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jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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issues installing dms_tools2 #69

Open dylanc-14 opened 1 year ago

dylanc-14 commented 1 year ago

Hello,

I followed the following steps to install dms_tools2 on a 2019 MacBook Air with the following hardware information:

Model Identifier: MacBookAir8,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1.6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0) OS Loader Version: 540.120.3~22

Installation Steps:

  1. installed Anaconda Navigator 2.3.2
  2. Created a python 3.6.10 environment titled Python
  3. ran command conda config --append channels conda-forge in terminal, which resolved a previous issue installing several of the dependency packages in step 4.
  4. individually ran the following dms_tools2 dependencies:
conda install numpy==1.19.5
conda install pandas==0.25.3
conda install matplotlib==3.2.2
conda install typing-extensions==3.10.0.2
conda install biopython
conda install attrs
conda install pysam
conda install IPython
conda install jupyter
conda install mizani==0.6.0
conda install plotnine==0.6.0
conda install natsort
conda install pystan==2.19.1.1
conda install scipy
conda install seaborn
conda install statsmodels
conda install regex
conda install packaging
conda install umi_tools
  1. conda install dms_tools2 yielded the following error message: 
PackagesNotFoundError: The following packages are not available from current channels:

  - dms_tools2

Current channels:

  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://conda.anaconda.org/conda-forge/osx-64
  - https://conda.anaconda.org/conda-forge/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to https://anaconda.org and use the search bar at the top of the page.

Thus, we tried a pip install with the following command: pip install dms_tools2 --user . This yielded the following error message: 

