0.2o h20670df_0
pandas 0.22.0 <pip>
pip 10.0.1 <pip>
pip 9.0.3 py36_0
ppca 0.0.3 <pip>
pyparsing 2.2.0 <pip>
python 3.6.5 hc3d631a_0
python-dateutil 2.7.2 <pip>
pytz 2018.4 <pip>
readline 7.0 ha6073c6_4
requests 2.18.4 <pip>
scikit-learn 0.19.1 <pip>
scipy 1.0.1 <pip>
seaborn 0.8.1 <pip>
setuptools 39.0.1 py36_0
six 1.11.0 <pip>
sqlite 3.23.1 he433501_0
tables 3.4.3 <pip>
tk 8.6.7 hc745277_3
umap-learn 0.2.3 <pip>
urllib3 1.22 <pip>
wheel 0.31.0 py36_0
xz 5.2.3 h55aa19d_2
zlib 1.2.11 ha838bed_2 I prefer not to run
apt-get install python3-devsince I'm afraid it will clobber something.
andrewheusser
commented
6 years ago It looks like ipython is using a different version of python Python 3.5.2 (default, Nov 23 2017, 16:37:01) (not the one installed in your test env). looks like you may need to install ipython in your text env
andrewheusser
commented
6 years ago @galenwilkerson were you able to resolve this?
galenwilkerson
commented
6 years ago Nope, I don't think your suggestion was correct about ipython. Let me know if you get it working.
On Sun, Apr 22, 2018, 12:36 PM Andy Heusser notifications@github.com wrote:
@galenwilkerson https://github.com/galenwilkerson were you able to resolve this?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ContextLab/hypertools/issues/195#issuecomment-383371412, or mute the thread https://github.com/notifications/unsubscribe-auth/AAMumIfG3eV2pzRE0hzRLQxXyRNStTrLks5trF0jgaJpZM4TdAHe .
andrewheusser
commented
6 years ago ok, the issue is likely related to installing hdbscan using pip instead of conda for anaconda environments, see https://github.com/scikit-learn-contrib/hdbscan/issues/143.
can you try installing hdbscan with conda? conda install -c conda-forge hdbscan. if that works, i'll add a note to the readme
jeremymanning
commented
5 years ago @andrewheusser let's remove hdbscan from requirements (and all hdbscan-related features) until we can work this one out. i'm also encountering hdbscan install issues...
if the user wants to use hdbscan, we could:
that way if the user has hdbscan installed already, they can use it. but if not, it won't mess up the installation of hypertools.
galenwilkerson
commented
5 years ago Unsubscribe please
Thanks
On Mon, Jul 16, 2018, 10:34 PM Jeremy Manning notifications@github.com wrote:
@andrewheusser https://github.com/andrewheusser let's remove hdbscan from requirements (and all hdbscan-related features) until we can work this one out. i'm also encountering hdbscan install issues...
if the user wants to use hdbscan, we could:
- try importing hdbscan and running the analysis
- if that fails, throw a "hdbscan not installed" error
that way if the user has hdbscan installed already, they can use it. but if not, it won't mess up the installation of hypertools.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ContextLab/hypertools/issues/195#issuecomment-405440373, or mute the thread https://github.com/notifications/unsubscribe-auth/AAMumFFdc3U2JeUFayVjuhSSIiA7QrAnks5uHU0lgaJpZM4TdAHe .
lmcinnes
commented
5 years ago @andrewheusser It seems more likely that the issue is scikitlearn-contrib/hdbscan@222 -- at least as far as the build failure is concerned. That should be fixed in master. I can try pushing a new sdist to PyPI to resolve?
andrewheusser
commented
5 years ago @jeremymanning - what is the error that you are getting? is it related to dist_metrics.pyx?
