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biocore / q2-mislabeled

A QIIME 2 plugin for assessing sample mislabeling and contamination
BSD 3-Clause "New" or "Revised" License
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Installation errors #2

Closed joycelyny closed 1 year ago

joycelyny commented 1 year ago

ERROR: Failed building wheel for scikit-bio Running setup.py clean for scikit-bio Successfully built sourcetracker Failed to build biom-format scikit-bio ERROR: Could not build wheels for biom-format which use PEP 517 and cannot be installed directly

wasade commented 1 year ago

Thanks, but is there any other context, the rest of the error output, and the commands run that were used to generate the error?

joycelyny commented 1 year ago

I believe I may have an error within my virtual environment:

Compiling skbio/metadata/_intersection.pyx because it changed. Compiling skbio/stats/__subsample.pyx because it changed. Compiling skbio/alignment/_ssw_wrapper.pyx because it changed. Compiling skbio/diversity/_phylogenetic.pyx because it changed. Compiling skbio/stats/ordination/_cutils.pyx because it changed. Compiling skbio/stats/distance/_cutils.pyx because it changed. [1/6] Cythonizing skbio/alignment/_ssw_wrapper.pyx Traceback (most recent call last): File "/opt/python-3.8.12/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 280, in main() File "/opt/python-3.8.12/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 263, in main json_out['return_val'] = hook(*hook_input['kwargs']) File "/opt/python-3.8.12/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 114, in get_requires_for_build_wheel return hook(config_settings) File "/tmp/pip-build-env-c5iu3cvy/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 163, in get_requires_for_build_wheel config_settings, requirements=['wheel']) File "/tmp/pip-build-env-c5iu3cvy/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 143, in _get_build_requires self.run_setup() File "/tmp/pip-build-env-c5iu3cvy/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 268, in run_setup self).run_setup(setup_script=setup_script) File "/tmp/pip-build-env-c5iu3cvy/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 158, in run_setup exec(compile(code, file, 'exec'), locals()) File "setup.py", line 130, in extensions = cythonize(extensions) File "/tmp/pip-build-env-c5iu3cvy/overlay/lib64/python3.6/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize cythonize_one(args) File "/tmp/pip-build-env-c5iu3cvy/overlay/lib64/python3.6/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one raise CompileError(None, pyx_file) Cython.Compiler.Errors.CompileError: skbio/alignment/_ssw_wrapper.pyx

WARNING: Discarding https://files.pythonhosted.org/packages/8c/a4/6ec875ba9a56f7705529aecc745ca3eaee6d90b87cd103281be7a032b412/scikit-bio-0.5.7.tar.gz#sha256=6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9 (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: /opt/jupyterhub/bin/python3 /opt/python-3.8.12/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py get_requires_for_build_wheel /tmp/tmphe5e4v0c Check the logs for full command output. Using cached scikit-bio-0.5.6.tar.gz (8.4 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_5a22f756716d496d8b99b1fa6d91cb03/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_5a22f756716d496d8b99b1fa6d91cb03/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-ka595i8d cwd: /tmp/pip-install-u7nx04ro/scikit-bio_5a22f756716d496d8b99b1fa6d91cb03/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_5a22f756716d496d8b99b1fa6d91cb03/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/66/b0/054ef21e024d24422882958072973cd192b492e004a3ce4e9614ef173d9b/scikit-bio-0.5.6.tar.gz#sha256=48b73ec53ce0ff2c2e3e05f3cfcf93527c1525a8d3e9dd4ae317b4219c37f0ea (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.5.5.tar.gz (8.3 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_fa3b5f7c8b754230a17296292b3bd600/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_fa3b5f7c8b754230a17296292b3bd600/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-2wu2yrhf cwd: /tmp/pip-install-u7nx04ro/scikit-bio_fa3b5f7c8b754230a17296292b3bd600/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_fa3b5f7c8b754230a17296292b3bd600/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/2d/ff/3a909ae8c212305846f7e87f86f3902408b55b958eccedf5d4349e76c671/scikit-bio-0.5.5.tar.gz#sha256=9fa813be66e88a994f7b7a68b8ba2216e205c525caa8585386ebdeebed6428df (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.5.4.tar.gz (8.3 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_7c0ec6b991c543b8b2097b33ec9d3c4b/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_7c0ec6b991c543b8b2097b33ec9d3c4b/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-_xnuc9cl cwd: /tmp/pip-install-u7nx04ro/scikit-bio_7c0ec6b991c543b8b2097b33ec9d3c4b/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_7c0ec6b991c543b8b2097b33ec9d3c4b/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/ed/e0/3ae790c5c260be0968a6d41108e35f327365e5460c9d8672714fd136817d/scikit-bio-0.5.4.tar.gz#sha256=3243f1995ef24643c09ff4d9391a79528aadd8232e5aa5d66c38d7b2e0c92f24 (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.5.3.tar.gz (8.3 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_5814775e34c04cdfb49564179765356c/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_5814775e34c04cdfb49564179765356c/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-f1jw36ls cwd: /tmp/pip-install-u7nx04ro/scikit-bio_5814775e34c04cdfb49564179765356c/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_5814775e34c04cdfb49564179765356c/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/39/07/4e3bcf7a7c254154ac445684d5f646ccc4a6ce6bfc3b0cc8030136215b8a/scikit-bio-0.5.3.tar.gz#sha256=fbeebe39b0026601fa0f641fdad45abc7c2810fa75d43142f3c5473aff07ff59 (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.5.2.tar.gz (8.3 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_f2f8a9194bb8471dbf6fa35b92246d28/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_f2f8a9194bb8471dbf6fa35b92246d28/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-3yh22yas cwd: /tmp/pip-install-u7nx04ro/scikit-bio_f2f8a9194bb8471dbf6fa35b92246d28/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_f2f8a9194bb8471dbf6fa35b92246d28/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/98/ee/08995b89efccf2bf8a0307a1eb7825dceb199e64a3db24cec832c0ca0baf/scikit-bio-0.5.2.tar.gz#sha256=566c83249d2d338104d106c3a8ba36fa1afeabf10ead8e95b84605b71c65b743 (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.5.1.tar.gz (8.2 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_d20d322ffba144acb69c01dceb361483/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_d20d322ffba144acb69c01dceb361483/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-xcgdx50p cwd: /tmp/pip-install-u7nx04ro/scikit-bio_d20d322ffba144acb69c01dceb361483/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_d20d322ffba144acb69c01dceb361483/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/e5/7e/cf03a7e53da18ae6a847894384838e9a36a98b48909a3f347ff6077c7304/scikit-bio-0.5.1.tar.gz#sha256=2d606f0bbd50df3e5814c10260d0e1a35484ecf141e5e5c809d9c9dbf87a3655 (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.5.0.zip (8.4 MB) ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_6836c495dd9243b7a95478dca0c8ec6e/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_6836c495dd9243b7a95478dca0c8ec6e/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'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-wcpjjs6p cwd: /tmp/pip-install-u7nx04ro/scikit-bio_6836c495dd9243b7a95478dca0c8ec6e/ Complete output (5 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-u7nx04ro/scikit-bio_6836c495dd9243b7a95478dca0c8ec6e/setup.py", line 20, in import numpy as np ModuleNotFoundError: No module named 'numpy'