Collecting dms_tools2
  Using cached dms_tools2-2.6.12.tar.gz (42.0 MB)
Requirement already satisfied: attrs>=17.4.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (21.4.0)
Requirement already satisfied: biopython>=1.68 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (1.78)
Requirement already satisfied: pysam>=0.13 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (0.14.1)
Requirement already satisfied: pandas<1.0,>=0.23 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (0.25.3)
Requirement already satisfied: numpy<1.20,>=1.16 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (1.19.5)
Requirement already satisfied: IPython>=5.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (7.16.1)
Requirement already satisfied: jupyter>=1.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (1.0.0)
Requirement already satisfied: matplotlib<3.3,>=2.1.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (3.2.2)
Requirement already satisfied: plotnine<0.7,>=0.3 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (0.6.0)
Requirement already satisfied: mizani<0.7 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (0.6.0)
Requirement already satisfied: natsort>=5.0.3 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (7.1.1)
Requirement already satisfied: pystan<3,>=2.19 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (2.19.1.1)
Requirement already satisfied: scipy>=1.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (1.3.1)
Requirement already satisfied: seaborn>=0.8 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (0.11.2)
Collecting phydms>=2.4.1
  Using cached phydms-2.4.1.tar.gz (4.1 MB)
Requirement already satisfied: statsmodels>=0.8 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (0.12.2)
Requirement already satisfied: regex>=2.4.153 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (2021.8.3)
Requirement already satisfied: packaging in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (21.3)
Requirement already satisfied: umi_tools>=1.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from dms_tools2) (1.1.0)
Requirement already satisfied: setuptools>=18.5 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (58.0.4)
Requirement already satisfied: jedi>=0.10 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (0.17.0)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (3.0.20)
Requirement already satisfied: pygments in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (2.11.2)
Requirement already satisfied: traitlets>=4.2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (4.3.3)
Requirement already satisfied: pexpect in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (4.8.0)
Requirement already satisfied: decorator in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (5.1.1)
Requirement already satisfied: appnope in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (0.1.2)
Requirement already satisfied: backcall in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (0.2.0)
Requirement already satisfied: pickleshare in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from IPython>=5.1->dms_tools2) (0.7.5)
Requirement already satisfied: parso>=0.7.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jedi>=0.10->IPython>=5.1->dms_tools2) (0.8.3)
Requirement already satisfied: qtconsole in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter>=1.0.0->dms_tools2) (5.2.2)
Requirement already satisfied: ipykernel in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter>=1.0.0->dms_tools2) (5.3.4)
Requirement already satisfied: nbconvert in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter>=1.0.0->dms_tools2) (6.0.7)
Requirement already satisfied: notebook in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter>=1.0.0->dms_tools2) (6.4.3)
Requirement already satisfied: jupyter-console in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter>=1.0.0->dms_tools2) (6.4.3)
Requirement already satisfied: ipywidgets in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter>=1.0.0->dms_tools2) (7.6.5)
Requirement already satisfied: python-dateutil>=2.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib<3.3,>=2.1.1->dms_tools2) (2.8.2)
Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib<3.3,>=2.1.1->dms_tools2) (1.3.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib<3.3,>=2.1.1->dms_tools2) (3.0.4)
Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib<3.3,>=2.1.1->dms_tools2) (0.11.0)
Requirement already satisfied: palettable in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from mizani<0.7->dms_tools2) (3.3.0)
Requirement already satisfied: pytz>=2017.2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from pandas<1.0,>=0.23->dms_tools2) (2021.3)
Requirement already satisfied: cython>=0.28 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms>=2.4.1->dms_tools2) (0.29.24)
Requirement already satisfied: sympy>=1.0 in ./.local/lib/python3.6/site-packages (from phydms>=2.4.1->dms_tools2) (1.9)
Requirement already satisfied: six>=1.10 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms>=2.4.1->dms_tools2) (1.16.0)
Requirement already satisfied: pyvolve>=1.0.3 in ./.local/lib/python3.6/site-packages (from phydms>=2.4.1->dms_tools2) (1.0.3)
Requirement already satisfied: weblogo<3.6,>=3.4 in ./.local/lib/python3.6/site-packages (from phydms>=2.4.1->dms_tools2) (3.5.0)
Requirement already satisfied: PyPDF2>=1.26 in ./.local/lib/python3.6/site-packages (from phydms>=2.4.1->dms_tools2) (2.11.1)
Requirement already satisfied: descartes>=1.1.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from plotnine<0.7,>=0.3->dms_tools2) (1.1.0)
Requirement already satisfied: patsy>=0.4.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from plotnine<0.7,>=0.3->dms_tools2) (0.5.1)
Requirement already satisfied: wcwidth in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->IPython>=5.1->dms_tools2) (0.2.5)
Requirement already satisfied: typing-extensions>=3.10.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from PyPDF2>=1.26->phydms>=2.4.1->dms_tools2) (3.10.0.2)
Requirement already satisfied: dataclasses in ./.local/lib/python3.6/site-packages (from PyPDF2>=1.26->phydms>=2.4.1->dms_tools2) (0.8)
Requirement already satisfied: mpmath>=0.19 in ./.local/lib/python3.6/site-packages (from sympy>=1.0->phydms>=2.4.1->dms_tools2) (1.2.1)
Requirement already satisfied: ipython-genutils in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from traitlets>=4.2->IPython>=5.1->dms_tools2) (0.2.0)
Requirement already satisfied: pybktree in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from umi_tools>=1.0.0->dms_tools2) (1.1)
Requirement already satisfied: future in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from umi_tools>=1.0.0->dms_tools2) (0.18.2)
Requirement already satisfied: jupyter-client in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from ipykernel->jupyter>=1.0.0->dms_tools2) (7.1.2)