@galenwilkerson - you can unsubscribe from this issue by clicking unsubscribe on the right side of this page under 'notifications': https://help.github.com/articles/subscribing-to-and-unsubscribing-from-notifications/
jeremymanning
commented
5 years ago @andrewheusser here's the full output (this is on Python 3.7 and MacOS 10.13):
$ pip install --user hypertools
Collecting hypertools
Requirement already satisfied: six in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (1.11.0)
Requirement already satisfied: future in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.16.0)
Collecting requests (from hypertools)
Using cached https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl
Requirement already satisfied: seaborn>=0.8.1 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.8.1)
Requirement already satisfied: umap-learn>=0.1.5 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.3.0)
Requirement already satisfied: matplotlib>=1.5.1 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (2.2.2)
Requirement already satisfied: scikit-learn>=0.19.1 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.19.2)
Collecting hdbscan>=0.8.11 (from hypertools)
Using cached https://files.pythonhosted.org/packages/c7/6a/92ecddb0d8c28266d8d4f9ab6f58ee543059aaade98e73b35de44a1c99f9/hdbscan-0.8.13.tar.gz
Requirement already satisfied: deepdish in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.3.6)
Requirement already satisfied: pandas>=0.18.0 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.23.3)
Requirement already satisfied: numpy>=1.10.4 in /usr/local/lib/python3.7/site-packages (from hypertools) (1.14.5)
Requirement already satisfied: PPCA>=0.0.2 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (0.0.3)
Requirement already satisfied: scipy>=1.0.0 in ./Library/Python/3.7/lib/python/site-packages (from hypertools) (1.1.0)
Collecting idna<2.8,>=2.5 (from requests->hypertools)
Using cached https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests->hypertools)
Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting urllib3<1.24,>=1.21.1 (from requests->hypertools)
Using cached https://files.pythonhosted.org/packages/bd/c9/6fdd990019071a4a32a5e7cb78a1d92c53851ef4f56f62a3486e6a7d8ffb/urllib3-1.23-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests->hypertools)
Using cached https://files.pythonhosted.org/packages/7c/e6/92ad559b7192d846975fc916b65f667c7b8c3a32bea7372340bfe9a15fa5/certifi-2018.4.16-py2.py3-none-any.whl
Requirement already satisfied: numba>=0.37 in ./Library/Python/3.7/lib/python/site-packages (from umap-learn>=0.1.5->hypertools) (0.39.0)
Requirement already satisfied: python-dateutil>=2.1 in ./Library/Python/3.7/lib/python/site-packages (from matplotlib>=1.5.1->hypertools) (2.7.3)
Requirement already satisfied: cycler>=0.10 in ./Library/Python/3.7/lib/python/site-packages (from matplotlib>=1.5.1->hypertools) (0.10.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./Library/Python/3.7/lib/python/site-packages (from matplotlib>=1.5.1->hypertools) (2.2.0)
Requirement already satisfied: kiwisolver>=1.0.1 in ./Library/Python/3.7/lib/python/site-packages (from matplotlib>=1.5.1->hypertools) (1.0.1)
Requirement already satisfied: pytz in ./Library/Python/3.7/lib/python/site-packages (from matplotlib>=1.5.1->hypertools) (2018.5)
Requirement already satisfied: cython>=0.17 in /usr/local/lib/python3.7/site-packages (from hdbscan>=0.8.11->hypertools) (0.28.4)
Requirement already satisfied: tables in ./Library/Python/3.7/lib/python/site-packages (from deepdish->hypertools) (3.4.4)
Requirement already satisfied: llvmlite>=0.24.0dev0 in ./Library/Python/3.7/lib/python/site-packages (from numba>=0.37->umap-learn>=0.1.5->hypertools) (0.24.0)
Requirement already satisfied: setuptools in /usr/local/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib>=1.5.1->hypertools) (39.2.0)
Requirement already satisfied: numexpr>=2.5.2 in ./Library/Python/3.7/lib/python/site-packages (from tables->deepdish->hypertools) (2.6.5)
Building wheels for collected packages: hdbscan
Running setup.py bdist_wheel for hdbscan ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-install-o9metzua/hdbscan/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 /private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-wheel-joqi8nwm --python-tag cp37:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.7
creating build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/validity.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/prediction.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/plots.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/hdbscan_.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/robust_single_linkage_.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
creating build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
copying hdbscan/tests/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
copying hdbscan/tests/test_rsl.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
copying hdbscan/tests/test_hdbscan.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
running build_ext
cythoning hdbscan/_hdbscan_tree.pyx to hdbscan/_hdbscan_tree.c
building 'hdbscan._hdbscan_tree' extension
creating build/temp.macosx-10.13-x86_64-3.7
creating build/temp.macosx-10.13-x86_64-3.7/hdbscan
/usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/opt/llvm/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_tree.c -o build/temp.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_tree.o
In file included from hdbscan/_hdbscan_tree.c:567:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
1 warning generated.