WARNING: Discarding https://files.pythonhosted.org/packages/95/60/f4c269a6dfaf9d027adba6a81497e5d238cf5e604f53206b4ea50ed1145f/scikit-bio-0.5.0.zip#sha256=482194dd827b86fdf340d1576b07d70f8c62158d471d733fa3e73fe316afaa3a (from https://pypi.org/simple/scikit-bio/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. Using cached scikit-bio-0.4.2.tar.gz (8.1 MB) Collecting bz2file>=0.98 Using cached bz2file-0.98-py3-none-any.whl Collecting CacheControl>=0.11.5 Using cached CacheControl-0.12.14-py2.py3-none-any.whl (21 kB) Collecting contextlib2>=0.4.0 Using cached contextlib2-21.6.0-py2.py3-none-any.whl (13 kB) Collecting future>=0.14.3 Using cached future-0.18.3-py3-none-any.whl Requirement already satisfied: IPython>=3.2.0 in /opt/jupyterhub/lib/python3.6/site-packages (from scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (7.16.3) Requirement already satisfied: requests in /opt/jupyterhub/lib/python3.6/site-packages (from CacheControl>=0.11.5->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (2.27.1) Collecting msgpack>=0.5.2 Using cached msgpack-1.0.5-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (300 kB) Requirement already satisfied: setuptools>=18.5 in /opt/python-3.8.12/lib/python3.8/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (56.0.0) Requirement already satisfied: pexpect in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (4.8.0) Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (3.0.33) Requirement already satisfied: pickleshare in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.7.5) Requirement already satisfied: jedi<=0.17.2,>=0.10 in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.17.2) Requirement already satisfied: backcall in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.2.0) Requirement already satisfied: traitlets>=4.2 in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (4.3.3) Requirement already satisfied: pygments in /opt/jupyterhub/lib/python3.6/site-packages (from IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (2.13.0) Requirement already satisfied: parso<0.8.0,>=0.7.0 in /opt/jupyterhub/lib/python3.6/site-packages (from jedi<=0.17.2,>=0.10->IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.7.1) Collecting cycler>=0.10 Using cached cycler-0.11.0-py3-none-any.whl (6.4 kB) Collecting pillow>=6.2.0 Using cached Pillow-8.4.0-cp36-cp36m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB) Collecting kiwisolver>=1.0.1 Using cached kiwisolver-1.3.1-cp36-cp36m-manylinux1_x86_64.whl (1.1 MB) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /opt/jupyterhub/lib/python3.6/site-packages (from matplotlib>=1.4.3->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (3.0.9) Requirement already satisfied: wcwidth in /opt/jupyterhub/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.2.5) Requirement already satisfied: ipython-genutils in /opt/jupyterhub/lib/python3.6/site-packages (from traitlets>=4.2->IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.2.0) Requirement already satisfied: ptyprocess>=0.5 in /opt/jupyterhub/lib/python3.6/site-packages (from pexpect->IPython>=3.2.0->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (0.7.0) Requirement already satisfied: charset-normalizer~=2.0.0 in /opt/jupyterhub/lib/python3.6/site-packages (from requests->CacheControl>=0.11.5->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (2.0.12) Requirement already satisfied: idna<4,>=2.5 in /opt/jupyterhub/lib/python3.6/site-packages (from requests->CacheControl>=0.11.5->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (3.4) Requirement already satisfied: certifi>=2017.4.17 in /opt/jupyterhub/lib/python3.6/site-packages (from requests->CacheControl>=0.11.5->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (2022.9.24) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /opt/jupyterhub/lib/python3.6/site-packages (from requests->CacheControl>=0.11.5->scikit-bio->sourcetracker@ https://github.com/wasade/sourcetracker2/archive/be_sparse.zip->q2-mislabeled) (1.26.13) Collecting threadpoolctl>=2.0.0 Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB) Collecting joblib>=0.11 Using cached joblib-1.1.1-py2.py3-none-any.whl (309 kB) Building wheels for collected packages: sourcetracker, biom-format, scikit-bio Building wheel for sourcetracker (setup.py) ... done Created wheel for sourcetracker: filename=sourcetracker-2.0.1.dev0-py3-none-any.whl size=33818 sha256=26220dde8423a942d08749e0afab1757fe5bd9763a98bc050fd915a04fc0a45a Stored in directory: /tmp/pip-ephem-wheel-cache-l54l6_q2/wheels/9c/ba/72/8f3564ff25fc30f68be2fca92ee2bba6ac5753218d3bbf7268 Building wheel for biom-format (PEP 517) ... error ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 /opt/python-3.8.12/lib/python3.8/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpufghk2_2 cwd: /tmp/pip-install-u7nx04ro/biom-format_31f2da2b8a4e4068a9c0a582a2c84832 Complete output (189 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/biom copying biom/exception.py -> build/lib.linux-x86_64-3.6/biom copying biom/err.py -> build/lib.linux-x86_64-3.6/biom copying biom/util.py -> build/lib.linux-x86_64-3.6/biom copying biom/table.py -> build/lib.linux-x86_64-3.6/biom copying biom/parse.py -> build/lib.linux-x86_64-3.6/biom copying biom/init.py -> build/lib.linux-x86_64-3.6/biom creating build/lib.linux-x86_64-3.6/biom/tests copying biom/tests/test_table.py -> build/lib.linux-x86_64-3.6/biom/tests copying biom/tests/test_util.py -> build/lib.linux-x86_64-3.6/biom/tests copying biom/tests/test_parse.py -> build/lib.linux-x86_64-3.6/biom/tests copying biom/tests/init.py -> build/lib.linux-x86_64-3.6/biom/tests copying biom/tests/long_lines.py -> build/lib.linux-x86_64-3.6/biom/tests copying biom/tests/test_err.py -> build/lib.linux-x86_64-3.6/biom/tests creating build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_converter.