Requirement already satisfied: tornado>=4.2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from ipykernel->jupyter>=1.0.0->dms_tools2) (6.1)
Requirement already satisfied: nbformat>=4.2.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from ipywidgets->jupyter>=1.0.0->dms_tools2) (5.1.3)
Requirement already satisfied: jupyterlab-widgets>=1.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from ipywidgets->jupyter>=1.0.0->dms_tools2) (1.0.0)
Requirement already satisfied: widgetsnbextension~=3.5.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from ipywidgets->jupyter>=1.0.0->dms_tools2) (3.5.1)
Requirement already satisfied: jupyter-core in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets->jupyter>=1.0.0->dms_tools2) (4.8.1)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets->jupyter>=1.0.0->dms_tools2) (3.2.0)
Requirement already satisfied: pyrsistent>=0.14.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter>=1.0.0->dms_tools2) (0.17.3)
Requirement already satisfied: importlib-metadata in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter>=1.0.0->dms_tools2) (4.8.1)
Requirement already satisfied: argon2-cffi in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from notebook->jupyter>=1.0.0->dms_tools2) (20.1.0)
Requirement already satisfied: Send2Trash>=1.5.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from notebook->jupyter>=1.0.0->dms_tools2) (1.8.0)
Requirement already satisfied: pyzmq>=17 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from notebook->jupyter>=1.0.0->dms_tools2) (22.2.1)
Requirement already satisfied: terminado>=0.8.3 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from notebook->jupyter>=1.0.0->dms_tools2) (0.9.4)
Requirement already satisfied: jinja2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from notebook->jupyter>=1.0.0->dms_tools2) (3.0.3)
Requirement already satisfied: prometheus-client in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from notebook->jupyter>=1.0.0->dms_tools2) (0.13.1)
Requirement already satisfied: nest-asyncio>=1.5 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter-client->ipykernel->jupyter>=1.0.0->dms_tools2) (1.5.1)
Requirement already satisfied: entrypoints in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jupyter-client->ipykernel->jupyter>=1.0.0->dms_tools2) (0.3)
Requirement already satisfied: ptyprocess in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from terminado>=0.8.3->notebook->jupyter>=1.0.0->dms_tools2) (0.7.0)
Requirement already satisfied: cffi>=1.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter>=1.0.0->dms_tools2) (1.14.0)
Requirement already satisfied: pycparser in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter>=1.0.0->dms_tools2) (2.21)
Requirement already satisfied: zipp>=0.5 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from importlib-metadata->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets->jupyter>=1.0.0->dms_tools2) (3.6.0)
Requirement already satisfied: MarkupSafe>=2.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from jinja2->notebook->jupyter>=1.0.0->dms_tools2) (2.0.1)
Requirement already satisfied: bleach in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (4.1.0)
Requirement already satisfied: defusedxml in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (0.7.1)
Requirement already satisfied: mistune<2,>=0.8.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (0.8.4)
Requirement already satisfied: jupyterlab-pygments in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (0.1.2)
Requirement already satisfied: nbclient<0.6.0,>=0.5.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (0.5.3)
Requirement already satisfied: testpath in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (0.5.0)
Requirement already satisfied: pandocfilters>=1.4.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbconvert->jupyter>=1.0.0->dms_tools2) (1.5.0)
Requirement already satisfied: async-generator in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->jupyter>=1.0.0->dms_tools2) (1.10)
Requirement already satisfied: webencodings in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from bleach->nbconvert->jupyter>=1.0.0->dms_tools2) (0.5.1)
Requirement already satisfied: qtpy in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from qtconsole->jupyter>=1.0.0->dms_tools2) (2.0.1)
Building wheels for collected packages: dms-tools2, phydms
  Building wheel for dms-tools2 (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/dms-tools2_389bcd5400d044d18ce7ae046d9aa32c/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/dms-tools2_389bcd5400d044d18ce7ae046d9aa32c/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-wheel-p9xie52j
       cwd: /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/dms-tools2_389bcd5400d044d18ce7ae046d9aa32c/
  Complete output (36 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.6
  creating build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/pacbio.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/dssp.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/_metadata.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/plot.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/rplot.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/compareprefs.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/minimap2.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/sra.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/parseargs.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/syn_selection.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/fracsurvive.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/prefs.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/diffsel.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/utils.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/ipython_utils.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/protstruct.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/barcodes.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/seqnumbering.py -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  copying dms_tools2/rplot_Rcode.R -> build/lib.macosx-10.9-x86_64-3.6/dms_tools2
  running build_ext
  building 'dms_tools2._cutils' extension
  creating build/temp.macosx-10.9-x86_64-3.6
  creating build/temp.macosx-10.9-x86_64-3.6/dms_tools2
  x86_64-apple-darwin13.4.0-clang -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -I/Users/dylanclark/opt/anaconda3/envs/Python/include/python3.6m -c dms_tools2/_cutils.c -o build/temp.macosx-10.9-x86_64-3.6/dms_tools2/_cutils.o -Wno-error=declaration-after-statement
  x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/dms_tools2/_cutils.o -o build/lib.macosx-10.9-x86_64-3.6/dms_tools2/_cutils.cpython-36m-darwin.so
  ld: warning: -pie being ignored. It is only used when linking a main executable
  ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
  clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
