2024-10-15T14:47:37,718 Created temporary directory: /tmp/pip-build-tracker-_6p8gt6d
2024-10-15T14:47:37,719 Initialized build tracking at /tmp/pip-build-tracker-_6p8gt6d
2024-10-15T14:47:37,720 Created build tracker: /tmp/pip-build-tracker-_6p8gt6d
2024-10-15T14:47:37,720 Entered build tracker: /tmp/pip-build-tracker-_6p8gt6d
2024-10-15T14:47:37,721 Created temporary directory: /tmp/pip-wheel-fc6372ic
2024-10-15T14:47:37,725 Created temporary directory: /tmp/pip-ephem-wheel-cache-dugmvntt
2024-10-15T14:47:37,768 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-10-15T14:47:37,771 2 location(s) to search for versions of streamd:
2024-10-15T14:47:37,771 * https://pypi.org/simple/streamd/
2024-10-15T14:47:37,771 * https://www.piwheels.org/simple/streamd/
2024-10-15T14:47:37,771 Fetching project page and analyzing links: https://pypi.org/simple/streamd/
2024-10-15T14:47:37,772 Getting page https://pypi.org/simple/streamd/
2024-10-15T14:47:37,774 Found index url https://pypi.org/simple/
2024-10-15T14:47:37,994 Fetched page https://pypi.org/simple/streamd/ as application/vnd.pypi.simple.v1+json
2024-10-15T14:47:37,996   Found link https://files.pythonhosted.org/packages/8d/96/dd06d3cfc2b8f66a791d39120d88fc8a735168ebc8ff7e5638850a02bdb7/streamd-0.2.4.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.4
2024-10-15T14:47:37,997   Found link https://files.pythonhosted.org/packages/3c/33/e67ff9cffede4a4390020db9ba6f6823898845e3c8bba06b3b5ff85c9c70/streamd-0.2.5.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.5
2024-10-15T14:47:37,998   Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/44/4e/ff6c13b62f53b4037ae42649009dce5a32b8ac0ad0eac5eec3df5cfbb557/streamd-0.2.6-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6)
2024-10-15T14:47:37,999   Found link https://files.pythonhosted.org/packages/72/53/dc71d524afdcfe34821f994e1affe793bbc44b984a73134cdea2ef641300/streamd-0.2.6.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.6
2024-10-15T14:47:38,000   Skipping link: No binaries permitted for streamd: https://files.pythonhosted.org/packages/4f/10/22028ea2fffc91921a979a6e5ac95b1f2b490e16abb5942b8ed978990ef7/streamd-0.2.7-py3-none-any.whl (from https://pypi.org/simple/streamd/) (requires-python:>=3.6)
2024-10-15T14:47:38,001   Found link https://files.pythonhosted.org/packages/0f/8e/371666f0b05ae834174fb94cf0f7bd3871c13f87754cb346c767547c4fd6/streamd-0.2.7.tar.gz (from https://pypi.org/simple/streamd/) (requires-python:>=3.6), version: 0.2.7
2024-10-15T14:47:38,002 Fetching project page and analyzing links: https://www.piwheels.org/simple/streamd/
2024-10-15T14:47:38,003 Getting page https://www.piwheels.org/simple/streamd/
2024-10-15T14:47:38,004 Found index url https://www.piwheels.org/simple/
2024-10-15T14:47:38,180 Fetched page https://www.piwheels.org/simple/streamd/ as text/html
2024-10-15T14:47:38,182   Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.6-py3-none-any.whl#sha256=f7888c07d9836354ded91c5e344bbb7b1d4552d11e37e32321cde4b50262a040 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6)
2024-10-15T14:47:38,183   Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.5-py3-none-any.whl#sha256=23e92bac46dff5622fbf91e611c2277c5c87967d2a26965933d6f33e03b63818 (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6)
2024-10-15T14:47:38,184   Skipping link: No binaries permitted for streamd: https://www.piwheels.org/simple/streamd/streamd-0.2.4-py3-none-any.whl#sha256=411cca8c59b01f0e7b8e18520e025a61e135cc2a6db0f374d2d5b80b171dbb2e (from https://www.piwheels.org/simple/streamd/) (requires-python:>=3.6)
2024-10-15T14:47:38,185 Skipping link: not a file: https://www.piwheels.org/simple/streamd/