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/installation_informer.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_validator.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_head.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/util.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/metadata_exporter.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/uc_processor.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_ids.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/metadata_adder.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/init.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_normalizer.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_subsetter.py -> build/lib.linux-x86_64-3.6/biom/cli copying biom/cli/table_summarizer.py -> build/lib.linux-x86_64-3.6/biom/cli creating build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/init.py -> build/lib.linux-x86_64-3.6/biom/tests/test_data creating build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_table_converter.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_add_metadata.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_summarize_table.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_table_normalizer.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_validate_table.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_uc_processor.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/init.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_show_install_info.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli copying biom/tests/test_cli/test_subset_table.py -> build/lib.linux-x86_64-3.6/biom/tests/test_cli running egg_info writing biom_format.egg-info/PKG-INFO writing dependency_links to biom_format.egg-info/dependency_links.txt writing entry points to biom_format.egg-info/entry_points.txt writing requirements to biom_format.egg-info/requires.txt writing top-level names to biom_format.egg-info/top_level.txt reading manifest file 'biom_format.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no directories found matching 'support_files' warning: no directories found matching 'tests/test_data' no previously-included directories found matching 'docs/_build' warning: no previously-included files matching '.pyc' found anywhere in distribution warning: no previously-included files matching '.pyo' found anywhere in distribution warning: no previously-included files matching '.git' found anywhere in distribution warning: no previously-included files matching '.so' found anywhere in distribution warning: no previously-included files matching '..swp' found anywhere in distribution adding license file 'COPYING.txt' writing manifest file 'biom_format.egg-info/SOURCES.txt' copying biom/_filter.pyx -> build/lib.linux-x86_64-3.6/biom copying biom/_subsample.pyx -> build/lib.linux-x86_64-3.6/biom copying biom/_transform.pyx -> build/lib.linux-x86_64-3.6/biom creating build/lib.linux-x86_64-3.6/biom/assets copying biom/assets/exercise_api.py -> build/lib.linux-x86_64-3.6/biom/assets copying biom/assets/exercise_cli.sh -> build/lib.linux-x86_64-3.6/biom/assets creating build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/1000x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/100x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x1000x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x100x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.001_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.010_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/bench_tables/10x10x0.100_bench_hdf5.biom.gz -> build/lib.linux-x86_64-3.6/biom/tests/bench_tables copying biom/tests/test_data/bad_table.txt -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/bad_table.txt.gz -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/empty.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/no-contents.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/test.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/test.json -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/test.json.gz -> build/lib.linux-x86_64-3.6/biom/tests/test_data copying biom/tests/test_data/test_grp_metadata.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_data creating build/lib.linux-x86_64-3.6/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_obs_collapsed.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/json_sample_collapsed.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.biom -> build/lib.linux-x86_64-3.6/biom/tests/test_cli/test_data copying biom/tests/test_cli/test_data/test.json -> build/lib.linux-x86_64-3.6/biom/tests/test_cli/test_data running build_ext building 'biom._filter' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/biom gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/tmp/pip-build-env-_eai_mkp/overlay/lib64/python3.6/site-packages/numpy/core/include -I/tmp/pip-build-env-_eai_mkp/overlay/lib64/python3.6/site-packages/numpy/core/include -I/opt/jupyterhub/include -I/usr/include/python3.6m -c biom/_filter.c -o build/temp.linux-x86_64-3.6/biom/_filter.o biom/_filter.c:38:20: fatal error: Python.h: No such file or directory