  error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for dms-tools2
  Running setup.py clean for dms-tools2
  Building wheel for phydms (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-wheel-4dlao_li
       cwd: /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/
  Complete output (35 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.6
  creating build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/treelikelihood.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/_metadata.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/models.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/parsearguments.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/constants.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/simulate.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/utils.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/file_io.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/weblogo.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/_weblogo_template.eps -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  running build_ext
  building 'phydmslib.numutils' extension
  creating build/temp.macosx-10.9-x86_64-3.6
  creating build/temp.macosx-10.9-x86_64-3.6/phydmslib
  x86_64-apple-darwin13.4.0-clang -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -I/Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include -I/Users/dylanclark/opt/anaconda3/envs/Python/include/python3.6m -c phydmslib/numutils.c -o build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -Wno-unused-function
  In file included from phydmslib/numutils.c:642:
  In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
  In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
  /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
  #warning "Using deprecated NumPy API, disable it with " \
   ^
  1 warning generated.
  x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -o build/lib.macosx-10.9-x86_64-3.6/phydmslib/numutils.cpython-36m-darwin.so
  ld: warning: -pie being ignored. It is only used when linking a main executable
  ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
  clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
  error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for phydms
  Running setup.py clean for phydms
Failed to build dms-tools2 phydms
Installing collected packages: phydms, dms-tools2
    Running setup.py install for phydms ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-record-9_qmi7fv/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/dylanclark/.local/include/python3.6m/phydms
         cwd: /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/
    Complete output (35 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.6
    creating build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/treelikelihood.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/_metadata.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/models.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/parsearguments.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/constants.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/simulate.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/utils.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/file_io.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/weblogo.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/_weblogo_template.eps -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    running build_ext
    building 'phydmslib.numutils' extension
    creating build/temp.macosx-10.9-x86_64-3.6
    creating build/temp.macosx-10.9-x86_64-3.6/phydmslib
    x86_64-apple-darwin13.4.0-clang -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -I/Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include -I/Users/dylanclark/opt/anaconda3/envs/Python/include/python3.6m -c phydmslib/numutils.c -o build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -Wno-unused-function
    In file included from phydmslib/numutils.c:642:
    In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
    In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
    /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it with " \
     ^
    1 warning generated.
    x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -o build/lib.macosx-10.9-x86_64-3.6/phydmslib/numutils.cpython-36m-darwin.so
    ld: warning: -pie being ignored. It is only used when linking a main executable
    ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
    clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
    error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-i7hiaww3/phydms_85b1cec06207412f820cbc4ac0b4a2b9/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-record-9_qmi7fv/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/dylanclark/.local/include/python3.6m/phydms Check the logs for full command output.
  1. It appeared like the sole issue was installing the phydms dependency, thus we tried installing the phydms separately via pip with pip install phydms --user. The following error message was produced:
Collecting phydms
  Using cached phydms-2.4.1.tar.gz (4.1 MB)
Requirement already satisfied: biopython>=1.67 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (1.78)
Requirement already satisfied: cython>=0.28 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (0.29.24)
Requirement already satisfied: numpy>=1.16.5 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (1.19.5)
Requirement already satisfied: scipy>=0.18 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (1.3.1)
Requirement already satisfied: matplotlib>=2.0.2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (3.2.2)
Requirement already satisfied: natsort>=5.0.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (7.1.1)
Requirement already satisfied: sympy>=1.0 in ./.local/lib/python3.6/site-packages (from phydms) (1.9)
Requirement already satisfied: six>=1.10 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (1.16.0)
Requirement already satisfied: pandas>=0.20.2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (0.25.3)
Requirement already satisfied: pyvolve>=1.0.3 in ./.local/lib/python3.6/site-packages (from phydms) (1.0.3)
Requirement already satisfied: statsmodels>=0.8 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from phydms) (0.12.2)
Requirement already satisfied: weblogo<3.6,>=3.4 in ./.local/lib/python3.6/site-packages (from phydms) (3.5.0)
Requirement already satisfied: PyPDF2>=1.26 in ./.local/lib/python3.6/site-packages (from phydms) (2.11.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib>=2.0.2->phydms) (3.0.4)
Requirement already satisfied: kiwisolver>=1.0.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib>=2.0.2->phydms) (1.3.1)
Requirement already satisfied: cycler>=0.10 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib>=2.0.2->phydms) (0.11.0)