2024-10-15T14:47:38,186 Skipping link: not a file: https://pypi.org/simple/streamd/
2024-10-15T14:47:38,206 Given no hashes to check 1 links for project 'streamd': discarding no candidates
2024-10-15T14:47:38,208 Collecting streamd==0.2.7
2024-10-15T14:47:38,212   Created temporary directory: /tmp/pip-unpack-nvc_9urh
2024-10-15T14:47:38,434   Downloading streamd-0.2.7.tar.gz (161 kB)
2024-10-15T14:47:38,646   Added streamd==0.2.7 from https://files.pythonhosted.org/packages/0f/8e/371666f0b05ae834174fb94cf0f7bd3871c13f87754cb346c767547c4fd6/streamd-0.2.7.tar.gz to build tracker '/tmp/pip-build-tracker-_6p8gt6d'
2024-10-15T14:47:38,648   Running setup.py (path:/tmp/pip-wheel-fc6372ic/streamd_29ed48542b4747f3b0ca1731bffe2845/setup.py) egg_info for package streamd
2024-10-15T14:47:38,649   Created temporary directory: /tmp/pip-pip-egg-info-fvt7pk3z
2024-10-15T14:47:38,649   Preparing metadata (setup.py): started
2024-10-15T14:47:38,651   Running command python setup.py egg_info
2024-10-15T14:47:39,747   running egg_info
2024-10-15T14:47:39,749   creating /tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info
2024-10-15T14:47:39,776   writing /tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/PKG-INFO
2024-10-15T14:47:39,781   writing dependency_links to /tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/dependency_links.txt
2024-10-15T14:47:39,782   writing entry points to /tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/entry_points.txt
2024-10-15T14:47:39,784   writing requirements to /tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/requires.txt
2024-10-15T14:47:39,785   writing top-level names to /tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/top_level.txt
2024-10-15T14:47:39,786   writing manifest file '/tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/SOURCES.txt'
2024-10-15T14:47:39,881   reading manifest file '/tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/SOURCES.txt'
2024-10-15T14:47:39,883   reading manifest template 'MANIFEST.in'
2024-10-15T14:47:39,889   adding license file 'LICENSE.txt'
2024-10-15T14:47:39,893   writing manifest file '/tmp/pip-pip-egg-info-fvt7pk3z/streamd.egg-info/SOURCES.txt'
2024-10-15T14:47:40,001   Preparing metadata (setup.py): finished with status 'done'
2024-10-15T14:47:40,007   Source in /tmp/pip-wheel-fc6372ic/streamd_29ed48542b4747f3b0ca1731bffe2845 has version 0.2.7, which satisfies requirement streamd==0.2.7 from https://files.pythonhosted.org/packages/0f/8e/371666f0b05ae834174fb94cf0f7bd3871c13f87754cb346c767547c4fd6/streamd-0.2.7.tar.gz
2024-10-15T14:47:40,008   Removed streamd==0.2.7 from https://files.pythonhosted.org/packages/0f/8e/371666f0b05ae834174fb94cf0f7bd3871c13f87754cb346c767547c4fd6/streamd-0.2.7.tar.gz from build tracker '/tmp/pip-build-tracker-_6p8gt6d'
2024-10-15T14:47:40,016 Created temporary directory: /tmp/pip-unpack-5qi4_9j1
2024-10-15T14:47:40,018 Created temporary directory: /tmp/pip-unpack-4_12wp6s
2024-10-15T14:47:40,018 Building wheels for collected packages: streamd
2024-10-15T14:47:40,022   Created temporary directory: /tmp/pip-wheel-xjfo6kys
2024-10-15T14:47:40,023   Building wheel for streamd (setup.py): started
2024-10-15T14:47:40,024   Destination directory: /tmp/pip-wheel-xjfo6kys
2024-10-15T14:47:40,025   Running command python setup.py bdist_wheel
2024-10-15T14:47:41,057   running bdist_wheel
2024-10-15T14:47:41,190   running build
2024-10-15T14:47:41,190   running build_py
2024-10-15T14:47:41,221   creating build/lib/streamd
2024-10-15T14:47:41,223   copying streamd/run_gbsa.py -> build/lib/streamd
2024-10-15T14:47:41,226   copying streamd/__init__.py -> build/lib/streamd
2024-10-15T14:47:41,228   copying streamd/run_md.py -> build/lib/streamd