include "Python.h"

                  ^

compilation terminated. error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for biom-format Building wheel for scikit-bio (setup.py) ... error ERROR: Command errored out with exit status 1: command: /opt/jupyterhub/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u7nx04ro/scikit-bio_dfe3954c420a4a6db6697075215a11b5/setup.py'"'"'; file='"'"'/tmp/pip-install-u7nx04ro/scikit-bio_dfe3954c420a4a6db6697075215a11b5/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 /tmp/pip-wheel-fb5srevz cwd: /tmp/pip-install-u7nx04ro/scikit-bio_dfe3954c420a4a6db6697075215a11b5/ Complete output (602 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/skbio copying skbio/test.py -> build/lib.linux-x86_64-3.6/skbio copying skbio/workflow.py -> build/lib.linux-x86_64-3.6/skbio copying skbio/_base.py -> build/lib.linux-x86_64-3.6/skbio copying skbio/init.py -> build/lib.linux-x86_64-3.6/skbio creating build/lib.linux-x86_64-3.6/benchmarks copying benchmarks/benchmarks.py -> build/lib.linux-x86_64-3.6/benchmarks copying benchmarks/init.py -> build/lib.linux-x86_64-3.6/benchmarks creating build/lib.linux-x86_64-3.6/skbio/stats copying skbio/stats/_subsample.py -> build/lib.linux-x86_64-3.6/skbio/stats copying skbio/stats/power.py -> build/lib.linux-x86_64-3.6/skbio/stats copying skbio/stats/composition.py -> build/lib.linux-x86_64-3.6/skbio/stats copying skbio/stats/_misc.py -> build/lib.linux-x86_64-3.6/skbio/stats copying skbio/stats/init.py -> build/lib.linux-x86_64-3.6/skbio/stats copying skbio/stats/gradient.py -> build/lib.linux-x86_64-3.6/skbio/stats creating build/lib.linux-x86_64-3.6/skbio/tests copying skbio/tests/test_workflow.py -> build/lib.linux-x86_64-3.6/skbio/tests copying skbio/tests/test_base.py -> build/lib.linux-x86_64-3.6/skbio/tests copying skbio/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/tests creating build/lib.linux-x86_64-3.6/skbio/tree copying skbio/tree/_exception.py -> build/lib.linux-x86_64-3.6/skbio/tree copying skbio/tree/_nj.py -> build/lib.linux-x86_64-3.6/skbio/tree copying skbio/tree/_majority_rule.py -> build/lib.linux-x86_64-3.6/skbio/tree copying skbio/tree/init.py -> build/lib.linux-x86_64-3.6/skbio/tree copying skbio/tree/_tree.py -> build/lib.linux-x86_64-3.6/skbio/tree creating build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/_testing.py -> build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/_exception.py -> build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/_decorator.py -> build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/_warning.py -> build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/_misc.py -> build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/init.py -> build/lib.linux-x86_64-3.6/skbio/util copying skbio/util/_metadata_repr.py -> build/lib.linux-x86_64-3.6/skbio/util creating build/lib.linux-x86_64-3.6/skbio/diversity copying skbio/diversity/_driver.py -> build/lib.linux-x86_64-3.6/skbio/diversity copying skbio/diversity/_util.py -> build/lib.linux-x86_64-3.6/skbio/diversity copying skbio/diversity/init.py -> build/lib.linux-x86_64-3.6/skbio/diversity creating build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/distance.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_nucleotide_mixin.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_repr.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_genetic_code.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_sequence.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_dna.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/init.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_grammared_sequence.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_protein.py -> build/lib.linux-x86_64-3.6/skbio/sequence copying skbio/sequence/_rna.py -> build/lib.linux-x86_64-3.6/skbio/sequence creating build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/_exception.py -> build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/_fileobject.py -> build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/util.py -> build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/_warning.py -> build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/init.py -> build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/registry.py -> build/lib.linux-x86_64-3.6/skbio/io copying skbio/io/_iosources.py -> build/lib.linux-x86_64-3.6/skbio/io creating build/lib.linux-x86_64-3.6/skbio/alignment copying skbio/alignment/_repr.py -> build/lib.linux-x86_64-3.6/skbio/alignment copying skbio/alignment/_tabular_msa.py -> build/lib.linux-x86_64-3.6/skbio/alignment copying skbio/alignment/_indexing.py -> build/lib.linux-x86_64-3.6/skbio/alignment copying skbio/alignment/_pairwise.py -> build/lib.linux-x86_64-3.6/skbio/alignment copying skbio/alignment/init.py -> build/lib.linux-x86_64-3.6/skbio/alignment creating build/lib.linux-x86_64-3.6/skbio/stats/ordination copying skbio/stats/ordination/_utils.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination copying skbio/stats/ordination/_correspondence_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination copying skbio/stats/ordination/_principal_coordinate_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination copying skbio/stats/ordination/_canonical_correspondence_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination copying skbio/stats/ordination/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination copying skbio/stats/ordination/_redundancy_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination creating build/lib.linux-x86_64-3.6/skbio/stats/tests copying skbio/stats/tests/test_gradient.py -> build/lib.linux-x86_64-3.6/skbio/stats/tests copying skbio/stats/tests/test_composition.py -> build/lib.linux-x86_64-3.6/skbio/stats/tests copying skbio/stats/tests/test_subsample.py -> build/lib.linux-x86_64-3.6/skbio/stats/tests copying skbio/stats/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/tests copying skbio/stats/tests/test_misc.py -> build/lib.linux-x86_64-3.6/skbio/stats/tests copying skbio/stats/tests/test_power.py -> build/lib.linux-x86_64-3.6/skbio/stats/tests creating build/lib.linux-x86_64-3.6/skbio/stats/evolve copying skbio/stats/evolve/_hommola.py -> build/lib.linux-x86_64-3.6/skbio/stats/evolve copying skbio/stats/evolve/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/evolve creating build/lib.linux-x86_64-3.6/skbio/stats/distance copying skbio/stats/distance/_anosim.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance copying skbio/stats/distance/_mantel.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance copying skbio/stats/distance/_bioenv.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance copying skbio/stats/distance/_base.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance copying skbio/stats/distance/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance copying skbio/stats/distance/_permanova.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance creating build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_redundancy_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_util.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_correspondence_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/test_principal_coordinate_analysis.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests copying skbio/stats/ordination/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests creating build/lib.linux-x86_64-3.6/skbio/stats/evolve/tests copying skbio/stats/evolve/tests/test_hommola.py -> build/lib.linux-x86_64-3.6/skbio/stats/evolve/tests copying skbio/stats/evolve/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/evolve/tests creating build/lib.linux-x86_64-3.6/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_anosim.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_base.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_mantel.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_permanova.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests copying skbio/stats/distance/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests copying skbio/stats/distance/tests/test_bioenv.py -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests creating build/lib.linux-x86_64-3.6/skbio/tree/tests copying skbio/tree/tests/test_majority_rule.py -> build/lib.linux-x86_64-3.6/skbio/tree/tests copying skbio/tree/tests/test_nj.py -> build/lib.linux-x86_64-3.6/skbio/tree/tests copying skbio/tree/tests/test_tree.py -> build/lib.linux-x86_64-3.6/skbio/tree/tests copying skbio/tree/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/tree/tests creating build/lib.linux-x86_64-3.6/skbio/util/tests copying skbio/util/tests/test_testing.py -> build/lib.linux-x86_64-3.6/skbio/util/tests copying skbio/util/tests/test_decorator.py -> build/lib.linux-x86_64-3.6/skbio/util/tests copying skbio/util/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/util/tests copying skbio/util/tests/test_misc.py -> build/lib.linux-x86_64-3.6/skbio/util/tests creating build/lib.linux-x86_64-3.6/skbio/diversity/beta copying skbio/diversity/beta/_unifrac.py -> build/lib.linux-x86_64-3.6/skbio/diversity/beta copying skbio/diversity/beta/init.py -> build/lib.linux-x86_64-3.6/skbio/diversity/beta creating build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/_chao1.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/_gini.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/_lladser.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/_base.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/_ace.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/_faith_pd.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha copying skbio/diversity/alpha/init.