Requirement already satisfied: python-dateutil>=2.1 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from matplotlib>=2.0.2->phydms) (2.8.2)
Requirement already satisfied: pytz>=2017.2 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from pandas>=0.20.2->phydms) (2021.3)
Requirement already satisfied: dataclasses in ./.local/lib/python3.6/site-packages (from PyPDF2>=1.26->phydms) (0.8)
Requirement already satisfied: typing-extensions>=3.10.0.0 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from PyPDF2>=1.26->phydms) (3.10.0.2)
Requirement already satisfied: patsy>=0.5 in ./opt/anaconda3/envs/Python/lib/python3.6/site-packages (from statsmodels>=0.8->phydms) (0.5.1)
Requirement already satisfied: mpmath>=0.19 in ./.local/lib/python3.6/site-packages (from sympy>=1.0->phydms) (1.2.1)
Building wheels for collected packages: phydms
  Building wheel for phydms (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-wheel-dmhd0af9
       cwd: /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/
  Complete output (35 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-10.9-x86_64-3.6
  creating build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/treelikelihood.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/_metadata.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/models.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/parsearguments.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/constants.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/simulate.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/utils.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/file_io.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/weblogo.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  copying phydmslib/_weblogo_template.eps -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
  running build_ext
  building 'phydmslib.numutils' extension
  creating build/temp.macosx-10.9-x86_64-3.6
  creating build/temp.macosx-10.9-x86_64-3.6/phydmslib
  x86_64-apple-darwin13.4.0-clang -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -I/Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include -I/Users/dylanclark/opt/anaconda3/envs/Python/include/python3.6m -c phydmslib/numutils.c -o build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -Wno-unused-function
  In file included from phydmslib/numutils.c:642:
  In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
  In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
  In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
  /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
  #warning "Using deprecated NumPy API, disable it with " \
   ^
  1 warning generated.
  x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -o build/lib.macosx-10.9-x86_64-3.6/phydmslib/numutils.cpython-36m-darwin.so
  ld: warning: -pie being ignored. It is only used when linking a main executable
  ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
  clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
  error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for phydms
  Running setup.py clean for phydms
Failed to build phydms
Installing collected packages: phydms
    Running setup.py install for phydms ... error
    ERROR: Command errored out with exit status 1:
     command: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-record-ofoh0bkm/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/dylanclark/.local/include/python3.6m/phydms
         cwd: /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/
    Complete output (35 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.macosx-10.9-x86_64-3.6
    creating build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/treelikelihood.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/_metadata.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/models.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/parsearguments.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/constants.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/simulate.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/__init__.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/utils.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/file_io.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/weblogo.py -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    copying phydmslib/_weblogo_template.eps -> build/lib.macosx-10.9-x86_64-3.6/phydmslib
    running build_ext
    building 'phydmslib.numutils' extension
    creating build/temp.macosx-10.9-x86_64-3.6
    creating build/temp.macosx-10.9-x86_64-3.6/phydmslib
    x86_64-apple-darwin13.4.0-clang -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -I/Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include -I/Users/dylanclark/opt/anaconda3/envs/Python/include/python3.6m -c phydmslib/numutils.c -o build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -Wno-unused-function
    In file included from phydmslib/numutils.c:642:
    In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
    In file included from /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
    /Users/dylanclark/opt/anaconda3/envs/Python/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it with " \
     ^
    1 warning generated.
    x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -Wl,-export_dynamic -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/dylanclark/opt/anaconda3/envs/Python/lib -L/Users/dylanclark/opt/anaconda3/envs/Python/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -isystem /Users/dylanclark/opt/anaconda3/envs/Python/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/phydmslib/numutils.o -o build/lib.macosx-10.9-x86_64-3.6/phydmslib/numutils.cpython-36m-darwin.so
    ld: warning: -pie being ignored. It is only used when linking a main executable
    ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd' for architecture x86_64
    clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
    error: command 'x86_64-apple-darwin13.4.0-clang' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /Users/dylanclark/opt/anaconda3/envs/Python/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/setup.py'"'"'; __file__='"'"'/private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-install-p73dchj7/phydms_79a3ea60bb0042e6ab4f03ba0dca84b3/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/td/w4kgvgj12hl6d1q_15h0rjlm0000gn/T/pip-record-ofoh0bkm/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /Users/dylanclark/.local/include/python3.6m/phydms Check the logs for full command output.

Any ideas on how we should proceed? Thank you!

jbloom commented 1 year ago

I'm sorry for the glacial response to this... @ckikawa, do you have any tips since you clearly got this installed.

ckikawa commented 1 year ago

@jbloom I have not tried to install directly on my machine. I build a conda virtual environment that specifies dms_tools2 version 2.6.10 and I have no issues.