2024-10-15T14:47:41,231   creating build/lib/streamd/mcpbpy_md
2024-10-15T14:47:41,233   copying streamd/mcpbpy_md/mcbpy_md.py -> build/lib/streamd/mcpbpy_md
2024-10-15T14:47:41,235   copying streamd/mcpbpy_md/__init__.py -> build/lib/streamd/mcpbpy_md
2024-10-15T14:47:41,238   creating build/lib/streamd/prolif
2024-10-15T14:47:41,239   copying streamd/prolif/run_prolif.py -> build/lib/streamd/prolif
2024-10-15T14:47:41,241   copying streamd/prolif/prolif2png.py -> build/lib/streamd/prolif
2024-10-15T14:47:41,244   copying streamd/prolif/__init__.py -> build/lib/streamd/prolif
2024-10-15T14:47:41,246   copying streamd/prolif/prolif_frame_map.py -> build/lib/streamd/prolif
2024-10-15T14:47:41,248   creating build/lib/streamd/analysis
2024-10-15T14:47:41,249   copying streamd/analysis/plot_build.py -> build/lib/streamd/analysis
2024-10-15T14:47:41,252   copying streamd/analysis/md_system_analysis.py -> build/lib/streamd/analysis
2024-10-15T14:47:41,254   copying streamd/analysis/xvg2png.py -> build/lib/streamd/analysis
2024-10-15T14:47:41,256   copying streamd/analysis/__init__.py -> build/lib/streamd/analysis
2024-10-15T14:47:41,257   copying streamd/analysis/run_analysis.py -> build/lib/streamd/analysis
2024-10-15T14:47:41,260   creating build/lib/streamd/preparation
2024-10-15T14:47:41,264   copying streamd/preparation/ligand_preparation.py -> build/lib/streamd/preparation
2024-10-15T14:47:41,266   copying streamd/preparation/mcpbpy_preparation.py -> build/lib/streamd/preparation
2024-10-15T14:47:41,269   copying streamd/preparation/__init__.py -> build/lib/streamd/preparation
2024-10-15T14:47:41,270   copying streamd/preparation/complex_preparation.py -> build/lib/streamd/preparation
2024-10-15T14:47:41,273   copying streamd/preparation/md_files_preparation.py -> build/lib/streamd/preparation
2024-10-15T14:47:41,275   creating build/lib/streamd/utils
2024-10-15T14:47:41,276   copying streamd/utils/dask_init.py -> build/lib/streamd/utils
2024-10-15T14:47:41,278   copying streamd/utils/__init__.py -> build/lib/streamd/utils
2024-10-15T14:47:41,280   copying streamd/utils/utils.py -> build/lib/streamd/utils
2024-10-15T14:47:41,282   creating build/lib/streamd/scripts
2024-10-15T14:47:41,284   copying streamd/scripts/prepare_Gaussian_input.py -> build/lib/streamd/scripts
2024-10-15T14:47:41,286   copying streamd/scripts/__init__.py -> build/lib/streamd/scripts
2024-10-15T14:47:41,287   copying streamd/scripts/pmed_amb2gmx.py -> build/lib/streamd/scripts
2024-10-15T14:47:41,289   copying streamd/scripts/mol2_fix_coordsbonds.py -> build/lib/streamd/scripts
2024-10-15T14:47:41,291   copying streamd/scripts/pdb2mol.py -> build/lib/streamd/scripts
2024-10-15T14:47:41,293   copying streamd/scripts/getcharge.py -> build/lib/streamd/scripts
2024-10-15T14:47:41,295   running egg_info
2024-10-15T14:47:41,323   writing streamd.egg-info/PKG-INFO
2024-10-15T14:47:41,327   writing dependency_links to streamd.egg-info/dependency_links.txt
2024-10-15T14:47:41,329   writing entry points to streamd.egg-info/entry_points.txt
2024-10-15T14:47:41,331   writing requirements to streamd.egg-info/requires.txt
2024-10-15T14:47:41,332   writing top-level names to streamd.egg-info/top_level.txt
2024-10-15T14:47:41,367   reading manifest file 'streamd.egg-info/SOURCES.txt'
2024-10-15T14:47:41,375   reading manifest template 'MANIFEST.in'
2024-10-15T14:47:41,378   adding license file 'LICENSE.txt'
2024-10-15T14:47:41,383   writing manifest file 'streamd.egg-info/SOURCES.txt'
2024-10-15T14:47:41,385   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'streamd.example' is absent from the `packages` configuration.
2024-10-15T14:47:41,386   !!