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha creating build/lib.linux-x86_64-3.6/skbio/diversity/tests copying skbio/diversity/tests/test_util.py -> build/lib.linux-x86_64-3.6/skbio/diversity/tests copying skbio/diversity/tests/test_driver.py -> build/lib.linux-x86_64-3.6/skbio/diversity/tests copying skbio/diversity/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/diversity/tests creating build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests copying skbio/diversity/beta/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests copying skbio/diversity/beta/tests/test_unifrac.py -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests creating build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_faith_pd.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_gini.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_base.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_lladser.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_chao1.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/test_ace.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests copying skbio/diversity/alpha/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests creating build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_nucleotide_sequences.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_rna.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_sequence.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_genetic_code.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_protein.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_distance.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_dna.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests copying skbio/sequence/tests/test_grammared_sequence.py -> build/lib.linux-x86_64-3.6/skbio/sequence/tests creating build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/stockholm.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/fastq.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/clustal.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/blast6.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/qseq.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/emptyfile.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/fasta.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/_base.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/blast7.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/phylip.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/init.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/ordination.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/lsmat.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/_blast.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/genbank.py -> build/lib.linux-x86_64-3.6/skbio/io/format copying skbio/io/format/newick.py -> build/lib.linux-x86_64-3.6/skbio/io/format creating build/lib.linux-x86_64-3.6/skbio/io/tests copying skbio/io/tests/test_util.py -> build/lib.linux-x86_64-3.6/skbio/io/tests copying skbio/io/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/io/tests copying skbio/io/tests/test_registry.py -> build/lib.linux-x86_64-3.6/skbio/io/tests copying skbio/io/tests/test_iosources.py -> build/lib.linux-x86_64-3.6/skbio/io/tests creating build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_qseq.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_fastq.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_phylip.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_blast6.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_newick.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_stockholm.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_genbank.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_base.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_emptyfile.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_clustal.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_lsmat.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_fasta.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_ordination.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests copying skbio/io/format/tests/test_blast7.py -> build/lib.linux-x86_64-3.6/skbio/io/format/tests creating build/lib.linux-x86_64-3.6/skbio/alignment/tests copying skbio/alignment/tests/test_tabular_msa.py -> build/lib.linux-x86_64-3.6/skbio/alignment/tests copying skbio/alignment/tests/test_pairwise.py -> build/lib.linux-x86_64-3.6/skbio/alignment/tests copying skbio/alignment/tests/test_ssw.py -> build/lib.linux-x86_64-3.6/skbio/alignment/tests copying skbio/alignment/tests/init.py -> build/lib.linux-x86_64-3.6/skbio/alignment/tests creating build/lib.linux-x86_64-3.6/skbio/alignment/_lib copying skbio/alignment/_lib/init.py -> build/lib.linux-x86_64-3.6/skbio/alignment/_lib creating build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/cr_data_out -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/cr_no_data_out -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/cr_data_raw -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/gr_w_msg_out -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/vr_real_raw -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/vr_out -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/gr_wo_msg_raw -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/gr_w_msg_raw -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/cr_no_data_raw -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/vr_raw -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/gr_wo_msg_out -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data copying skbio/stats/tests/data/vr_real_out -> build/lib.linux-x86_64-3.6/skbio/stats/tests/data creating build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_site_scaling1_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_species_scaling2_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_site_scaling1_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling1 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_species_scaling1_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_Y -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_site_scaling2_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling1 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_biplot_scaling1 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_site_scaling2_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_biplot_scaling1 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_3 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_X -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/exp_PCoAEigenResults_site -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_sample_constraints_scaling2 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_species_scaling2_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_biplot_scaling2 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_biplot_scaling2 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/PCoA_sample_data_2 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/L&L_CA_data -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_X -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_sample_constraints_scaling2 -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example3_species_scaling1_from_vegan -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/example2_Y -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data copying skbio/stats/ordination/tests/data/exp_PCoAzeros_site -> build/lib.linux-x86_64-3.6/skbio/stats/ordination/tests/data creating build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/mantel_env_dm_vegan.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm4.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/df_extra_column.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_dm_vegan.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_reordered_distance_matrices.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/mantel_veg_dm_vegan.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal_with_labels.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_na_p_value.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results_single_column.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_all_dms.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm2.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_minimal.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/exp_results_different_column_order.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/df.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm_reordered.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_exp_results_vegan.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm3.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_duplicate_dms.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/dm.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/pwmantel_exp_results_dm_dm2.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data copying skbio/stats/distance/tests/data/bioenv_df_vegan.txt -> build/lib.linux-x86_64-3.6/skbio/stats/distance/tests/data creating build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data creating build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/tree.nwk -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/unweighted_unifrac_dm.txt -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/otu-table.tsv -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/weighted_unifrac_dm.txt -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/weighted_normalized_unifrac_dm.txt -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt copying skbio/diversity/beta/tests/data/qiime-191-tt/README.md -> build/lib.linux-x86_64-3.6/skbio/diversity/beta/tests/data/qiime-191-tt creating build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests/data creating build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/tree.nwk -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/otu-table.tsv -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/faith-pd.txt -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests/data/qiime-191-tt copying skbio/diversity/alpha/tests/data/qiime-191-tt/README.md -> build/lib.linux-x86_64-3.6/skbio/diversity/alpha/tests/data/qiime-191-tt creating build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/big5_file -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/big5_file.bz2 -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/example_file.gz -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/example_file -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/big5_file.gz -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/real_file -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/example_file.bz2 -> build/lib.linux-x86_64-3.6/skbio/io/tests/data copying skbio/io/tests/data/real_file_2 -> build/lib.linux-x86_64-3.6/skbio/io/tests/data creating build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_multi_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error11 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_escape.