/usr/local/opt/llvm/bin/clang -bundle -undefined dynamic_lookup -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include build/temp.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_tree.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_tree.cpython-37m-darwin.so
skipping 'hdbscan/_hdbscan_linkage.c' Cython extension (up-to-date)
building 'hdbscan._hdbscan_linkage' extension
/usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/opt/llvm/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_linkage.c -o build/temp.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_linkage.o
In file included from hdbscan/_hdbscan_linkage.c:274:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
hdbscan/_hdbscan_linkage.c:4936:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4936:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:4904:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4904:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:4872:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4872:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:4840:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4840:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:22783:21: error: no member named 'exc_type' in 'struct _ts'
*type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22784:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22785:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22792:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22793:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22794:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22795:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22796:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22797:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22852:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22853:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22854:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22855:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = local_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22856:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22857:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22879:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22880:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22881:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22882:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = *type;
~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
5 warnings and 20 errors generated.
error: command '/usr/local/opt/llvm/bin/clang' failed with exit status 1
----------------------------------------
Failed building wheel for hdbscan
Running setup.py clean for hdbscan
Failed to build hdbscan
Installing collected packages: idna, chardet, urllib3, certifi, requests, hdbscan, hypertools
The script chardetect is installed in '/Users/jmanning/Library/Python/3.7/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Running setup.py install for hdbscan ... error
Complete output from command /usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-install-o9metzua/hdbscan/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-record-rm_gnaot/install-record.txt --single-version-externally-managed --compile --user --prefix=:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.13-x86_64-3.7
creating build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/validity.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/prediction.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/plots.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/hdbscan_.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
copying hdbscan/robust_single_linkage_.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan
creating build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
copying hdbscan/tests/__init__.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
copying hdbscan/tests/test_rsl.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
copying hdbscan/tests/test_hdbscan.py -> build/lib.macosx-10.13-x86_64-3.7/hdbscan/tests
running build_ext
skipping 'hdbscan/_hdbscan_tree.c' Cython extension (up-to-date)
building 'hdbscan._hdbscan_tree' extension
creating build/temp.macosx-10.13-x86_64-3.7
creating build/temp.macosx-10.13-x86_64-3.7/hdbscan
/usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/opt/llvm/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_tree.c -o build/temp.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_tree.o
In file included from hdbscan/_hdbscan_tree.c:567:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
1 warning generated.