2024-10-15T14:47:41,387           ********************************************************************************
2024-10-15T14:47:41,387           ############################
2024-10-15T14:47:41,388           # Package would be ignored #
2024-10-15T14:47:41,388           ############################
2024-10-15T14:47:41,389           Python recognizes 'streamd.example' as an importable package[^1],
2024-10-15T14:47:41,390           but it is absent from setuptools' `packages` configuration.

2024-10-15T14:47:41,391           This leads to an ambiguous overall configuration. If you want to distribute this
2024-10-15T14:47:41,391           package, please make sure that 'streamd.example' is explicitly added
2024-10-15T14:47:41,392           to the `packages` configuration field.

2024-10-15T14:47:41,393           Alternatively, you can also rely on setuptools' discovery methods
2024-10-15T14:47:41,394           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-10-15T14:47:41,394           instead of `find_packages(...)`/`find:`).

2024-10-15T14:47:41,395           You can read more about "package discovery" on setuptools documentation page:

2024-10-15T14:47:41,396           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-10-15T14:47:41,397           If you don't want 'streamd.example' to be distributed and are
2024-10-15T14:47:41,397           already explicitly excluding 'streamd.example' via
2024-10-15T14:47:41,398           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-10-15T14:47:41,398           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-10-15T14:47:41,399           combination with a more fine grained `package-data` configuration.

2024-10-15T14:47:41,399           You can read more about "package data files" on setuptools documentation page:

2024-10-15T14:47:41,400           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-10-15T14:47:41,402           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-10-15T14:47:41,402                 even if it does not contain any `.py` files.
2024-10-15T14:47:41,403                 On the other hand, currently there is no concept of package data
2024-10-15T14:47:41,403                 directory, all directories are treated like packages.
2024-10-15T14:47:41,404           ********************************************************************************

2024-10-15T14:47:41,405   !!
2024-10-15T14:47:41,409     check.warn(importable)
2024-10-15T14:47:41,410   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'streamd.scripts.com' is absent from the `packages` configuration.
2024-10-15T14:47:41,411   !!

2024-10-15T14:47:41,413           ********************************************************************************
2024-10-15T14:47:41,414           ############################
2024-10-15T14:47:41,414           # Package would be ignored #
2024-10-15T14:47:41,415           ############################
2024-10-15T14:47:41,416           Python recognizes 'streamd.scripts.com' as an importable package[^1],
2024-10-15T14:47:41,417           but it is absent from setuptools' `packages` configuration.

2024-10-15T14:47:41,418           This leads to an ambiguous overall configuration. If you want to distribute this
2024-10-15T14:47:41,419           package, please make sure that 'streamd.scripts.com' is explicitly added
2024-10-15T14:47:41,420           to the `packages` configuration field.

2024-10-15T14:47:41,421           Alternatively, you can also rely on setuptools' discovery methods
2024-10-15T14:47:41,422           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-10-15T14:47:41,423           instead of `find_packages(...)`/`find:`).

2024-10-15T14:47:41,425           You can read more about "package discovery" on setuptools documentation page:

2024-10-15T14:47:41,426           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-10-15T14:47:41,427           If you don't want 'streamd.scripts.com' to be distributed and are
2024-10-15T14:47:41,428           already explicitly excluding 'streamd.scripts.com' via
2024-10-15T14:47:41,429           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-10-15T14:47:41,430           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-10-15T14:47:41,431           combination with a more fine grained `package-data` configuration.

2024-10-15T14:47:41,432           You can read more about "package data files" on setuptools documentation page:

2024-10-15T14:47:41,434           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-10-15T14:47:41,437           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-10-15T14:47:41,438                 even if it doe2024-10-15T14:47:42,765   running clean
2024-10-15T14:47:42,826   removing 'build/lib' (and everything under it)
2024-10-15T14:47:42,837   'build/bdist.linux-armv7l' does not exist -- can't clean it
2024-10-15T14:47:42,838   'build/scripts-3.11' does not exist -- can't clean it
2024-10-15T14:47:42,839   removing 'build'
2024-10-15T14:47:42,945 Failed to build streamd
2024-10-15T14:47:42,946 ERROR: Failed to build one or more wheels
2024-10-15T14:47:42,948 Exception information:
2024-10-15T14:47:42,948 Traceback (most recent call last):
2024-10-15T14:47:42,948   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
2024-10-15T14:47:42,948     status = _inner_run()
2024-10-15T14:47:42,948              ^^^^^^^^^^^^
2024-10-15T14:47:42,948   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
2024-10-15T14:47:42,948     return self.run(options, args)
2024-10-15T14:47:42,948            ^^^^^^^^^^^^^^^^^^^^^^^
2024-10-15T14:47:42,948   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 67, in wrapper
2024-10-15T14:47:42,948     return func(self, options, args)
2024-10-15T14:47:42,948            ^^^^^^^^^^^^^^^^^^^^^^^^^
2024-10-15T14:47:42,948   File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 180, in run
2024-10-15T14:47:42,948     raise CommandError("Failed to build one or more wheels")
2024-10-15T14:47:42,948 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2024-10-15T14:47:42,949 Removed build tracker: '/tmp/pip-build-tracker-_6p8gt6d'