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_header_too_long -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_5_ws_lines_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_column_types -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_empty_str -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_3_seqs_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_gc_data_length -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_missing_locus_name -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_single_seq_sanger -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_illumina1.3_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_6_ws_lines_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/empty -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_rna_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error20 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_all_data_types -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_sanger_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_line_within_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_end_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_filter -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site_constraints -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_long -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_none -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error5 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_string -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_mixed_nans -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_between_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_gibberish -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_seq_data -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_before_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error4 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_mixed_qual_scores -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_vtab.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_default_single_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_within_qual -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_prot_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error18 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_title.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_seq_too_long -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gr_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_gr_data_length -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_for_sniffer_2 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_nuc_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_length_mismatch -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_invalid_differing_fields -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error9 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_6_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_last -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_6_ws_lines_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_rna_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_between_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_nonstring_labels -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_multi_char -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_6_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_max_width_5 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_multi_char -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_tabular_msa_different_type -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_single_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_end_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_rna -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_5_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_plus -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_1 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_whitespace_only_lines -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_original_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_dna_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_dna_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_multi_seq_illumina1.3 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_sequence -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_extra -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_line_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_6_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_species -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blank_lines_between_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_nonexistent_gs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_no_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_zero_seq_len -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_metadata_only -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_zero_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_2 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_2_seqs_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error23 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error19 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_negative -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_minimal -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_after_10_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_multi_seq_roundtrip -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error3 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_ws_line_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_seq.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_dna_seq_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_gr -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error1 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_tab.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_end_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_data_only -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_as_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error12 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_blank_line_within_sequence -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_middle -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_multi_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gf_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_line_within_sequence -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_tabular_msa_different_type -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_nonexistent_gr -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record_lower -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_single_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_blank_sequence -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_unrecognized_field -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_1 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_first -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_differing_fields -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_8_fields -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site_constraints -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error13 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_original_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/solexa_full_range_original_solexa.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example2_scores -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_prot_seqs_odd_labels -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_sequence_names -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_as_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/whitespace_only -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_plus.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_species -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_in_qual.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_multi_char -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_none -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_tile -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_id_mismatch -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_data_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_original_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_multi_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_single_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error8 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_as_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_missing_footer -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_tabs.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_multi_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_lane -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_rna_original_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_example3_scores -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_minimal -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_id_whitespace_replacement_multi_char -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_none -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/misc_dna_as_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error15 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error16 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/wrapping_as_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_spaces.