/usr/local/opt/llvm/bin/clang -bundle -undefined dynamic_lookup -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -I/usr/local/opt/llvm/include build/temp.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_tree.o -L/usr/local/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/sqlite/lib -o build/lib.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_tree.cpython-37m-darwin.so
skipping 'hdbscan/_hdbscan_linkage.c' Cython extension (up-to-date)
building 'hdbscan._hdbscan_linkage' extension
/usr/local/opt/llvm/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/opt/llvm/include -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m -I/usr/local/lib/python3.7/site-packages/numpy/core/include -c hdbscan/_hdbscan_linkage.c -o build/temp.macosx-10.13-x86_64-3.7/hdbscan/_hdbscan_linkage.o
In file included from hdbscan/_hdbscan_linkage.c:274:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18:
In file included from /usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:
/usr/local/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
hdbscan/_hdbscan_linkage.c:4936:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4936:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:4904:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4904:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:4872:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4872:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:4840:15: warning: code will never be executed [-Wunreachable-code]
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^~~~~~~~~~~~~
hdbscan/_hdbscan_linkage.c:4840:9: note: silence by adding parentheses to mark code as explicitly dead
if (0 && (__pyx_tmp_idx < 0 || __pyx_tmp_idx >= __pyx_tmp_shape)) {
^
/* DISABLES CODE */ ( )
hdbscan/_hdbscan_linkage.c:22783:21: error: no member named 'exc_type' in 'struct _ts'
*type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22784:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
*value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22785:19: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
*tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22792:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22793:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22794:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22795:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22796:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22797:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22852:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22853:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22854:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22855:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = local_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22856:13: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tstate->exc_value = local_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22857:13: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tstate->exc_traceback = local_tb;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22879:24: error: no member named 'exc_type' in 'struct _ts'
tmp_type = tstate->exc_type;
~~~~~~ ^
hdbscan/_hdbscan_linkage.c:22880:25: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
tmp_value = tstate->exc_value;
^~~~~~~~~
curexc_value
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:237:15: note: 'curexc_value' declared here
PyObject *curexc_value;
^
hdbscan/_hdbscan_linkage.c:22881:22: error: no member named 'exc_traceback' in 'struct _ts'; did you mean 'curexc_traceback'?
tmp_tb = tstate->exc_traceback;
^~~~~~~~~~~~~
curexc_traceback
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/include/python3.7m/pystate.h:238:15: note: 'curexc_traceback' declared here
PyObject *curexc_traceback;
^
hdbscan/_hdbscan_linkage.c:22882:13: error: no member named 'exc_type' in 'struct _ts'
tstate->exc_type = *type;
~~~~~~ ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
5 warnings and 20 errors generated.
error: command '/usr/local/opt/llvm/bin/clang' failed with exit status 1
----------------------------------------
Command "/usr/local/opt/python/bin/python3.7 -u -c "import setuptools, tokenize;__file__='/private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-install-o9metzua/hdbscan/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-record-rm_gnaot/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /private/var/folders/zz/9lqw9wnd6d747mxyvfrbcpy80000gn/T/pip-install-o9metzua/hdbscan/thanks! hey @lmcinnes - are you familiar with this error? its looks like a different issue than what Galen ran into. perhaps something new introduced in python 3.7?
@jeremymanning - we don't test python 3.7 yet, i'll put that on the list for the next release
lmcinnes
commented
5 years ago Yes, I'm familiar with this -- it's a Cython/python3.7 issue. I was going to try to fix it in the next few days. It will require people to have cython to install hdbscan which is annoying, but I know of no other way to work aropund the binary incompatibilities between 3.x and 3.7.
On Tue, Jul 17, 2018 at 9:30 AM Andy Heusser notifications@github.com wrote:
thanks! hey @lmcinnes https://github.com/lmcinnes - are you familiar with this error? its looks like a different issue than what Galen ran into. perhaps something new introduced in python 3.7?
@jeremymanning https://github.com/jeremymanning - we don't test python 3.7 yet, i'll put that on the list for the next release
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ContextLab/hypertools/issues/195#issuecomment-405582138, or mute the thread https://github.com/notifications/unsubscribe-auth/ALaKBcBoHVxBhroZpS6-hXVofbOKNvMGks5uHebdgaJpZM4TdAHe .
jeremymanning
commented
5 years ago @lmcinnes that sounds great. I agree that it's annoying to add another requirement, but it seems like the right way to go.
More generally for the toolbox, I'm wondering if we should take a slightly different approach to dependencies, now that we're starting to rely more and more on external dependencies. I'll add a new issue about this, but my general thinking is that we could:
This will allow us to increase the reliability of the installation while still maintaining support for advanced users.
andrewheusser
commented
5 years ago In the hypertools 0.5.1 release, hdbscan is an optional install. We are planning to move to this model for all non-core dependencies to keep hypertools as stable as possible
I've gotten this error for both methods of installation. Using an anaconda 3.6 environment.