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error22 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_blank_lines_between_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_double_seq.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_none -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_only_sequence -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_mixed_nans -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_blanks_end_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_many_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_end_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_w_beginning_whitespace -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_prot_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_differing_seq_lengths -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_extensive_mixed -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_gc -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_CCA_site -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_read -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_L&L_CA_data_scores -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_after_plus -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_no_qual.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/sanger_full_range_as_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_varied_whitespace_in_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_10_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_single_seq_short -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_PCoA_sample_data_3_scores -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_bio_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_empty_line_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_middle -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_runon_gf -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_double_qual.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_seq.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_max_width_5 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_prot_seqs_odd_labels -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gc_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_space.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_null.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_original_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error7 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_invalid_data_type -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_missing_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_blanks_end_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_float -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_5_blanks_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error24 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_type_in_column -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_whitespace_in_header_3 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_trees -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_without_id -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_for_sniffer -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_ws_lines_between_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_description_newline_replacement_empty_str -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_RDA_site -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_no_data -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_blank_lines -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_legacy_format -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_custom_multi_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_multiple_msa -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error17 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_two_of_each_metadata -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_two_chunks -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_original_sanger_no_description -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_plus.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_header_too_short -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_seq_data_last -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_multi_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_malformed_gs_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_single_tree_with_id -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_too_few_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_no_data -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/genbank_single_record_upper -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_qual_scores_over_255 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_missing_qual_scores_first -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_between_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_missing_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_multi_seq_roundtrip -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_max_width_1 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_y -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error10 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_unit_sep.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_description_newline_replacement_empty_str -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_qual_del.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_and_blast7_default -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_ws_lines_between_records -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_invalid_number_of_columns -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error21 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_ws_line_within_qual -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_id_whitespace_replacement_empty_str -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_whitespace_stripping -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_original_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_3_seqs_defaults_desc_mismatch -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error2 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_illumina_no_description -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/legacy9_invalid_too_many_columns -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error14 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_exp_Ordination_PCoA_site -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_3_seqs_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_bio_seq_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_trunc_at_qual.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_single_seq_illumina1.3 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_5_ws_lines_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_invalid_whitespace_line_in_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_short_qual.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qual_single_bio_seq_non_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_only_sequence -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_invalid_seq_too_short -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/ordination_error6 -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_prot_seq_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/illumina_full_range_as_illumina.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_legacy_format -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_mixed_nans -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_within_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_blank_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_whitespace_only_lines -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_after_seq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_duplicate_tree_ids -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_invalid_blank_in_seq_at_symbol -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/tsv_10_fields -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_single_rna_seq_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_long_qual.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/qseq_invalid_x -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_invalid_too_many_columns -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_variable_length_ids -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/longreads_as_sanger.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_seq_sanger -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fasta_invalid_whitespace_line_after_header -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_5_ws_lines_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_wrapping_as_sanger_no_description -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/phylip_dna_3_seqs -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/error_diff_ids.fastq -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_writer_sanger_defaults -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/fastq_multi_ws_lines_start_of_file -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/stockholm_blank_lines -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast7_default_single_line -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data copying skbio/io/format/tests/data/blast6_custom_minimal -> build/lib.linux-x86_64-3.6/skbio/io/format/tests/data running build_ext building 'skbio.stats.subsample' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/skbio creating build/temp.linux-x86_64-3.6/skbio/stats gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/opt/jupyterhub/include -I/usr/include/python3.6m -I/tmp/pip-install-u7nx04ro/scikit-bio_dfe3954c420a4a6db6697075215a11b5/.eggs/numpy-1.19.5-py3.6-linux-x86_64.egg/numpy/core/include -c skbio/stats/__subsample.c -o build/temp.linux-x86_64-3.6/skbio/stats/subsample.o skbio/stats/__subsample.c:12:20: fatal error: Python.h: No such file or directory

include "Python.h"

                  ^

compilation terminated. error: command 'gcc' failed with exit status 1

ERROR: Failed building wheel for scikit-bio Running setup.py clean for scikit-bio Successfully built sourcetracker Failed to build biom-format scikit-bio ERROR: Could not build wheels for biom-format which use PEP 517 and cannot be installed directly WARNING: You are using pip version 21.1.1; however, version 21.3.1 is available. You should consider upgrading via the '/opt/jupyterhub/bin/python3 -m pip install --upgrade pip' command.

wasade commented 1 year ago

What command was run to generate this?

joycelyny commented 1 year ago

pip install q2-mislabeled

wasade commented 1 year ago

Thanks. This does assume the installation is occurring within a QIIME 2 environment, is that the case and if so what version of QIIME 2?

joycelyny commented 1 year ago

(qiime2-2022.11) bash-4.2$ qiime info System versions Python version: 3.8.15 QIIME 2 release: 2022.11 QIIME 2 version: 2022.11.1 q2cli version: 2022.11.1

Installed plugins alignment: 2022.11.1 composition: 2022.11.2 cutadapt: 2022.11.1 dada2: 2022.11.2 deblur: 2022.11.1 deicode: 0.2.4 demux: 2022.11.1 diversity: 2022.11.1 diversity-lib: 2022.11.1 emperor: 2022.11.1 empress: 1.2.0 feature-classifier: 2022.11.1 feature-table: 2022.11.1 fragment-insertion: 2022.11.1 gemelli: 0.0.9 gneiss: 2022.11.1 longitudinal: 2022.11.1 metadata: 2022.11.1 phylogeny: 2022.11.1 quality-control: 2022.11.1 quality-filter: 2022.11.1 qurro: 0.8.0 sample-classifier: 2022.11.1 sourcetracker2: 2.0.1-dev taxa: 2022.11.1 types: 2022.11.1 vsearch: 2022.11.1

wasade commented 1 year ago

and pip was run while that environment was active? That is odd. If yes, can you send the output of which conda, which pip and which qiime?

joycelyny commented 1 year ago

yes, here is the output:

(qiime2-2022.11) bash-4.2$ which conda /bin/conda (qiime2-2022.11) bash-4.2$ which pip /opt/jupyterhub/bin/pip (qiime2-2022.11) bash-4.2$ which qiime ~/miniconda3/envs/qiime2-2022.11/bin/qiime

wasade commented 1 year ago

The conda program doesn't correspond to your miniconda3 directory, same with pip, which is unusual. Are you able to install anything with pip and conda?

joycelyny commented 1 year ago

I run into permission errors for pip install, and have not tried conda install. I could try redirecting pip and conda to within the miniconda3 directory?

wasade commented 1 year ago

Ya i recommend using the install of pip associated with the environment

On Mon, Nov 6, 2023, 14:19 joycelyny @.***> wrote:

I run into permission errors for pip install, and have not tried conda install. I could try redirecting pip and conda to within the miniconda3 directory?

— Reply to this email directly, view it on GitHub https://github.com/biocore/q2-mislabeled/issues/2#issuecomment-1796859738, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADTZMU5RZ3MB7QSYIMBMK3YDFO5ZAVCNFSM6AAAAAA7ABTESKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJWHA2TSNZTHA . You are receiving this because you commented.Message ID: @.***>

joycelyny commented 1 year ago

It's working for me now, thanks for all the help!

wasade commented 1 year ago

Great, thanks!